Origin IGS: cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa .........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 ttcatctagaagggaatttagttgtatatcgcagcagtcgattgannnnnttaattaattaannnnntttttagctgctggttgccactgctgtggatttacatattacttctgtgttccatagccttagctggtctactcccgcgtttgtggtcgcattatcgatcgcttgtttcgctgcagctgccttgtctgcgctttctgctagcgttttggctttttcttcgtctgttaagtcatattgcgcgttgatggctgcttcttagcttttcagcgcatcttcgatggctttctaagcagccggtttagctgtgggtgttggagtgactgatgatacacttgtcgctccgtcgtttttagcttgcg Mask Tandem Repeat Region ================================================ cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Find is-nt database================================================ Query_seq: SMT_2111:SMT_2112|SMT_2111:SMT_2112:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:-><-:2000097..2000462 366 cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2111:SMT_2112|SMT_2111:SMT_2112:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:-><-:2000097..2000462 366 cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2111:SMT_2112|SMT_2111:SMT_2112:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:-><-:2000097..2000462 366 cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 114 End: 293 ................................................................................................................. M N A Q Y D L T D E E K A K T L A E S A D K A A A A K Q A I D N A T T N A G V D Q L R L W N T E V I C K S T A V A T S S ......................................................................... Protein_Len: 60 Strand: - Start: 118 End: 309 ..................................................................................................................... S L L R L F L W F A L L F R L C P L Q L S V L S R Y H S W L R P L L G A L A I S C L L L I Y I W L L P L W C S F X X X M ......................................................... Protein_Len: 60 Strand: - Start: 104 End: 292 ....................................................................................................... M L A C Y S K V S S S F A L V S A S L A S L A A A A F C A I S L A V V F A P T S W S L S H F V S T I H L D V A T A V L M .......................................................................... Protein_Len: 30 Strand: - Start: 39 End: 128 ...................................... D S W C G C S F R S S L F G D F I R Q F A L F C G D V R L M .............................................................................................................................................................................................................................................. cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa 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================================================ cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2111:SMT_2112|SMT_2111:SMT_2112:hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor:-><-:2000097..2000462 366 cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Intra-Species Hit: Count: 1 Min: 1 Max: 366 Len: 366 Subject: smit_SMT_2111_SMT_2112|hypothetical protein predicted by Glimmer/Critica:transcription-repair coupling factor|POSITIVE:NEGATIVE|[2000097,2000462]|366 HSP 1 e-value: 0.0 bit: 666.0 Len: 366 Query Start:1 Query End:366 Subject Strand: POSITIVE Subject Start: 1 Subject End: 366 cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa cgcaagctaaaaacgacggagcgacaagtgtatcatcagtcactccaacacccacagctaaaccggctgcttagaaagccatcgaagatgcgctgaaaagctaagaagcagccatcaacgcgcaatatgacttaacagacgaagaaaaagccaaaacgctagcagaaagcgcagacaaggcagctgcagcgaaacaagcgatcgataatgcgaccacaaacgcgggagtagaccagctaaggctatggaacacagaagtaatatgtaaatccacagcagtggcaaccagcagctaaaaannnnnttaattaattaannnnntcaatcgactgctgcgatatacaactaaattcccttctagatgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCAAGCUAAAAACGACGGAGCGACAAGUGUAUCAUCAGUCACUCCAACACCCACAGCUAAACCGGCUGCUUAGAAAGCCAUCGAAGAUGCGCUGAAAAGCUAAGAAGCAGCCAUCAACGCGCAAUAUGACUUAACAGACGAAGAAAAAGCCAAAACGCUAGCAGAAAGCGCAGACAAGGCAGCUGCAGCGAAACAAGCGAUCGAUAAUGCGACCACAAACGCGGGAGUAGACCAGCUAAGGCUAUGGAACACAGAAGUAAUAUGUAAAUCCACAGCAGUGGCAACCAGCAGCUAAAAANNNNNUUAAUUAAUUAANNNNNUCAAUCGACUGCUGCGAUAUACAACUAAAUUCCCUUCUAGAUGAA ((((((((.........((((.(((..(((...)))..))).)))).........)))).....((((((((.......((((...)))).(((....)))....)))))))).....(((.........(((........)))............((((.((((...((.(......)))..))))))))......)))........))))...........((((((......((((..(((.((((..(((.........)))...)))).)))..)))).....(((((......................................))))).............))))))........... (-85.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAUCUAGAAGGGAAUUUAGUUGUAUAUCGCAGCAGUCGAUUGANNNNNUUAAUUAAUUAANNNNNUUUUUAGCUGCUGGUUGCCACUGCUGUGGAUUUACAUAUUACUUCUGUGUUCCAUAGCCUUAGCUGGUCUACUCCCGCGUUUGUGGUCGCAUUAUCGAUCGCUUGUUUCGCUGCAGCUGCCUUGUCUGCGCUUUCUGCUAGCGUUUUGGCUUUUUCUUCGUCUGUUAAGUCAUAUUGCGCGUUGAUGGCUGCUUCUUAGCUUUUCAGCGCAUCUUCGAUGGCUUUCUAAGCAGCCGGUUUAGCUGUGGGUGUUGGAGUGACUGAUGAUACACUUGUCGCUCCGUCGUUUUUAGCUUGCG ........((((..((...............(((((((..(.........((((....))))........)..)))))))...((((..((((((((...(((((.......)))))))))))))....((((((........(((...(((((((......)))))))......))).(((((......).)))).......))))))....)))).))..))))..((((((((((((.....(((((((.(((((.....)))))..))))))).......)))))))....)))))...((..(((((.(..((.(((((((((.............))))))))).))..).))))).)). (-108.65) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 357 216 172 175 123 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 355 85 42 197 155 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 352 297 270 44 17 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 352 297 270 44 17 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 343 192 161 57 23 smit:SMT_134|5end_LysM_domain_protein_85427..85657_POSITIVE 340 243 201 95 59 smit:SMT_712|5end_alcohol_dehydrogenase,_zinc-containing_620381..620611_NEGATIVE 338 200 157 211 168 smit:SMT_1982|5end_conserved_hypothetical_protein_1913036..1913266_POSITIVE 338 200 157 199 156 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 338 200 157 224 181 smit:SMT_1156|5end_K07485_transposase_1099938..1100168_POSITIVE 335 209 163 76 17 smit:SMT_563|5end_thioredoxin_reductase_480988..481218_POSITIVE 334 199 157 77 22 smit:SMT_274|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_215221..215451_POSITIVE 333 80 34 117 64 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 331 200 157 192 148 smit:SMT_1972|5end_uncharacterized_conserved_phage_related_protein_1903662..1903892_POSITIVE 326 208 169 226 193 smit:SMT_1827|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1797568..1797798_POSITIVE 326 208 169 66 33 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 326 110 63 180 124 smit:SMT_590|5end_tetratricopeptide_repeat_family_protein_506737..506967_POSITIVE 326 208 169 66 33 smit:SMT_586|5end_ATP_synthase_F1,_beta_subunit_502533..502763_POSITIVE 320 59 13 68 30 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 319 80 43 154 112 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 319 80 43 154 112 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 529 240 198 48 5 smit:SMT_2092|3end_malolactic_enzyme_1987040..1987190_NEGATIVE 397 90 42 67 22 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 320 59 13 52 14 smit:SMT_1621|3end_K09134_hypothetical_protein_1607256..1607406_NEGATIVE 319 80 43 45 3 smit:SMT_480|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416765..416915_NEGATIVE 303 249 202 82 31 smit:SMT_1484|3end_exonuclease_RexA_1464256..1464406_NEGATIVE 301 188 150 80 39 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE 298 130 83 84 31 smit:SMT_794|3end_hypothetical_protein_703245..703395_NEGATIVE 296 208 161 69 2 smit:SMT_1729|3end_exodeoxyribonuclease_VII_small_subunit_1714858..1715008_POSITIVE 295 90 42 67 21 smit:SMT_836|3end_cell_surface_protein_precursor_777664..777814_NEGATIVE 293 59 14 66 13 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 292 70 38 77 49 smit:SMT_1925|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867458..1867608_POSITIVE 288 228 184 67 19 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 288 228 184 62 14 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 285 200 154 77 33 smit:SMT_481|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417641..417791_NEGATIVE 285 190 151 138 105 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 279 215 178 46 2 smit:SMT_325|3end_K02029_polar_amino_acid_transport_system_permease_protein_262247..262397_NEGATIVE 278 123 81 67 14 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 277 53 12 113 63 smit:SMT_756|3end_3-dehydroquinate_dehydratase_659907..660057_NEGATIVE 277 207 163 151 106 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 276 96 65 132 103 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE