Origin IGS: gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct .........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 aggaacctctttctaaaaaagagggagatcaacctccctcttcattgcagttatgcgaattatagcttactactttttaaaataagcactaaaaaactaaagttttacaaggtatcgaagaaaaccctttcacaattatattttactccttttttaaaaataaaacaagtgatgataggacttcgtatagtagatattttcaaaaaattccccaatcttacaaaaatgtaagattaaagtctcttttgtaaggttaggttatggcaagcggtctttttttgatgtaaactagactcataaagaacaaaggagtaacatc Mask Tandem Repeat Region ================================================ gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Find is-nt database================================================ Query_seq: SMT_1422:SMT_1423|SMT_1422:SMT_1423:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1407558..1407876 319 gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1422:SMT_1423|SMT_1422:SMT_1423:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1407558..1407876 319 gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1422:SMT_1423|SMT_1422:SMT_1423:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1407558..1407876 319 gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 93 End: 212 ............................................................................................ M F V R L G N F L K I S T I R S P I I T C F I F K K G V K Y N C E R V F F D T L ........................................................................................................... Protein_Len: 60 Strand: - Start: 92 End: 292 ........................................................................................... K K F I D V I R L G I M V Q K I K L F P T F Y L Q S L T K K S V K Y F K L K K T S I K F L L L S Y N A Y S C H L P L N M ........................... Protein_Len: 45 Strand: - Start: 72 End: 206 ....................................................................... L L S K L R V N K Y S Q P I K Q F Y R S Y S T R D D S T K N K F F S Y F I I T F P N E E M ................................................................................................................. Protein_Len: 32 Strand: - Start: 31 End: 126 .............................. N V D F F S R K G Y G L R V F S V K I K C K Q L I P S N K S F M ................................................................................................................................................................................................. gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct 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: 82 Start: 151 End: 180 ......................................................................................................................................................CTTGTTTTATTTTTAAAAAAGGAGTAAAAT........................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.0 Tail_Score: -5.00616 Start: 280 End: 299 Full_Region: CATAACTGCAATGAA GAGGGAGG TTGA TCTCCCTC TTTTTTAGAAAGAGG .......................................................................................................................................................................................................................................................................................GAGGGAGGTTGATCTCCCTC.................... Find igs database================================================ Query_seq: SMT_1422:SMT_1423|SMT_1422:SMT_1423:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:<-->:1407558..1407876 319 gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Intra-Species Hit: Count: 1 Min: 1 Max: 319 Len: 319 Subject: smit_SMT_1422_SMT_1423|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|NEGATIVE:POSITIVE|[1407558,1407876]|319 HSP 1 e-value: 1.0E-168 bit: 591.0 Len: 319 Query Start:1 Query End:319 Subject Strand: POSITIVE Subject Start: 1 Subject End: 319 gatgttactcctttgttctttatgagtctagtttacatcnnnnnnngaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggggaattttttgaaaatatctactatacgaagtcctatcatcacttgttttatttttaaaaaaggagtaaaatataattgtgaaagggttttcttcgataccttgtaaaactttagttttttagtgcttattttaaaaagtagtaagctataattcgcataactgcaatgaagagggaggttgatctccctcttttttagaaagaggttcct Inter-species Hit: Count: 3 Min: 1 Max: 109 Len: 109 Subject: NC_008533_SPD_0803_SPD_0804|hypothetical protein:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[820178,821149]|972 HSP 1 e-value: 1.0E-42 bit: 174.0 Len: 109 Query Start:1 Query End:109 Subject Strand: NEGATIVE Subject Start: 739 Subject End: 847 gatgttactcctttgttctttatgagtctagtttacatcnnnnnnngaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggg.................................................................................................................................................................................................................. gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggg.................................................................................................................................................................................................................. Subject: NC_003098_spr0811_spr0812|hypothetical protein:ABC transporter ATP-binding protein - unknown substrate|NEGATIVE:POSITIVE|[813193,813562]|370 HSP 1 e-value: 1.0E-42 bit: 174.0 Len: 109 Query Start:1 Query End:109 Subject Strand: NEGATIVE Subject Start: 194 Subject End: 302 gatgttactcctttgttctttatgagtctagtttacatcnnnnnnngaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggg.................................................................................................................................................................................................................. gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggg.................................................................................................................................................................................................................. Subject: NC_003028_SP_0911_SP_0912|hypothetical protein:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[864280,864706]|427 HSP 1 e-value: 1.0E-42 bit: 174.0 Len: 109 Query Start:1 Query End:109 Subject Strand: NEGATIVE Subject Start: 194 Subject End: 302 gatgttactcctttgttctttatgagtctagtttacatcnnnnnnngaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggg.................................................................................................................................................................................................................. gatgttactcctttgttctttatgagtctagtttacatcaaaaaaagaccgcttgccataacctaaccttacaaaagagactttaatcttacatttttgtaagattggg.................................................................................................................................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGUUACUCCUUUGUUCUUUAUGAGUCUAGUUUACAUCAAAAAAAGACCGCUUGCCAUAACCUAACCUUACAAAAGAGACUUUAAUCUUACAUUUUUGUAAGAUUGGG (((((.(((..((..(.....)..))...)))..)))))......................(((((.(((((((((((((......))))....))))))))).))))) (-19.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCAAUCUUACAAAAAUGUAAGAUUAAAGUCUCUUUUGUAAGGUUAGGUUAUGGCAAGCGGUCUUUUUUUGAUGUAAACUAGACUCAUAAAGAACAAAGGAGUAACAUC ...(((((((((....)))))))))...(((((((((((...((((.....))))....(((((..(((......)))..)))))........)))))))))..))... (-23.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 70 21 161 112 smit:SMT_1422|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1407467..1407697_NEGATIVE 269 70 24 71 30 smit:SMT_228|5end_hypothetical_protein_164384..164614_POSITIVE 244 94 52 125 82 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 239 40 2 128 90 smit:SMT_784|5end_hypothetical_protein_696298..696528_NEGATIVE 225 85 47 44 2 smit:SMT_1704|5end_D-alanine-D-alanine_ligase_1687431..1687661_POSITIVE 224 60 15 92 43 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 224 81 45 121 84 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 222 82 48 161 123 smit:SMT_1407|5end_ribonuclease_HII_1386309..1386539_NEGATIVE 219 93 52 151 107 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 218 47 7 135 97 smit:SMT_737|5end_hypothetical_protein_642746..642976_NEGATIVE 214 57 12 120 60 smit:SMT_1712|5end_excinuclease_ABC_subunit_A_1700351..1700581_NEGATIVE 213 57 12 200 154 smit:SMT_1091|5end_competence-specific_global_transcription_modulator_1033040..1033270_NEGATIVE 210 36 5 127 95 smit:SMT_901|5end_hypothetical_protein_851434..851664_NEGATIVE 209 48 4 172 124 smit:SMT_206|5end_K07720_two-component_system,_response_regulator_YesN_138237..138467_NEGATIVE 206 72 50 107 81 smit:SMT_910|5end_type_I_restriction_enzyme_R_protein_861889..862119_NEGATIVE 205 99 51 123 79 smit:SMT_1247|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1207409..1207639_POSITIVE 202 69 25 51 2 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 202 39 8 31 4 smit:SMT_492|5end_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_426373..426603_POSITIVE 200 39 2 216 185 smit:SMT_1957|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1890645..1890875_POSITIVE 200 68 46 206 183 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 70 47 25 3 smit:SMT_227|3end_hypothetical_protein_164418..164568_POSITIVE 249 70 23 86 38 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 243 98 55 148 101 smit:SMT_2048|3end_competence-specific_global_transcription_modulator_1957961..1958111_NEGATIVE 239 40 2 119 81 smit:SMT_785|3end_hypothetical_protein_696307..696457_NEGATIVE 237 89 46 151 102 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE 216 84 43 149 107 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 213 57 12 80 34 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 210 36 5 137 105 smit:SMT_902|3end_hypothetical_protein_851424..851574_NEGATIVE 209 40 8 98 51 smit:SMT_1043|3end_chaperonin_GroEL_985110..985260_NEGATIVE 208 57 12 150 105 smit:SMT_1615|3end_K02016_iron_complex_transport_system_substrate-binding_protein_1601734..1601884_NEGATIVE 204 56 11 54 13 smit:SMT_328|3end_23S_rRNA_methyltransferase_264863..265013_POSITIVE 202 39 8 31 4 smit:SMT_491|3end_K01998_branched-chain_amino_acid_transport_system_permease_protein_426453..426603_POSITIVE 199 29 1 122 96 smit:SMT_1058|3end_primosomal_protein_DnaI_997462..997612_POSITIVE 199 33 8 103 77 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 197 82 47 113 75 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 196 70 28 122 77 smit:SMT_1888|3end_K02026_multiple_sugar_transport_system_permease_protein_1842842..1842992_POSITIVE 194 58 14 108 60 smit:SMT_1717|3end_DNA-3-methyladenine_glycosylase_I_1703711..1703861_NEGATIVE 194 58 11 73 18 smit:SMT_911|3end_hypothetical_protein_862720..862870_POSITIVE 194 36 1 143 98 smit:SMT_183|3end_30S_ribosomal_protein_S14_121279..121429_POSITIVE 193 60 11 130 75 smit:SMT_1305|3end_glycerol_kinase_1269805..1269955_POSITIVE