Origin IGS: ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata .........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 tatattgcctccacagtcaacataaaagacaagttccttgtccgaagggcgaaaaaccgcggtaccaccttcattcaatgaacttgtcattctcatttcgtattctatttttcaagatgagtagcatgattctccgtctcagatggctcgcagcaccgccaattctctgaactaagaacttgaaaaatcaattctcaccagtcttattatacttgcttattctcttttcgtcaacc Mask Tandem Repeat Region ================================================ ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Find is-nt database================================================ Query_seq: SSA_0753:SSA_0755|SSA_0753:SSA_0755:Foldase protein prsA precursor, putative:hypothetical protein:->->:736116..736351 236 ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0753:SSA_0755|SSA_0753:SSA_0755:Foldase protein prsA precursor, putative:hypothetical protein:->->:736116..736351 236 ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0753:SSA_0755|SSA_0753:SSA_0755:Foldase protein prsA precursor, putative:hypothetical protein:->->:736116..736351 236 ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 74 End: 163 ......................................................................... M G G A A S H L R R R I M L L I L K N R I R N E N D K F I E ......................................................................... Protein_Len: 36 Strand: + Start: 129 End: 236 ................................................................................................................................ M E Y E M R M T S S L N E G G T A V F R P S D K E L V F Y V D C G G N I Protein_Len: 30 Strand: - Start: 70 End: 159 ..................................................................... L I P P A A L W R L R L I M S S M K F F L I R F S F S L N M ............................................................................. ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 2 End: 31 .GTTGACGAAAAGAGAATAAGCAAGTATAAT............................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -8.6 Tail_Score: -4.69326 Start: 195 End: 209 Full_Region: GTTTTTCGCCCTTCG GACAAG GAA CTTGTC TTTTATGTTGACTGT ..................................................................................................................................................................................................GACAAGGAACTTGTC........................... Find igs database================================================ Query_seq: SSA_0753:SSA_0755|SSA_0753:SSA_0755:Foldase protein prsA precursor, putative:hypothetical protein:->->:736116..736351 236 ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Intra-Species Hit: Count: 1 Min: 1 Max: 236 Len: 236 Subject: NC_009009_SSA_0753_SSA_0755|Foldase protein prsA precursor, putative:hypothetical protein|POSITIVE:POSITIVE|[736116,736351]|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 ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata ggttgacgaaaagagaataagcaagtataataagactggtgagaattgatttttcaagttcttagttcagagaattggcggtgctgcgagccatctgagacggagaatcatgctactcatcttgaaaaatagaatacgaaatgagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcggacaaggaacttgtcttttatgttgactgtggaggcaatata Inter-species Hit: Count: 4 Min: 26 Max: 194 Len: 169 Subject: smit_SMT_765_SMT_766|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[672711,673474]|764 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:143 Query End:194 Subject Strand: NEGATIVE Subject Start: 37 Subject End: 88 ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... HSP 2 e-value: 2.0E-9 bit: 63.9 Len: 71 Query Start:26 Query End:96 Subject Strand: NEGATIVE Subject Start: 135 Subject End: 205 .........................tataataagactggtgagaattgatttttcaagt-tcttagttcagagaattggcggtgctgcgagccatct............................................................................................................................................ .........................tataataagaaagttgagaattgatttt-caattatcttagtccagagaaatggcggtgctgcgagccatct............................................................................................................................................ Subject: NC_008533_SPD_1217_SPD_1218|hypothetical protein:spermidine/putrescine ABC transporter, spermidine/putrescine-binding protein|NEGATIVE:NEGATIVE|[1249544,1250317]|774 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:143 Query End:194 Subject Strand: NEGATIVE Subject Start: 37 Subject End: 88 ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 37 Query Start:60 Query End:96 Subject Strand: NEGATIVE Subject Start: 135 Subject End: 171 ...........................................................tcttagttcagagaattggcggtgctgcgagccatct............................................................................................................................................ ...........................................................tcttagtccagagaaatggcggtgctgcgagccatct............................................................................................................................................ Subject: NC_003098_spr1241_spr1242|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1242025,1242286]|262 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:143 Query End:194 Subject Strand: NEGATIVE Subject Start: 25 Subject End: 76 ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 37 Query Start:60 Query End:96 Subject Strand: NEGATIVE Subject Start: 123 Subject End: 159 ...........................................................tcttagttcagagaattggcggtgctgcgagccatct............................................................................................................................................ ...........................................................tcttagtccagagaaatggcggtgctgcgagccatct............................................................................................................................................ Subject: NC_003028_SP_1384_SP_1385|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1309465,1309726]|262 HSP 1 e-value: 3.0E-21 bit: 103.0 Len: 52 Query Start:143 Query End:194 Subject Strand: NEGATIVE Subject Start: 25 Subject End: 76 ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... ..............................................................................................................................................gagaatgacaagttcattgaatgaaggtggtaccgcggtttttcgcccttcg.......................................... HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 37 Query Start:60 Query End:96 Subject Strand: NEGATIVE Subject Start: 123 Subject End: 159 ...........................................................tcttagttcagagaattggcggtgctgcgagccatct............................................................................................................................................ ...........................................................tcttagtccagagaaatggcggtgctgcgagccatct............................................................................................................................................ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUAAGACUGGUGAGAAUUGAUUUUUCAAGUUCUUAGUUCAGAGAAUUGGCGGUGCUGCGAGCCAUCUGAGACGGAGAAUCAUGCUACUCAUCUUGAAAAAUAGAAUACGAAAUGAGAAUGACAAGUUCAUUGAAUGAAGGUGGUACCGCGGUUUUUCGCCCUUCG ..........((((((((((((((....)).))))))))..)))).(((..(((((.((((((.(((((((....(((.(((((((....(((((.(((............))).))))).))))....))).))).....)))))))..))))))...))))).))). (-43.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAGGGCGAAAAACCGCGGUACCACCUUCAUUCAAUGAACUUGUCAUUCUCAUUUCGUAUUCUAUUUUUCAAGAUGAGUAGCAUGAUUCUCCGUCUCAGAUGGCUCGCAGCACCGCCAAUUCUCUGAACUAAGAACUUGAAAAAUCAAUUCUCACCAGUCUUAUUAUA .(((..((((((......((.....)).......(((((.....)))))....)))))).))).((((((((((..((((......))))...((.(((((((((..........))))....)))))))......))))))))))....................... (-28.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 89 45 193 140 NC_009009:SSA_0351|5end_Signal_peptidase_I,_putative_344907..345137_NEGATIVE 346 83 53 40 11 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 344 78 34 60 18 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 343 78 32 186 137 NC_009009:SSA_1483|5end_Sphingosine_kinase_(diacylglycerol_kinase),_putative_1490220..1490450_NEGATIVE 340 78 40 163 120 NC_009009:SSA_1469|5end_Shikimate_dehydrogenase,_putative_1476317..1476547_NEGATIVE 340 100 53 69 7 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 339 100 51 69 16 NC_009009:SSA_1072|5end_Glutamate_5-kinase,_putative_1089755..1089985_POSITIVE 337 76 34 126 80 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 334 80 31 196 139 NC_009009:SSA_0972|5end_hypothetical_protein_979973..980203_POSITIVE 327 77 52 191 157 NC_009009:SSA_0115|5end_50S_ribosomal_protein_L29,_putative_112402..112632_POSITIVE 326 68 28 193 152 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 325 98 51 94 45 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 321 100 51 77 15 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 319 98 51 76 15 NC_009009:SSA_1003|5end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1003875..1004105_POSITIVE 318 96 53 71 28 NC_009009:SSA_0438|5end_Single-strand_binding_protein,_putative_440615..440845_POSITIVE 317 68 22 224 174 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 317 76 31 76 39 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 316 89 42 186 135 NC_009009:SSA_1499|5end_50S_ribosomal_protein_L35,_putative_1504357..1504587_NEGATIVE 315 90 43 69 10 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 312 96 51 231 188 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 78 33 44 2 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 344 78 34 44 2 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 333 78 32 105 60 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 333 89 45 149 101 NC_009009:SSA_2033|3end_30S_ribosomal_protein_S9,_putative_2038387..2038537_NEGATIVE 327 70 22 138 94 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 325 98 51 104 55 NC_009009:SSA_0495|3end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_496036..496186_POSITIVE 319 98 51 63 2 NC_009009:SSA_1002|3end_Alpha-galactosidase,_putative_1003942..1004092_POSITIVE 318 96 53 59 16 NC_009009:SSA_0437|3end_30S_ribosomal_protein_S6,_putative_440683..440833_POSITIVE 315 90 56 143 103 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 311 78 36 122 78 NC_009009:SSA_2148|3end_Alkaline_shock_stress_response_protein,_putative_2149449..2149599_NEGATIVE 307 77 42 135 101 NC_009009:SSA_1500|3end_Translation_initiation_factor_IF-3,_putative_1504391..1504541_NEGATIVE 297 87 41 57 21 NC_009009:SSA_2258|3end_hypothetical_protein_2253389..2253539_NEGATIVE 297 78 43 119 83 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE 296 77 33 56 7 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 290 79 32 66 25 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 285 82 42 43 3 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 285 78 33 98 52 NC_009009:SSA_0705|3end_hypothetical_protein_690552..690702_NEGATIVE 284 97 52 64 16 NC_009009:SSA_2380|3end_hypothetical_protein_2385665..2385815_NEGATIVE 282 90 41 48 7 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 280 80 43 38 1 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE