Origin IGS: agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt .........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 aagagacgaagatattccatctcgaattattctcggcaaacgcggtctgtgagcgagtactttgtggtctgatttccgtatcagtaccgctccgcccacaggccgtatttgcttacttgtatttataatcatcaagacaatcctaccatataagtgaacagcgaattagtaattgacgttaagcccaaagaggtatct Mask Tandem Repeat Region ================================================ agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Find is-nt database================================================ Query_seq: PG1256:PG1257|PG1256:PG1257:ribonuclease, Rne/Rng family:hypothetical protein:<-<-:1334353..1334550 198 agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1256:PG1257|PG1256:PG1257:ribonuclease, Rne/Rng family:hypothetical protein:<-<-:1334353..1334550 198 agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1256:PG1257|PG1256:PG1257:ribonuclease, Rne/Rng family:hypothetical protein:<-<-:1334353..1334550 198 agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 58 End: 198 ......................................................... M V L M I I N T S K Q I R P V G G A V L I R K S D H K V L A H R P R L P R I I R D G I S S S L Protein_Len: 38 Strand: - Start: 74 End: 187 ......................................................................... L Y L Y A F V A Q P R L P V S V S I L G C L V R E C V A N A S F L E L H F M ........... Protein_Len: 31 Strand: - Start: 45 End: 137 ............................................ K Y P L I T K I I I F V L L C I R G T P P A T S I R F D S W M ............................................................. agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt 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================================================ agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1256:PG1257|PG1256:PG1257:ribonuclease, Rne/Rng family:hypothetical protein:<-<-:1334353..1334550 198 agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Intra-Species Hit: Count: 1 Min: 1 Max: 198 Len: 198 Subject: NC_002950_PG1256_PG1257|ribonuclease, Rne/Rng family:hypothetical protein|NEGATIVE:NEGATIVE|[1334353,1334550]|198 HSP 1 e-value: 1.0E-108 bit: 392.0 Len: 198 Query Start:1 Query End:198 Subject Strand: POSITIVE Subject Start: 1 Subject End: 198 agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt agatacctctttgggcttaacgtcaattactaattcgctgttcacttatatggtaggattgtcttgatgattataaatacaagtaagcaaatacggcctgtgggcggagcggtactgatacggaaatcagaccacaaagtactcgctcacagaccgcgtttgccgagaataattcgagatggaatatcttcgtctctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUACCUCUUUGGGCUUAACGUCAAUUACUAAUUCGCUGUUCACUUAUAUGGUAGGAUUGUCUUGAUGAUUAUAAAUACAAGUAAGCAAAUACGGCCUGUGGGCGGAGCGGUACUGAUACGGAAAUCAGACCACAAAGUACUCGCUCACAGACCGCGUUUGCCGAGAAUAAUUCGAGAUGGAAUAUCUUCGUCUCUU ......(((...........((((((..((.((((((((((........))))).))))))).)))))).................(((((..(((.((((((((((.(((((.(((((......)))))))).....)).).))))))))).)))..))))).)))........((((((((.....)))))))).. (-57.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAGACGAAGAUAUUCCAUCUCGAAUUAUUCUCGGCAAACGCGGUCUGUGAGCGAGUACUUUGUGGUCUGAUUUCCGUAUCAGUACCGCUCCGCCCACAGGCCGUAUUUGCUUACUUGUAUUUAUAAUCAUCAAGACAAUCCUACCAUAUAAGUGAACAGCGAAUUAGUAAUUGACGUUAAGCCCAAAGAGGUAUCU ..((((.(((....)))..)))).(((((((.((((((((..(((((((((.(((.(......((((((((((......))))).))))).)))).)))))))))..)))))((((((((((.........................))))))))))....)))...)))))))........(((......))).... (-54.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1043 140 91 231 182 NC_002950:PG1256|5end_ribonuclease,_Rne/Rng_family_1334262..1334492_NEGATIVE 407 170 121 73 13 NC_002950:PG1480|5end_conjugative_transposon_protein_TraI_1555895..1556125_NEGATIVE 402 188 142 52 1 NC_002950:PG0529|5end_carbamoyl-phosphate_synthase_small_subunit_574637..574867_POSITIVE 375 124 82 155 119 NC_002950:PG0412|5end_DNA_mismatch_repair_protein_MutL_451440..451670_NEGATIVE 368 123 87 104 62 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 351 135 93 210 162 NC_002950:PG0125|5end_hypothetical_protein_146786..147016_NEGATIVE 350 140 95 231 170 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 346 145 105 228 186 NC_002950:PG0756|5end_hypothetical_protein_805673..805903_NEGATIVE 346 138 92 187 122 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 343 130 81 192 131 NC_002950:PG0076|5end_N-acetylmuramoyl-L-alanine_amidase,_family_4_91333..91563_NEGATIVE 339 130 87 222 164 NC_002950:PG0541|5end_hypothetical_protein_594757..594987_POSITIVE 334 134 95 229 195 NC_002950:PG1996|5end_deoxyribose-phosphate_aldolase_2085921..2086151_POSITIVE 332 133 96 141 105 NC_002950:PG0788|5end_hypothetical_protein_840676..840906_NEGATIVE 331 124 88 186 143 NC_002950:PG1102|5end_hypothetical_protein_1173637..1173867_NEGATIVE 331 123 82 80 16 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 328 130 81 212 155 NC_002950:PG1825|5end_hypothetical_protein_1919671..1919901_NEGATIVE 327 142 101 67 24 NC_002950:PG0613|5end_hypothetical_protein_665186..665416_POSITIVE 324 134 94 63 12 NC_002950:PG1565|5end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1645859..1646089_NEGATIVE 324 129 86 180 130 NC_002950:PG0515|5end_hypothetical_protein_557958..558188_NEGATIVE 323 140 96 58 15 NC_002950:PG1611|5end_hypothetical_protein_1691487..1691717_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 123 87 97 55 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 338 125 82 43 6 NC_002950:PG1393|3end_penicillin-binding_protein_2,_putative_1474406..1474556_NEGATIVE 332 133 96 115 79 NC_002950:PG0789|3end_hypothetical_protein_840702..840852_NEGATIVE 331 147 101 92 37 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE 329 129 85 125 77 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 328 183 141 144 101 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 327 134 97 60 8 NC_002950:PG0639|3end_signal_peptide_peptidase_SppA,_67K_type_691213..691363_NEGATIVE 321 135 94 73 25 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 320 170 139 46 7 NC_002950:PG1481|3end_conjugative_transposon_protein_TraG_1555922..1556072_NEGATIVE 318 132 91 54 6 NC_002950:PG2200|3end_TPR_domain_protein_2306720..2306870_NEGATIVE 313 182 143 142 94 NC_002950:PG0087|3end_SIS_domain_protein_102505..102655_NEGATIVE 310 131 95 62 19 NC_002950:PG2144|3end_hypothetical_protein_2253290..2253440_POSITIVE 310 142 102 43 1 NC_002950:PG0612|3end_hypothetical_protein_665242..665392_POSITIVE 309 110 82 147 122 NC_002950:PG0413|3end_hypothetical_protein_451437..451587_NEGATIVE 308 117 82 48 4 NC_002950:PG0985|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1047516..1047666_POSITIVE 308 128 93 148 105 NC_002950:PG0228|3end_DdaH_family_protein_264024..264174_NEGATIVE 306 134 94 86 33 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 306 182 142 134 91 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 305 133 94 99 48 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 305 189 142 151 108 NC_002950:PG1181|3end_transcriptional_regulator,_tetR_family_1263656..1263806_NEGATIVE