Origin IGS: tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc .........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 gagccgctaagcggactcgtcggcctcgatgagcgaggccggagaccgataaggacgaatcacttccccaatctacaatcgcgctacgatcaagggcgcaaccaacaaattatttaagaaccggttttgagttcaattggataggcttaaacagggttgagtaaatgctccggcgggagcgttgaagacaaaaatgaaacggcaaccaatcgacaaaaacgaaattttttgagaca Mask Tandem Repeat Region ================================================ tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Find is-nt database================================================ Query_seq: PG1941:PG1942|PG1941:PG1942:30S ribosomal protein S7:30S ribosomal protein S12:<-<-:2027800..2028035 236 tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1941:PG1942|PG1941:PG1942:30S ribosomal protein S7:30S ribosomal protein S12:<-<-:2027800..2028035 236 tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1941:PG1942|PG1941:PG1942:30S ribosomal protein S7:30S ribosomal protein S12:<-<-:2027800..2028035 236 tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 12 End: 101 ........... M S F L S I G C R F I F V F N A P A G A F T Q P C L S L S N ....................................................................................................................................... Protein_Len: 31 Strand: + Start: 32 End: 124 ............................... M P F H F C L Q R S R R S I Y S T L F K P I Q L N S K P V L K ................................................................................................................ tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc 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================================================ tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1941:PG1942|PG1941:PG1942:30S ribosomal protein S7:30S ribosomal protein S12:<-<-:2027800..2028035 236 tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_002950_PG1941_PG1942|30S ribosomal protein S7:30S ribosomal protein S12|NEGATIVE:NEGATIVE|[2027800,2028035]|236 HSP 1 e-value: 1.0E-131 bit: 468.0 Len: 236 Query Start:1 Query End:236 Subject Strand: POSITIVE Subject Start: 1 Subject End: 236 tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc tgtctcaaaaaatttcgtttttgtcgattggttgccgtttcatttttgtcttcaacgctcccgccggagcatttactcaaccctgtttaagcctatccaattgaactcaaaaccggttcttaaataatttgttggttgcgcccttgatcgtagcgcgattgtagattggggaagtgattcgtccttatcggtctccggcctcgctcatcgaggccgacgagtccgcttagcggctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUCAAAAAAUUUCGUUUUUGUCGAUUGGUUGCCGUUUCAUUUUUGUCUUCAACGCUCCCGCCGGAGCAUUUACUCAACCCUGUUUAAGCCUAUCCAAUUGAACUCAAAACCGGUUCUUAAAUAAUUUGUUGGUUGCGCCCUUGAUCGUAGCGCGAUUGUAGAUUGGGGAAGUGAUUCGUCCUUAUCGGUCUCCGGCCUCGCUCAUCGAGGCCGACGAGUCCGCUUAGCGGCUC .....((((((......))))))..(((((((.(.((..(((((....((((((..(((((....))))).(((((.((((..((((((((...(((...(((....)))....))).))))))))....)))).((((((...........))))))..))))).)))))))))))..)).)...)))))))..((((((((.....))))))))..(((.((((...))))))) (-64.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGCCGCUAAGCGGACUCGUCGGCCUCGAUGAGCGAGGCCGGAGACCGAUAAGGACGAAUCACUUCCCCAAUCUACAAUCGCGCUACGAUCAAGGGCGCAACCAACAAAUUAUUUAAGAACCGGUUUUGAGUUCAAUUGGAUAGGCUUAAACAGGGUUGAGUAAAUGCUCCGGCGGGAGCGUUGAAGACAAAAAUGAAACGGCAACCAAUCGACAAAAACGAAAUUUUUUGAGACA (((((.((((..((((((..((((((((.....)))))))).((((((....(((.(.....).))).............(((((.(......))))))......................)))))).))))))..))))...)))))......(((((.((.((((((((....)))))))).....((....))..))..)))))......((((((......))))))..... (-70.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 998 70 21 161 112 NC_002950:PG1941|5end_30S_ribosomal_protein_S7_2027709..2027939_NEGATIVE 449 228 189 120 64 NC_002950:PG1494|5end_hypothetical_protein_1569841..1570071_POSITIVE 437 229 181 208 147 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 432 225 181 196 155 NC_002950:PG1285|5end_glucosamine-6-phosphate_deaminase_1362894..1363124_POSITIVE 422 229 182 81 25 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 416 229 181 86 35 NC_002950:PG0004|5end_NAD-dependent_deacetylase_2968..3198_POSITIVE 411 200 157 113 70 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 409 228 188 230 171 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 404 221 190 231 198 NC_002950:PG1565|5end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1645859..1646089_NEGATIVE 403 200 154 140 97 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 395 199 153 158 116 NC_002950:PG2021|5end_hypothetical_protein_2114852..2115082_NEGATIVE 395 227 190 178 142 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 388 223 186 214 162 NC_002950:PG2099|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2207932..2208162_NEGATIVE 382 226 182 50 8 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 379 226 181 187 141 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 378 198 154 63 26 NC_002950:PG1648|5end_RelA/SpoT_family_protein_1727762..1727992_POSITIVE 376 174 132 81 33 NC_002950:PG1753|5end_selenide,_water_dikinase_1838615..1838845_POSITIVE 376 70 22 205 152 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 376 70 22 205 152 NC_002950:PG1266|5end_hypothetical_protein_1346987..1347217_NEGATIVE 376 227 183 194 152 NC_002950:PG1134|5end_thioredoxin_reductase_1214350..1214580_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 424 228 181 144 85 NC_002950:PG0344|3end_purple_acid_phosphatase_378543..378693_NEGATIVE 412 216 171 120 72 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 411 200 157 132 89 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 406 223 187 141 97 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 403 200 154 103 60 NC_002950:PG1043|3end_ferrous_iron_transport_protein_B_1110675..1110825_NEGATIVE 395 69 22 55 3 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 387 226 183 149 98 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 384 60 14 141 94 NC_002950:PG0472|3end_iron-sulfur_cluster_binding_protein,_putative_514414..514564_POSITIVE 382 226 182 53 11 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 376 174 132 84 36 NC_002950:PG1752|3end_hypothetical_protein_1838698..1838848_POSITIVE 376 226 188 66 18 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 375 216 175 139 92 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 372 174 131 134 89 NC_002950:PG0582|3end_cell_division_protein_FtsQ,_putative_640456..640606_POSITIVE 370 223 186 50 7 NC_002950:PG0633|3end_hypothetical_protein_686208..686358_POSITIVE 370 228 190 132 76 NC_002950:PG0158|3end_competence_protein_F-related_protein_180995..181145_POSITIVE 366 215 172 130 80 NC_002950:PG1578|3end_quinolinate_synthetase_1656472..1656622_POSITIVE 366 219 178 61 23 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 363 168 132 145 113 NC_002950:PG1960|3end_ribosomal_protein_L28_2048424..2048574_NEGATIVE 363 78 33 123 73 NC_002950:PG1225|3end_ABC_transporter,_ATP-binding_protein_1303336..1303486_POSITIVE 361 225 189 43 6 NC_002950:PG0958|3end_ribonuclease_BN,_putative_1018135..1018285_NEGATIVE