Origin IGS: aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaaaaaagctggagctccaccgcggtggcggccgctctagaactagtggatcccccgggctgcaggtttttttataatctcacaactgcaagaaaattcatttatactactcaggaaaatttttggatttcagtgataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca .........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 tgcactagaaaagaacactgattcaaattgcctgacatacaatttagcacacagaaataagaaatttaaggttgttgctcatggtacctcaattgtaacactagcaagagatgtttttgtaggttgagaacttgtaatattttcaagacaatgcggctacctcatttttaatctacttccttgttctctgtgattatcactgaaatccaaaaattttcctgagtagtataaatgaattttcttgcagttgtgagattataaaaaaacctgcagcccgggggatccactagttctagagcggccgccaccgcggtggagctccagcttttttccctttagtgagggtaatttcgagctnnnnnttaattaattaannnnncttagcttgtcacttctacaaaaacttagcattgctagtagttgagacaggaagataagatt Mask Tandem Repeat Region ================================================ aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaaaaaagctggagctccaccgcggtggcggccgctctagaactagtggatcccccgggctgcaggtttttttataatctcacaactgcaagaaaattcatttatactactcaggaaaatttttggatttcagtgataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca Find is-nt database================================================ Query_seq: SMT_2041:SMT_2042|SMT_2041:SMT_2042:transcription-repair coupling factor:K04077 chaperonin GroEL (Hsp60):<-<-:1952609..1953049 441 aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaaaaaagctggagctccaccgcggtggcggccgctctagaactagtggatcccccgggctgcaggtttttttataatctcacaactgcaagaaaattcatttatactactcaggaaaatttttggatttcagtgataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2041:SMT_2042|SMT_2041:SMT_2042:transcription-repair coupling factor:K04077 chaperonin GroEL (Hsp60):<-<-:1952609..1953049 441 aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaaaaaagctggagctccaccgcggtggcggccgctctagaactagtggatcccccgggctgcaggtttttttataatctcacaactgcaagaaaattcatttatactactcaggaaaatttttggatttcagtgataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2041:SMT_2042|SMT_2041:SMT_2042:transcription-repair coupling factor:K04077 chaperonin GroEL (Hsp60):<-<-:1952609..1953049 441 aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaaaaaagctggagctccaccgcggtggcggccgctctagaactagtggatcccccgggctgcaggtttttttataatctcacaactgcaagaaaattcatttatactactcaggaaaatttttggatttcagtgataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 113 Max: 244 Len: 132 Subject: UniRef90_Q4YAZ4 Cluster: Hypothetical protein; n=1; Plasmodium berghei|Rep: Hypothetical protein - Plasmodium berghei HSP 1 e-value: 8.0E-6 bit: 51.6 Len: 132 Query Start:113 Query End:244 Subject Strand: null Subject Start: 6 Subject End: 41 ................................................................................................................ K S W S S T A V A A A L E L V D P P G C R F F Y N L T T A R K F I Y T T Q E N F W I S V ..................................................................................................................................................................................................... ................................................................................................................ K S W S S T A V A A A L E L V D P P G C R - - - - - - - - N S I L W T V Q R N C F I S V ..................................................................................................................................................................................................... aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 134 End: 271 ..................................................................................................................................... M A A A L E L V D P P G C R F F Y N L T T A R K F I Y T T Q E N F W I S V I I T E N K E V D .......................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 318 End: 410 ............................................................................................................................................................................................................................................................................................................................. G V F V D R A L T V I S T G H A V V K F K K N R H A L N Y T M ............................... aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca 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================================================ aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -2.3 Tail_Score: -5.22943 Start: 117 End: 130 Full_Region: agcggccgccaccgc ggtgg agct ccagc ttttttccctttagt ....................................................................................................................ggtggagctccagc....................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 51 HP_score: -2.9 Tail_Score: -3.72139 Start: 118 End: 149 Full_Region: ggggatccactagtt ctagagcggccgcc accgc ggtggagctccag cttttttccctttag .....................................................................................................................ctagagcggccgccaccgcggtggagctccag.................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_2041:SMT_2042|SMT_2041:SMT_2042:transcription-repair coupling factor:K04077 chaperonin GroEL (Hsp60):<-<-:1952609..1953049 441 aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca Intra-Species Hit: Count: 1 Min: 1 Max: 441 Len: 441 Subject: smit_SMT_2041_SMT_2042|transcription-repair coupling factor:K04077 chaperonin GroEL (Hsp60)|NEGATIVE:NEGATIVE|[1952609,1953049]|441 HSP 1 e-value: 1.0E-107 bit: 391.0 Len: 197 Query Start:245 Query End:441 Subject Strand: POSITIVE Subject Start: 245 Subject End: 441 ....................................................................................................................................................................................................................................................ataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca ....................................................................................................................................................................................................................................................ataatcacagagaacaaggaagtagattaaaaatgaggtagccgcattgtcttgaaaatattacaagttctcaacctacaaaaacatctcttgctagtgttacaattgaggtaccatgagcaacaaccttaaatttcttatttctgtgtgctaaattgtatgtcaggcaatttgaatcagtgttcttttctagtgca HSP 2 e-value: 6.0E-39 bit: 163.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaa......................................................................................................................................................................................................................................................................................................................................... aatcttatcttcctgtctcaactactagcaatgctaagtttttgtagaagtgacaagctaagnnnnnttaattaattaannnnnagctcgaaattaccctcactaaagggaa......................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUUAUCUUCCUGUCUCAACUACUAGCAAUGCUAAGUUUUUGUAGAAGUGACAAGCUAAGNNNNNUUAAUUAAUUAANNNNNAGCUCGAAAUUACCCUCACUAAAGGGAAAAAAGCUGGAGCUCCACCGCGGUGGCGGCCGCUCUAGAACUAGUGGAUCCCCCGGGCUGCAGGUUUUUUUAUAAUCUCACAACUGCAAGAAAAUUCAUUUAUACUACUCAGGAAAAUUUUUGGAUUUCAGUGAUAAUCACAGAGAACAAGGAAGUAGAUUAAAAAUGAGGUAGCCGCAUUGUCUUGAAAAUAUUACAAGUUCUCAACCUACAAAAACAUCUCUUGCUAGUGUUACAAUUGAGGUACCAUGAGCAACAACCUUAAAUUUCUUAUUUCUGUGUGCUAAAUUGUAUGUCAGGCAAUUUGAAUCAGUGUUCUUUUCUAGUGCA (((((...((((((.((((......((((...))))..(((((((((..((((..((((........((((....)))).....))))........((((......)))).(((((.(((.(((((..((((....))))(((((........))))).......))))).))).)))))........))))..)))))))))................((((((....))))))......(((.....))).))))...)))))).)))))...............((((((....(((((...(((..(((((((((((.(((.(((((.........)))))....)))))))....)))).)))..........(((..((((((((((((......))))).)))).)))..)))...)))...))))))))))). (-95.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCACUAGAAAAGAACACUGAUUCAAAUUGCCUGACAUACAAUUUAGCACACAGAAAUAAGAAAUUUAAGGUUGUUGCUCAUGGUACCUCAAUUGUAACACUAGCAAGAGAUGUUUUUGUAGGUUGAGAACUUGUAAUAUUUUCAAGACAAUGCGGCUACCUCAUUUUUAAUCUACUUCCUUGUUCUCUGUGAUUAUCACUGAAAUCCAAAAAUUUUCCUGAGUAGUAUAAAUGAAUUUUCUUGCAGUUGUGAGAUUAUAAAAAAACCUGCAGCCCGGGGGAUCCACUAGUUCUAGAGCGGCCGCCACCGCGGUGGAGCUCCAGCUUUUUUCCCUUUAGUGAGGGUAAUUUCGAGCUNNNNNUUAAUUAAUUAANNNNNCUUAGCUUGUCACUUCUACAAAAACUUAGCAUUGCUAGUAGUUGAGACAGGAAGAUAAGAUU .......(((.((....))..)))......((((...(((.....((((.((((....((....)).....))))))))....))).(((((((.....((((((((.....(((((((((((.((((((.........)))))).(((((.((((((...((((((.....((((((...........(((.....))).((((.........))))..))))))...))))))....(((..(....)..)))................))))..((((.((((((.........((((......)))))))))).)))).((((....(((((....))))).......))))...........................)))))))...)))))))))))......))))))))))))))).))))........... (-98.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1030 140 91 231 182 smit:SMT_2041|5end_transcription-repair_coupling_factor_1952518..1952748_NEGATIVE 443 176 131 176 124 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 385 158 115 199 142 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 381 175 131 186 124 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 375 170 121 187 143 smit:SMT_959|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_905283..905513_POSITIVE 375 169 123 77 15 smit:SMT_482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_418536..418766_NEGATIVE 371 145 116 65 29 smit:SMT_1593|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1581417..1581647_POSITIVE 370 169 123 174 111 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 369 170 128 157 119 smit:SMT_174|5end_30S_ribosomal_protein_S19_117431..117661_POSITIVE 365 146 102 216 159 smit:SMT_755|5end_shikimate_5-dehydrogenase_659917..660147_NEGATIVE 361 60 11 205 150 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 361 174 134 48 5 smit:SMT_319|5end_K02356_elongation_factor_EF-P_258864..259094_NEGATIVE 358 169 123 77 15 smit:SMT_470|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_407303..407533_NEGATIVE 356 149 101 107 52 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 351 156 115 77 22 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 350 177 131 59 16 smit:SMT_928|5end_hypothetical_protein_883218..883448_NEGATIVE 349 179 132 207 143 smit:SMT_416|5end_ribonuclease_Z_359423..359653_POSITIVE 349 163 126 190 140 smit:SMT_104|5end_DNA_repair_protein_49623..49853_POSITIVE 348 169 126 168 126 smit:SMT_311|5end_3-oxoacyl-_252123..252353_POSITIVE 343 169 124 129 67 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 464 58 11 95 43 smit:SMT_1904|3end_transcription-repair_coupling_factor_1853263..1853413_NEGATIVE 395 170 121 74 30 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 395 170 121 63 19 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 395 170 121 74 30 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 395 170 121 79 35 smit:SMT_1971|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903526..1903676_POSITIVE 395 170 121 63 19 smit:SMT_1966|3end_DNA_polymerase_III_alpha_subunit_1898328..1898478_POSITIVE 395 170 121 74 30 smit:SMT_1942|3end_zinc_metalloprotease_ZmpB,_truncated_1878384..1878534_POSITIVE 395 170 121 63 19 smit:SMT_1927|3end_cell_division_protein_FtsH_1868408..1868558_NEGATIVE 395 170 121 74 30 smit:SMT_1926|3end_mevalonate_kinase_1868062..1868212_POSITIVE 395 170 121 74 30 smit:SMT_1887|3end_LicC_protein_1841740..1841890_POSITIVE 395 170 121 63 19 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE 395 170 121 63 19 smit:SMT_1873|3end_K02006_cobalt_transport_system_ATP-binding_protein_1832351..1832501_POSITIVE 395 170 121 79 35 smit:SMT_1852|3end_1,4-alpha-glucan_branching_enzyme_1816467..1816617_NEGATIVE 395 170 121 79 35 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 377 168 123 66 18 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 375 170 121 63 19 smit:SMT_958|3end_hypothetical_protein_predicted_by_Glimmer/Critica_905239..905389_POSITIVE 369 170 128 53 15 smit:SMT_173|3end_50S_ribosomal_protein_L2_117407..117557_POSITIVE 364 170 122 71 28 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 361 153 116 148 100 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 356 149 101 137 82 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE