Origin IGS: agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcacttaaaccagatacactatttacatctactttaatgtctgtatctgctgcatcgattgcgtcttttgcctcattagctttattttctacttcagcttttgctgcagttttctcttcagttgttaaatcatctcgagcatcgatttcttctattttcttct Mask Tandem Repeat Region ================================================ agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Find is-nt database================================================ Query_seq: SMT_1940:SMT_1941|SMT_1940:SMT_1941:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1877167..1877330 164 agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1940:SMT_1941|SMT_1940:SMT_1941:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1877167..1877330 164 agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1940:SMT_1941|SMT_1940:SMT_1941:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1877167..1877330 164 agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 9 End: 164 ........ M E E I D A R D D L T T E E K T A A K A E V E N K A N E A K D A I D A A D T D I K V D V N S V S G L S D Protein_Len: 35 Strand: - Start: 39 End: 143 ...................................... C S F L F S C C F S F Y F I F S I L C F V C D I C C I C V N F Y I Y M ..................... Protein_Len: 42 Strand: - Start: 2 End: 127 . F F I S S I S A R S S K V V S S F V A A F A S T S F L A L S A F S A I S A A S V S M ..................................... agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat 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================================================ agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -5.4 Tail_Score: -4.58419 Start: 19 End: 29 Full_Region: agttgttaaatcatc tcga gca tcga tttcttctattttct ..................tcgagcatcga....................................................................................................................................... TransTerm Strand: - Conf: 73 HP_score: -5.5 Tail_Score: -4.7033 Start: 55 End: 72 Full_Region: tagctttattttcta cttcagc tttt gctgcag ttttctcttcagttg ......................................................cttcagcttttgctgcag............................................................................................ Find igs database================================================ Query_seq: SMT_1940:SMT_1941|SMT_1940:SMT_1941:hypothetical protein predicted by Glimmer/Critica:hypothetical protein:->->:1877167..1877330 164 agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Intra-Species Hit: Count: 2 Min: 1 Max: 164 Len: 164 Subject: smit_SMT_2006_SMT_2007|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:POSITIVE|[1926864,1927652]|789 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 626 Subject End: 789 agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat HSP 2 e-value: 1.0E-13 bit: 77.8 Len: 63 Query Start:102 Query End:164 Subject Strand: POSITIVE Subject Start: 496 Subject End: 558 .....................................................................................................gcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat .....................................................................................................gcaatcgatgaagctgatacagatattaaggttgatgtaaatagtatatctggtttaagtgat HSP 3 e-value: 2.0E-11 bit: 69.9 Len: 63 Query Start:102 Query End:164 Subject Strand: POSITIVE Subject Start: 268 Subject End: 329 .....................................................................................................gcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat .....................................................................................................gcaatcgatggagctgatacagatattaaggt-gatgtaaatagtatatctggtttaagtgat Subject: smit_SMT_1940_SMT_1941|hypothetical protein predicted by Glimmer/Critica:hypothetical protein|POSITIVE:POSITIVE|[1877167,1877330]|164 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat agaagaaaatagaagaaatcgatgctcgagatgatttaacaactgaagagaaaactgcagcaaaagctgaagtagaaaataaagctaatgaggcaaaagacgcaatcgatgcagcagatacagacattaaagtagatgtaaatagtgtatctggtttaagtgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAGAAAAUAGAAGAAAUCGAUGCUCGAGAUGAUUUAACAACUGAAGAGAAAACUGCAGCAAAAGCUGAAGUAGAAAAUAAAGCUAAUGAGGCAAAAGACGCAAUCGAUGCAGCAGAUACAGACAUUAAAGUAGAUGUAAAUAGUGUAUCUGGUUUAAGUGAU .................((((((((((..........................(((.((((....)))).)))..........(((.....)))....)).)).))))))....((((((((.(((((......)))))......))))))))........... (-30.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCACUUAAACCAGAUACACUAUUUACAUCUACUUUAAUGUCUGUAUCUGCUGCAUCGAUUGCGUCUUUUGCCUCAUUAGCUUUAUUUUCUACUUCAGCUUUUGCUGCAGUUUUCUCUUCAGUUGUUAAAUCAUCUCGAGCAUCGAUUUCUUCUAUUUUCUUCU ...........((((((((......((((........)))).))))))))....((((((.((......((......(((((.........(((.((((....)))).))).........)))))......))......))))))))................. (-26.27) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 126 83 217 171 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 284 120 85 61 24 smit:SMT_1449|5end_K08591_putative_membrane_protein_1431937..1432167_POSITIVE 277 120 82 81 42 smit:SMT_927|5end_KH_domain_protein_882677..882907_NEGATIVE 276 100 51 77 36 smit:SMT_1923|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1866021..1866251_POSITIVE 261 128 84 222 174 smit:SMT_154|5end_K03647_protein_involved_in_ribonucleotide_reduction_101930..102160_POSITIVE 253 120 74 153 104 smit:SMT_1630|5end_hypothetical_protein_1617291..1617521_POSITIVE 253 120 74 153 104 smit:SMT_1241|5end_hypothetical_protein_1201040..1201270_POSITIVE 247 130 83 102 59 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 239 130 83 75 29 smit:SMT_2037|5end_lysine_decarboxylase_1948260..1948490_NEGATIVE 237 115 77 66 23 smit:SMT_947|5end_ferredoxin_896405..896635_POSITIVE 235 150 102 74 24 smit:SMT_147|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_97406..97636_POSITIVE 235 150 102 74 24 smit:SMT_119|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_70457..70687_POSITIVE 234 88 41 61 8 smit:SMT_1220|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1183775..1184005_NEGATIVE 234 100 57 71 27 smit:SMT_559|5end_D-alanyl-D-alanine_carboxypeptidase_478042..478272_NEGATIVE 231 74 41 224 185 smit:SMT_1924|5end_isoleucyl-tRNA_synthetase_1866188..1866418_POSITIVE 231 100 51 195 155 smit:SMT_1800|5end_exonuclease_RexA_1773788..1774018_NEGATIVE 230 128 83 77 44 smit:SMT_1862|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1824094..1824324_POSITIVE 230 128 83 77 44 smit:SMT_1763|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1738537..1738767_POSITIVE 230 125 88 176 140 smit:SMT_1337|5end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312812..1313042_NEGATIVE 226 157 111 77 27 smit:SMT_1999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1922792..1923022_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 136 99 39 1 smit:SMT_2092|3end_malolactic_enzyme_1987040..1987190_NEGATIVE 218 120 71 68 13 smit:SMT_974|3end_DNA-binding_response_regulator_922170..922320_NEGATIVE 214 59 19 71 23 smit:SMT_1191|3end_phosphoribosylamine--glycine_ligase_1148475..1148625_NEGATIVE 212 108 64 52 13 smit:SMT_1594|3end_oligopeptide_transport_system_permease_protein_OppB_1585048..1585198_POSITIVE 210 68 24 66 28 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 210 120 71 145 98 smit:SMT_1626|3end_undecaprenyl-diphosphatase_1615183..1615333_NEGATIVE 210 70 23 88 42 smit:SMT_433|3end_cell_division_protein_DivIB_375954..376104_POSITIVE 210 149 106 53 1 smit:SMT_191|3end_adenylate_kinase_126463..126613_POSITIVE 209 119 83 53 17 smit:SMT_1410|3end_exonuclease_RexA_1388532..1388682_NEGATIVE 208 123 84 82 39 smit:SMT_357|3end_tRNA_(guanine-N7-)-methyltransferase_293900..294050_POSITIVE 204 125 92 135 103 smit:SMT_763|3end_alpha-amylase_669280..669430_POSITIVE 201 151 111 87 39 smit:SMT_1959|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1892967..1893117_POSITIVE 201 125 83 43 8 smit:SMT_1299|3end_MutT/NUDIX_family_protein_1262572..1262722_POSITIVE 201 115 92 81 50 smit:SMT_323|3end_amino_acid_transport_ATP-binding_protein_261519..261669_NEGATIVE 201 151 111 87 39 smit:SMT_286|3end_polysaccharide_transporter,_PST_family_230150..230300_POSITIVE 200 120 80 151 97 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 197 115 95 84 58 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 195 73 40 33 3 smit:SMT_1033|3end_K07485_transposase_971164..971314_POSITIVE 195 70 25 51 6 smit:SMT_264|3end_hypothetical_protein_203321..203471_NEGATIVE 194 66 23 50 2 smit:SMT_1252|3end_hypothetical_protein_1212763..1212913_POSITIVE