Origin IGS: ttaannnnnccatatgcggtgtgaaataccgcacagatgcgtaaggagaaaataccgcatcaggcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagaattcgagctcggtacccctgagtctaggtcggactagaccttgtaaaacgacggccagtccagtgtgctggaaagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat .........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 attctttctcttttcattatagcacattttcaaatctaggtttactggattctctgactctatctatttattcggaaaaaggatgaaaaatactcggtctggctcttcccaatggtactttccagcacactggactggccgtcgttttacaaggtctagtccgacctagactcaggggtaccgagctcgaattctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcctgatgcggtattttctccttacgcatctgtgcggtatttcacaccgcatatggnnnnnttaa Mask Tandem Repeat Region ================================================ ttaannnnnccatatgcggtgtgaaataccgcacagatgcgtaaggagaaaataccgcatcaggcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagaattcgagctcggtacccctgagtctaggtcggactagaccttgtaaaacgacggccagtccagtgtgctggaaagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Find is-nt database================================================ Query_seq: SMT_1970:SMT_1971|SMT_1970:SMT_1971:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1903093..1903421 329 ttaannnnnccatatgcggtgtgaaataccgcacagatgcgtaaggagaaaataccgcatcaggcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagaattcgagctcggtacccctgagtctaggtcggactagaccttgtaaaacgacggccagtccagtgtgctggaaagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1970:SMT_1971|SMT_1970:SMT_1971:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1903093..1903421 329 ttaannnnnccatatgcggtgtgaaataccgcacagatgcgtaaggagaaaataccgcatcaggcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagaattcgagctcggtacccctgagtctaggtcggactagaccttgtaaaacgacggccagtccagtgtgctggaaagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1970:SMT_1971|SMT_1970:SMT_1971:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1903093..1903421 329 ttaannnnnccatatgcggtgtgaaataccgcacagatgcgtaaggagaaaataccgcatcaggcgccattcgccattcaggctgcgcaactgttgggaagggcgatcggtgcgggcctcttcgctattacgccagaattcgagctcggtacccctgagtctaggtcggactagaccttgtaaaacgacggccagtccagtgtgctggaaagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 5 Min: 10 Max: 210 Len: 201 Subject: UniRef90_A0ZLG1 Cluster: Beta-D-galactosidase; n=1; Nodularia spumigena CCY9414|Rep: Beta-D-galactosidase - Nodularia spumigena CCY9414 HSP 1 e-value: 6.0E-22 bit: 105.0 Len: 153 Query Start:58 Query End:210 Subject Strand: null Subject Start: 22 Subject End: 72 ......................................................... F Q H T G L A V V L Q G L V R P R L R G T E L E F W R N S E E A R T D R P S Q Q L R S L N G E W R L M ....................................................................................................................... ......................................................... F Q H T G L A V V L Q G L V R P R L T G T E L E F W R N S E E A R T D R P S Q Q L R S L N G E W R L M ....................................................................................................................... Subject: UniRef90_Q6QI34 Cluster: LRRGT00174; n=1; Rattus norvegicus|Rep: LRRGT00174 - Rattus norvegicus (Rat) HSP 1 e-value: 2.0E-13 bit: 76.6 Len: 141 Query Start:10 Query End:150 Subject Strand: null Subject Start: 307 Subject End: 353 ......... P Y A V * N T A Q M R K E K I P H Q A P F A I Q A A Q L L G R A I G A G L F A I T P E F E L G ................................................................................................................................................................................... ......... P Y A V C N T A Q M R K E K I T H Q A P F A I Q D A H M L G R A I G A G L F A I T P A G E R G ................................................................................................................................................................................... Subject: UniRef90_UPI0000ECAFAB Cluster: UPI0000ECAFAB related cluster; n=1; Gallus gallus|Rep: UPI0000ECAFAB UniRef100 entry - Gallus gallus HSP 1 e-value: 9.0E-12 bit: 54.7 Len: 69 Query Start:11 Query End:79 Subject Strand: null Subject Start: 50 Subject End: 72 .......... E W R M A P D A V F S P Y A S V R Y F T P H M .......................................................................................................................................................................................................................................................... .......... E W R M A P D A V F S P Y A S V R Y F T P H M .......................................................................................................................................................................................................................................................... HSP 2 e-value: 9.0E-12 bit: 34.7 Len: 63 Query Start:61 Query End:123 Subject Strand: null Subject Start: 36 Subject End: 53 ............................................................ E E A R T D R P S Q Q L R S L N G E W R L .............................................................................................................................................................................................................. ............................................................ E E A R T D R P S Q Q L R S - - - E W R M .............................................................................................................................................................................................................. HSP 3 e-value: 9.0E-12 bit: 21.9 Len: 30 Query Start:174 Query End:203 Subject Strand: null Subject Start: 1 Subject End: 10 ............................................................................................................................................................................. T L D W P S F Y K V .............................................................................................................................. ............................................................................................................................................................................. T I H W P S F Y N V .............................................................................................................................. Subject: UniRef90_O21999 Cluster: LacZ-alpha; n=1; Cloning vector pAL-Z|Rep: LacZ-alpha - Cloning vector pAL-Z HSP 1 e-value: 4.0E-8 bit: 59.3 Len: 105 Query Start:31 Query End:135 Subject Strand: null Subject Start: 70 Subject End: 106 .............................. W R N S E E A R T D R P S Q Q L R S L N G E W R - - L M R Y F L L T H L C .................................................................................................................................................................................................. .............................. W R N S E E A R T D R P S Q Q L R S L N G E W R D K L A L Y A L M Q F L C .................................................................................................................................................................................................. Subject: UniRef90_Q8GEG0 Cluster: Hypothetical protein; n=1; Erwinia amylovora|Rep: Hypothetical protein - Erwinia amylovora (Fire blight bacteria) HSP 1 e-value: 1.0E-6 bit: 54.7 Len: 135 Query Start:64 Query End:198 Subject Strand: null Subject Start: 67 Subject End: 120 ............................................................... G L A V V L Q - - - - - - - G L V R P R L R G T E L E F - - W R N S E E A R T D R P S Q Q L R S L N G E W R ................................................................................................................................... ............................................................... G L A V V L Q R R D W E N P G V T Q L N R L A A H P P F A S W R N S E E A R T D R P S Q Q L R X L N G E W R ................................................................................................................................... ttaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 37 End: 171 .................................... M R K E K I P H Q A P F A I Q A A Q L L G R A I G A G L F A I T P E F E L G T P E S R S D .............................................................................................................................................................. Protein_Len: 60 Strand: + Start: 14 End: 259 ............. M R C E I P H R C V R R K Y R I R R H S P F R L R N C W E G R S V R A S S L L R Q N S S S V P L S L G R T R P C K T T A ...................................................................... Protein_Len: 47 Strand: - Start: 164 End: 304 ................................................................................................................................................................... T P S S R T F R R G T W H A P F Y W Q S S G S R T N K M R K G F L Y I S D S F G T F R S K F M ......................... Protein_Len: 60 Strand: - Start: 4 End: 240 ... L R W E G N L S R L Q Q S P R D T R A E E S N R W F E L E T G R L R P R V L G Q L V V A L G T H Q F T G N P L A L G L M ......................................................................................... ttaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat 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================================================ ttaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1970:SMT_1971|SMT_1970:SMT_1971:hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica:->->:1903093..1903421 329 ttaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Intra-Species Hit: Count: 1 Min: 211 Max: 329 Len: 119 Subject: smit_SMT_1970_SMT_1971|hypothetical protein predicted by Glimmer/Critica:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1903093,1903421]|329 HSP 1 e-value: 4.0E-61 bit: 236.0 Len: 119 Query Start:211 Query End:329 Subject Strand: POSITIVE Subject Start: 211 Subject End: 329 ..................................................................................................................................................................................................................agtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat ..................................................................................................................................................................................................................agtaccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataatgaaaagagaaagaat Inter-species Hit: Count: 3 Min: 213 Max: 314 Len: 102 Subject: NC_008533_SPD_0037_SPD_0038|hypothetical protein:DNA polymerase I|NEGATIVE:POSITIVE|[31054,31305]|252 HSP 1 e-value: 2.0E-29 bit: 131.0 Len: 102 Query Start:213 Query End:314 Subject Strand: NEGATIVE Subject Start: 121 Subject End: 222 ....................................................................................................................................................................................................................taccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataat............... ....................................................................................................................................................................................................................taccattgggaagagctagagcaagtatttttcaaactttttccgaataaatagatagagccagagaatttagtaaacctagatttaaaaatgtgctataat............... Subject: NC_003098_spr0031_spr0032|hypothetical protein:DNA polymerase I|NEGATIVE:POSITIVE|[31054,31305]|252 HSP 1 e-value: 2.0E-29 bit: 131.0 Len: 102 Query Start:213 Query End:314 Subject Strand: NEGATIVE Subject Start: 121 Subject End: 222 ....................................................................................................................................................................................................................taccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataat............... ....................................................................................................................................................................................................................taccattgggaagagctagagcaagtatttttcaaactttttccgaataaatagatagagccagagaatttagtaaacctagatttaaaaatgtgctataat............... Subject: NC_003028_SP_0031_SP_0032|hypothetical protein:DNA polymerase I|NEGATIVE:POSITIVE|[31244,31534]|291 HSP 1 e-value: 2.0E-29 bit: 131.0 Len: 102 Query Start:213 Query End:314 Subject Strand: NEGATIVE Subject Start: 160 Subject End: 261 ....................................................................................................................................................................................................................taccattgggaagagccagaccgagtatttttcatcctttttccgaataaatagatagagtcagagaatccagtaaacctagatttgaaaatgtgctataat............... ....................................................................................................................................................................................................................taccattgggaagagctagagcaagtatttttcaaactttttccgaataaatagatagagccagagaatttagtaaacctagatttaaaaatgtgctataat............... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCAUUGGGAAGAGCCAGACCGAGUAUUUUUCAUCCUUUUUCCGAAUAAAUAGAUAGAGUCAGAGAAUCCAGUAAACCUAGAUUUGAAAAUGUGCUAUAAU .....((((((((((...((..(((.....))).))))))))))))........((((...((..(((((.((.....)).))))).....))..))))... (-15.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUAGCACAUUUUCAAAUCUAGGUUUACUGGAUUCUCUGACUCUAUCUAUUUAUUCGGAAAAAGGAUGAAAAAUACUCGGUCUGGCUCUUCCCAAUGGUA .....(((.........(((((((.....)))))))....((((.......(((((((.......)))))))........))))..)))............. (-15.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 873 50 1 135 86 smit:SMT_1218|5end_DNA_polymerase_I_1179357..1179587_NEGATIVE 304 44 8 176 141 smit:SMT_1894|5end_K02025_multiple_sugar_transport_system_permease_protein_1846508..1846738_POSITIVE 304 44 8 176 141 smit:SMT_1764|5end_K02025_multiple_sugar_transport_system_permease_protein_1739943..1740173_POSITIVE 284 97 54 54 6 smit:SMT_672|5end_hypothetical_protein_580604..580834_POSITIVE 272 46 3 231 176 smit:SMT_1129|5end_hypothetical_protein_1063926..1064156_NEGATIVE 261 47 1 144 104 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 260 45 1 99 50 smit:SMT_1428|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1414622..1414852_NEGATIVE 257 74 35 224 165 smit:SMT_1886|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840984..1841214_POSITIVE 257 74 35 224 165 smit:SMT_1187|5end_adenylosuccinate_lyase_1146362..1146592_NEGATIVE 256 46 2 70 21 smit:SMT_1627|5end_hypothetical_protein_1616415..1616645_NEGATIVE 254 50 3 80 27 smit:SMT_2150|5end_threonyl-tRNA_synthetase_2024673..2024903_POSITIVE 254 50 3 80 27 smit:SMT_2146|5end_threonyl-tRNA_synthetase_2022048..2022278_POSITIVE 253 49 7 127 75 smit:SMT_1901|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1850537..1850767_POSITIVE 251 44 2 74 32 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 251 38 6 184 151 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 243 48 2 85 31 smit:SMT_2029|5end_acetyltransferase,_GNAT_family_1943749..1943979_POSITIVE 243 48 2 85 31 smit:SMT_1755|5end_acetyltransferase,_GNAT_family_1733042..1733272_POSITIVE 241 80 40 103 66 smit:SMT_211|5end_hypothetical_protein_predicted_by_Glimmer/Critica_144135..144365_POSITIVE 239 40 4 194 155 smit:SMT_915|5end_sucrose_operon_repressor_867574..867804_POSITIVE 239 36 13 32 7 smit:SMT_571|5end_putative_transposase,_ISSmu1_489261..489491_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 44 8 80 45 smit:SMT_1893|3end_ABC_transporter_substrate-binding_protein_-_sugar_transport_1846492..1846642_POSITIVE 304 44 8 80 45 smit:SMT_1763|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1739927..1740077_POSITIVE 283 98 51 86 17 smit:SMT_819|3end_hypothetical_protein_predicted_by_Glimmer/Critica_729966..730116_NEGATIVE 269 26 5 139 116 smit:SMT_452|3end_phosphomethylpyrimidine_kinase_389777..389927_NEGATIVE 254 50 3 61 8 smit:SMT_2149|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2024734..2024884_POSITIVE 253 49 7 130 78 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 235 67 22 148 83 smit:SMT_1188|3end_hypothetical_protein_1146426..1146576_NEGATIVE 234 97 57 46 1 smit:SMT_671|3end_hypothetical_protein_580676..580826_POSITIVE 231 66 23 81 29 smit:SMT_594|3end_lysyl-tRNA_synthetase_510348..510498_NEGATIVE 222 74 31 151 100 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 222 44 1 58 13 smit:SMT_1080|3end_CAAX_amino_terminal_protease_family_protein_1017783..1017933_NEGATIVE 221 47 2 71 15 smit:SMT_2040|3end_transcription-repair_coupling_factor_1950463..1950613_NEGATIVE 221 42 3 60 9 smit:SMT_98|3end_hypothetical_protein_30272..30422_POSITIVE 219 44 1 98 44 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 216 42 4 88 49 smit:SMT_1910|3end_pyruvate-formate_lyase_activating_enzyme_1857654..1857804_POSITIVE 216 70 24 50 2 smit:SMT_742|3end_hypothetical_protein_645784..645934_NEGATIVE 215 44 3 151 119 smit:SMT_1813|3end_amino_acid_transporter_1788232..1788382_POSITIVE 215 25 5 36 11 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 214 44 2 106 63 smit:SMT_402|3end_two-component_response_regulator_YesN_331663..331813_POSITIVE 209 86 49 71 32 smit:SMT_1073|3end_L-asparaginase_1012251..1012401_POSITIVE