Origin IGS: tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat .........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 atcgccaaagttacttgattgcaaagcaatctaagtaactaacgccaaatcctgtcaggaatttggctaggcacttcactagtaaagaaacataaatattatcgatttatgtttctttacgtcgtaaccagagacacttgcctaaacgcctcactaaattggtcaaccaaatctattaattggcttagtggctggtggcaatcttcaagtcactagaatgcaaggcaatctaagcaacga Mask Tandem Repeat Region ================================================ tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Find is-nt database================================================ Query_seq: SMT_1640:SMT_1641|SMT_1640:SMT_1641:hypothetical protein predicted by Glimmer/Critica:arginyl-tRNA synthetase:<-<-:1626412..1626651 240 tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1640:SMT_1641|SMT_1640:SMT_1641:hypothetical protein predicted by Glimmer/Critica:arginyl-tRNA synthetase:<-<-:1626412..1626651 240 tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1640:SMT_1641|SMT_1640:SMT_1641:hypothetical protein predicted by Glimmer/Critica:arginyl-tRNA synthetase:<-<-:1626412..1626651 240 tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 135 End: 227 ...................................................................................................................................... M D N I Y V S L L V K C L A K F L T G F G V S Y L D C F A I K ............. Protein_Len: 55 Strand: - Start: 28 End: 192 ........................... H S S S Q W W G S L W N I S K T S W N L S A N L C T D R T V V Y L F M F R Y Y K H K K V L S T G L W I G S L M ................................................ tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat 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================================================ tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -7.7 Tail_Score: -3.79251 Start: 126 End: 154 Full_Region: TGGTTACGACGTAAA GAAACATAAAT CGATAAT ATTTATGTTTC TTTACTAGTGAAGTG .............................................................................................................................GAAACATAAATCGATAATATTTATGTTTC...................................................................................... TransTerm Strand: - Conf: 70 HP_score: -7.7 Tail_Score: -3.68351 Start: 126 End: 154 Full_Region: cacttcactagtaaa gaaacataaat attatcg atttatgtttc tttacgtcgtaacca .............................................................................................................................gaaacataaatattatcgatttatgtttc...................................................................................... TransTerm Strand: + Conf: 62 HP_score: -2.7 Tail_Score: -4.51743 Start: 130 End: 150 Full_Region: TACGACGTAAAGAAA CATAAAT CGATAAT ATTTATG TTTCTTTACTAGTGA .................................................................................................................................CATAAATCGATAATATTTATG.......................................................................................... TransTerm Strand: - Conf: 60 HP_score: -2.7 Tail_Score: -4.47183 Start: 130 End: 150 Full_Region: tcactagtaaagaaa cataaat attatcg atttatg tttctttacgtcgta .................................................................................................................................cataaatattatcgatttatg.......................................................................................... Find igs database================================================ Query_seq: SMT_1640:SMT_1641|SMT_1640:SMT_1641:hypothetical protein predicted by Glimmer/Critica:arginyl-tRNA synthetase:<-<-:1626412..1626651 240 tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: smit_SMT_1640_SMT_1641|hypothetical protein predicted by Glimmer/Critica:arginyl-tRNA synthetase|NEGATIVE:NEGATIVE|[1626412,1626651]|240 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 240 Query Start:1 Query End:240 Subject Strand: POSITIVE Subject Start: 1 Subject End: 240 tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat tcgttgcttagattgccttgcattctagtgacttgaagattgccaccagccactaagccaattaatagatttggttgaccaatttagtgaggcgtttaggcaagtgtctctggttacgacgtaaagaaacataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat Inter-species Hit: Count: 1 Min: 84 Max: 240 Len: 157 Subject: NC_003098_spr1890_spr1891|arginyl-tRNA synthetase:Tranposase (orf2)|POSITIVE:NEGATIVE|[1870743,1871056]|314 HSP 1 e-value: 2.0E-28 bit: 127.0 Len: 112 Query Start:129 Query End:240 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 112 ................................................................................................................................acataaatcgataatatttatgtttctttactagtgaagtgcctagccaaattcctgacaggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat ................................................................................................................................acataaatcgatcatatttatgtcctaaaactagtgaagcgcctagccaaagtccgaataggatttggcgttagttacttagattgctttgcaatcaagtaactttggcgat HSP 2 e-value: 9.0E-9 bit: 61.9 Len: 39 Query Start:84 Query End:122 Subject Strand: NEGATIVE Subject Start: 243 Subject End: 281 ...................................................................................ttagtgaggcgtttaggcaagtgtctctggttacgacgt...................................................................................................................... ...................................................................................ttagtgaagtgtttaggcaagtgtctctggttacgacgt...................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUGAGGCGUUUAGGCAAGUGUCUCUGGUUACGACGUAAAGAAACAUAAAUCGAUAAUAUUUAUGUUUCUUUACUAGUGAAGUGCCUAGCCAAAUUCCUGACAGGAUUUGGCGUUAGUUACUUAGAUUGCUUUGCAAUCAAGUAACUUUGGCGAU .....(((((((((....)))))))))...((((...((((((((((((((((.......))))))))))))))))..))))..((((..(((((((((......)))))))))...((((((((.((((((...))))))))))))))..)))).. (-56.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGCCAAAGUUACUUGAUUGCAAAGCAAUCUAAGUAACUAACGCCAAAUCCUGUCAGGAAUUUGGCUAGGCACUUCACUAGUAAAGAAACAUAAAUAUUAUCGAUUUAUGUUUCUUUACGUCGUAACCAGAGACACUUGCCUAAACGCCUCACUAA ...((...((((((((((((((...)))))).))))))))...(((((((((.....)).)))))))((((((........((((((((((((((((.......))))))))))))))))(((.........)))...))))))...))........ (-51.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 898 50 1 224 175 smit:SMT_1640|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1626321..1626551_NEGATIVE 312 140 91 49 2 smit:SMT_1173|5end_CMP-N-acetylneuraminate-beta-galactosamide-alpha_-2,3-sialyltransferase_1125620..1125850_NEGATIVE 306 115 82 160 123 smit:SMT_596|5end_K03976_putative_transcription_regulator_513075..513305_NEGATIVE 302 120 71 76 25 smit:SMT_1616|5end_putative_ABC-type_cobalamin_Fe3+-siderophores_transport_system_ATPase_component_1603547..1603777_NEGATIVE 281 139 92 63 12 smit:SMT_1822|5end_hypothetical_protein_1794452..1794682_POSITIVE 273 117 74 186 142 smit:SMT_348|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_286456..286686_POSITIVE 267 115 75 77 33 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 263 99 53 213 170 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 263 50 1 122 75 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 259 111 71 60 25 smit:SMT_468|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_404710..404940_POSITIVE 257 120 71 142 101 smit:SMT_1053|5end_ABC_transporter_permease_protein_993671..993901_NEGATIVE 255 130 84 84 31 smit:SMT_1509|5end_phosphopentomutase_1492781..1493011_NEGATIVE 255 120 73 186 132 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 254 138 91 158 87 smit:SMT_866|5end_50S_ribosomal_protein_L11_816234..816464_NEGATIVE 254 41 2 230 192 smit:SMT_158|5end_putative_Holliday_junction_resolvase_103795..104025_POSITIVE 251 110 62 136 87 smit:SMT_933|5end_ATP-dependent_RNA_helicase_885631..885861_NEGATIVE 249 123 81 189 145 smit:SMT_848|5end_hypothetical_protein_795153..795383_NEGATIVE 248 44 1 41 3 smit:SMT_756|5end_3-dehydroquinate_dehydratase_660584..660814_NEGATIVE 247 108 62 228 176 smit:SMT_1238|5end_transposase,_TnpA_1198738..1198968_POSITIVE 247 108 67 57 7 smit:SMT_981|5end_hypothetical_protein_928709..928939_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 103 61 119 73 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 312 140 91 52 5 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE 302 120 71 79 28 smit:SMT_1617|3end_K02015_iron_complex_transport_system_permease_protein_1603544..1603694_NEGATIVE 273 38 1 151 108 smit:SMT_1848|3end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1812694..1812844_NEGATIVE 269 138 103 73 38 smit:SMT_1012|3end_xanthine_permease_949638..949788_POSITIVE 262 139 99 46 2 smit:SMT_1821|3end_Mg2+_and_Co2+_transporter_1794515..1794665_POSITIVE 259 111 71 50 15 smit:SMT_467|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_404780..404930_POSITIVE 257 120 71 126 85 smit:SMT_1054|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_993687..993837_NEGATIVE 256 104 61 145 93 smit:SMT_597|3end_K08974_putative_membrane_protein_513075..513225_NEGATIVE 255 130 84 60 7 smit:SMT_1510|3end_ribose_5-phosphate_isomerase_1492805..1492955_NEGATIVE 255 120 73 142 88 smit:SMT_309|3end_acyl-carrier-protein_S-malonyltransferase_251406..251556_POSITIVE 248 44 1 44 6 smit:SMT_757|3end_K06969_putative_SAM-dependent_methyltransferase_660581..660731_NEGATIVE 245 131 92 60 16 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 243 133 92 99 44 smit:SMT_953|3end_hypothetical_protein_900899..901049_NEGATIVE 241 41 1 60 19 smit:SMT_640|3end_PTS_system,_lactose-specific_IIBC_component_545099..545249_NEGATIVE 241 36 5 60 21 smit:SMT_207|3end_putative_two-component_sensor_histidine_kinase_138230..138380_NEGATIVE 240 140 91 108 61 smit:SMT_1742|3end_sodium-dependent_phosphate_transporter_1724991..1725141_POSITIVE 240 32 4 59 29 smit:SMT_1005|3end_possible_aluminum_resistance_protein_946679..946829_POSITIVE 240 117 79 64 14 smit:SMT_484|3end_hypothetical_protein_419659..419809_NEGATIVE 234 109 62 57 3 smit:SMT_693|3end_hypothetical_protein_604078..604228_POSITIVE