Origin IGS: atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgcaagtgcacgcgctagggcaacccgttgcttctgtccacctgataaatggcgaggacatcgctgctcttctggggtgccaatttgtcaaaccagaagacacacacttatcacctgatttattgaaataaagggaattttcctctctaactacacatcttatcaccatcgaaaagtctcacactaaacgctagcaactggaagttactctaagacgactctgttttagggctatttgtcgtgcacttttttcttagtcttttctcttttgaacctttatatatcaaaaaaagaaaaccagtggacgttagtctaagaagaatttctactgatttcacgcgattttctcatactacaggctaggttgcgggaaactggaannnnnttaattaattaannnnnggctgttcgtatcattccaaaaggaaaagaaggagat Mask Tandem Repeat Region ================================================ atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Find is-nt database================================================ Query_seq: SMT_2063:SMT_2064|SMT_2063:SMT_2064:hypothetical protein:amino acid ABC transporter, ATP-binding protein:<-->:1971883..1972321 439 atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2063:SMT_2064|SMT_2063:SMT_2064:hypothetical protein:amino acid ABC transporter, ATP-binding protein:<-->:1971883..1972321 439 atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2063:SMT_2064|SMT_2063:SMT_2064:hypothetical protein:amino acid ABC transporter, ATP-binding protein:<-->:1971883..1972321 439 atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 102 End: 227 ..................................................................................................... M K S V E I L L R L T S T G F L F L I Y K G S K E K R L R K K C T T N S P K T E S S .................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 333 End: 422 ............................................................................................................................................................................................................................................................................................................................................ M C V F W F D K L A P Q K S S D V L A I Y Q V D R S N G L P ................. Protein_Len: 56 Strand: + Start: 271 End: 438 .............................................................................................................................................................................................................................................................................. M V I R C V V R E E N S L Y F N K S G D K C V S S G L T N W H P R R A A M S S P F I R W T E A T G C P S A C T C . Protein_Len: 41 Strand: - Start: 312 End: 434 ....................................................................................................................................................................................................................................................................................................................... K L L D P S L H T D E P K V F Q C G L L A A I D E G N I L H V S A V P Q G L A H M ..... Protein_Len: 40 Strand: - Start: 80 End: 199 ............................................................................... G T T H S F R T F D T S I R R L S V D V P K R K K I Y L P E F S F L S L F F H M ................................................................................................................................................................................................................................................ atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg 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================================================ atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2063:SMT_2064|SMT_2063:SMT_2064:hypothetical protein:amino acid ABC transporter, ATP-binding protein:<-->:1971883..1972321 439 atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Intra-Species Hit: Count: 1 Min: 1 Max: 439 Len: 439 Subject: smit_SMT_2063_SMT_2064|hypothetical protein:amino acid ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[1971883,1972321]|439 HSP 1 e-value: 0.0 bit: 769.0 Len: 439 Query Start:1 Query End:439 Subject Strand: POSITIVE Subject Start: 1 Subject End: 439 atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttcnnnnnnngatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg atctccttcttttccttttggaatgatacgaacagccnnnnnttaattaattaannnnnttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttctttttttgatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagttgctagcgtttagtgtgagacttttcgatggtgataagatgtgtagttagagaggaaaattccctttatttcaataaatcaggtgataagtgtgtgtcttctggtttgacaaattggcaccccagaagagcagcgatgtcctcgccatttatcaggtggacagaagcaacgggttgccctagcgcgtgcacttgcg Inter-species Hit: Count: 3 Min: 60 Max: 244 Len: 185 Subject: NC_008533_SPD_0886_SPD_0887|thioredoxin family protein:amino acid permease family protein|POSITIVE:POSITIVE|[897068,897440]|373 HSP 1 e-value: 3.0E-50 bit: 200.0 Len: 185 Query Start:60 Query End:244 Subject Strand: POSITIVE Subject Start: 58 Subject End: 242 ...........................................................ttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttcnnnnnnn-gatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagtt................................................................................................................................................................................................... ...........................................................ttccagtttcccacaacctagcttttagtatgagaaaaacgcgtgacatcagtggaaatccgtcttagactaacttccactggttttctttttcttgatatataagggttcaaaagcgaaaagactcagaaaa-agtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagtt................................................................................................................................................................................................... Subject: NC_003098_spr0904_spr0905|hypothetical protein:Cationic amino acid transporter - APC Superfamily|POSITIVE:POSITIVE|[889537,889897]|361 HSP 1 e-value: 3.0E-50 bit: 200.0 Len: 185 Query Start:60 Query End:244 Subject Strand: POSITIVE Subject Start: 58 Subject End: 242 ...........................................................ttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttcnnnnnnn-gatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagtt................................................................................................................................................................................................... ...........................................................ttccagtttcccacaacctagcttttagtatgagaaaaacgcgtgacatcagtggaaatccgtcttagactaacttccactggttttctttttcttgatatataagggttcaaaagcgaaaagactcagaaaa-agtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagtt................................................................................................................................................................................................... Subject: NC_003028_SP_1000_SP_1001|thioredoxin family protein:amino acid permease family protein|POSITIVE:POSITIVE|[941432,941804]|373 HSP 1 e-value: 3.0E-50 bit: 200.0 Len: 185 Query Start:60 Query End:244 Subject Strand: POSITIVE Subject Start: 58 Subject End: 242 ...........................................................ttccagtttcccgcaacctagcctgtagtatgagaaaatcgcgtgaaatcagtagaaattcttcttagactaacgtccactggttttcnnnnnnn-gatatataaaggttcaaaagagaaaagactaagaaaaaagtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagtt................................................................................................................................................................................................... ...........................................................ttccagtttcccacaacctagcttttagtatgagaaaaacgcgtgacatcagtggaaatccgtcttagactaacttccactggttttctttttcttgatatataagggttcaaaagcgaaaagactcagaaaa-agtgcacgacaaatagccctaaaacagagtcgtcttagagtaacttccagtt................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCAGUUUCCCGCAACCUAGCCUGUAGUAUGAGAAAAUCGCGUGAAAUCAGUAGAAAUUCUUCUUAGACUAACGUCCACUGGUUUUCUUUUUUUGAUAUAUAAAGGUUCAAAAGAGAAAAGACUAAGAAAAAAGUGCACGACAAAUAGCCCUAAAACAGAGUCGUCUUAGAGUAACUUCCAGUU ....((((.(.(.......(((((...((((.((((((......(((((((((.(((....)))...(((....))).)))))))))..)))))).))))....))))).....((((...((((........((.((..........)).)).......)))).)))).).).))))....... (-28.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGGAAGUUACUCUAAGACGACUCUGUUUUAGGGCUAUUUGUCGUGCACUUUUUUCUUAGUCUUUUCUCUUUUGAACCUUUAUAUAUCAAAAAAAGAAAACCAGUGGACGUUAGUCUAAGAAGAAUUUCUACUGAUUUCACGCGAUUUUCUCAUACUACAGGCUAGGUUGCGGGAAACUGGAA ...((((((((..(((.((((..(((((...)))))........(((.((((.(((((((.(......)..((((((...........)))))).)))))))..)))).)))...)))).)))..))))))))((..((((.((((((((..((........))..)))))))).))))..)).. (-39.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 941 50 1 200 151 smit:SMT_2063|5end_hypothetical_protein_1971792..1972022_NEGATIVE 314 46 4 58 16 smit:SMT_622|5end_methionine_aminopeptidase_528939..529169_POSITIVE 289 34 3 179 137 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 267 42 1 70 31 smit:SMT_1891|5end_putative_dihydrolipoamide_S-acetyltransferase_1844373..1844603_POSITIVE 267 42 1 70 31 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 262 35 3 69 39 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 257 57 12 209 158 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 254 45 2 220 156 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 249 69 21 142 104 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 248 109 74 194 158 smit:SMT_401|5end_peptide_methionine_sulfoxide_reductase_329663..329893_POSITIVE 247 89 45 159 112 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 243 45 3 94 37 smit:SMT_894|5end_hypothetical_protein_841701..841931_NEGATIVE 242 44 4 66 25 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 240 47 3 213 162 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 237 44 2 198 155 smit:SMT_454|5end_hypothetical_protein_391289..391519_POSITIVE 236 46 9 189 155 smit:SMT_484|5end_hypothetical_protein_420180..420410_NEGATIVE 235 54 11 183 137 smit:SMT_1475|5end_K02004_1455873..1456103_POSITIVE 235 80 40 231 188 smit:SMT_501|5end_ABC_transporter,_ATP-binding_protein_433227..433457_POSITIVE 234 44 3 133 88 smit:SMT_1993|5end_hypothetical_protein_1919800..1920030_NEGATIVE 234 180 133 225 178 smit:SMT_699|5end_K03106_signal_recognition_particle,_subunit_SRP54_610336..610566_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 46 4 98 56 smit:SMT_621|3end_K03346_replication_initiation_and_membrane_attachment_protein_529059..529209_POSITIVE 310 180 160 21 1 smit:SMT_1246|3end_ISSag9,_transposase_1205938..1206088_NEGATIVE 310 67 21 53 9 smit:SMT_301|3end_hypothetical_protein_244402..244552_POSITIVE 304 166 127 72 34 smit:SMT_999|3end_hypothetical_protein_predicted_by_Glimmer/Critica_941496..941646_NEGATIVE 266 30 3 145 112 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 243 45 3 101 44 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE 242 44 4 108 67 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 236 46 9 140 106 smit:SMT_485|3end_hypothetical_protein_420229..420379_NEGATIVE 233 179 146 133 93 smit:SMT_1813|3end_amino_acid_transporter_1788232..1788382_POSITIVE 232 100 60 149 110 smit:SMT_1977|3end_endopeptidase_O_1908454..1908604_POSITIVE 232 100 60 149 110 smit:SMT_1466|3end_endopeptidase_O_1447905..1448055_POSITIVE 230 180 134 105 53 smit:SMT_1430|3end_hypothetical_protein_1415842..1415992_POSITIVE 229 66 23 102 57 smit:SMT_1896|3end_lysine_decarboxylase_1848073..1848223_NEGATIVE 224 42 1 118 75 smit:SMT_1836|3end_cytidine/deoxycytidylate_deaminase_family_protein_1804100..1804250_NEGATIVE 223 94 51 105 61 smit:SMT_2037|3end_lysine_decarboxylase_1947880..1948030_NEGATIVE 223 94 51 105 61 smit:SMT_1418|3end_lysine_decarboxylase_1401687..1401837_NEGATIVE 222 43 4 48 5 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 220 46 1 127 84 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 220 120 74 87 43 smit:SMT_741|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_644314..644464_NEGATIVE 220 44 1 59 13 smit:SMT_608|3end_laminin-binding_surface_protein_521187..521337_POSITIVE