Origin IGS: taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct .........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 agattttttctttttttgatgacaaaggtaattgtttttatcacaaaaccggtcattttttctccctatttatggggatataatctgataaatcaccataaaaggggatatcgtgaagccatttggattagcaggttctgttgaacgggattgagggaagatgagaagaggctatctgtgcacaacacacaaagacagcctcttcccaaaagaaaaccctacatctgcaactta Mask Tandem Repeat Region ================================================ taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct Find is-nt database================================================ Query_seq: TF0383:TF0385|TF0383:TF0385:alkyl hydroperoxide reductase, subunit C:conserved hypothetical protein:->->:406117..406350 234 taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0383:TF0385|TF0383:TF0385:alkyl hydroperoxide reductase, subunit C:conserved hypothetical protein:->->:406117..406350 234 taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0383:TF0385|TF0383:TF0385:alkyl hydroperoxide reductase, subunit C:conserved hypothetical protein:->->:406117..406350 234 taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 26 End: 139 ......................... M G R G C L C V L C T D S L F S S S L N P V Q Q N L L I Q M A S R Y P L L W ............................................................................................... Protein_Len: 30 Strand: + Start: 73 End: 162 ........................................................................ M F P Q S R S T E P A N P N G F T I S P F M V I Y Q I I S P ........................................................................ Protein_Len: 42 Strand: - Start: 94 End: 219 ............................................................................................. C F R S I W I A E R Y G R K H H N I L N Y G W L Y P S F I V P K T I F V I V K T M M ............... taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct 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================================================ taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -14.6 Tail_Score: -3.09878 Start: 27 End: 73 Full_Region: TGTAGGGTTTTCTTT TGGGAAGAGGCTGTCTTTGTGT GTT GTGCACAGATAGCCTCTTCTCA TCTTCCCTCAATCCC ..........................TGGGAAGAGGCTGTCTTTGTGTGTTGTGCACAGATAGCCTCTTCTCA................................................................................................................................................................. TransTerm Strand: + Conf: 72 HP_score: -8.6 Tail_Score: -3.52787 Start: 33 End: 67 Full_Region: GTTTTCTTTTGGGAA GAGGCTGTCTTTGTGT GTT GTGCACAGATAGCCTC TTCTCATCTTCCCTC ................................GAGGCTGTCTTTGTGTGTTGTGCACAGATAGCCTC....................................................................................................................................................................... TransTerm Strand: - Conf: 57 HP_score: -7.0 Tail_Score: -2.78715 Start: 127 End: 172 Full_Region: accggtcattttttc tccctatttatggggatata atctga taaatcaccataaaagggga tatcgtgaagccatt ..............................................................................................................................tccctatttatggggatataatctgataaatcaccataaaagggga.............................................................. Find igs database================================================ Query_seq: TF0383:TF0385|TF0383:TF0385:alkyl hydroperoxide reductase, subunit C:conserved hypothetical protein:->->:406117..406350 234 taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatcaaaaaaagaaaaaatct Intra-Species Hit: Count: 1 Min: 1 Max: 217 Len: 217 Subject: tfor_TF0383_TF0385|alkyl hydroperoxide reductase, subunit C:conserved hypothetical protein|POSITIVE:POSITIVE|[406117,406350]|234 HSP 1 e-value: 1.0E-120 bit: 430.0 Len: 217 Query Start:1 Query End:217 Subject Strand: POSITIVE Subject Start: 1 Subject End: 217 taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatc................. taagttgcagatgtagggttttcttttgggaagaggctgtctttgtgtgttgtgcacagatagcctcttctcatcttccctcaatcccgttcaacagaacctgctaatccaaatggcttcacgatatccccttttatggtgatttatcagattatatccccataaatagggagaaaaaatgaccggttttgtgataaaaacaattacctttgtcatc................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUUGCAGAUGUAGGGUUUUCUUUUGGGAAGAGGCUGUCUUUGUGUGUUGUGCACAGAUAGCCUCUUCUCAUCUUCCCUCAAUCCCGUUCAACAGAACCUGCUAAUCCAAAUGGCUUCACGAUAUCCCCUUUUAUGGUGAUUUAUCAGAUUAUAUCCCCAUAAAUAGGGAGAAAAAAUGACCGGUUUUGUGAUAAAAACAAUUACCUUUGUCAUC ......((((.((.((((........((((((((((((((((..((((.....))))))))))))))))))))....)))))).....((((....))))))))........(((((.........((((..(((((((.(((.((......)).))).)))))))..))))............(((.((((.......))))..)))...))))). (-68.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGACAAAGGUAAUUGUUUUUAUCACAAAACCGGUCAUUUUUUCUCCCUAUUUAUGGGGAUAUAAUCUGAUAAAUCACCAUAAAAGGGGAUAUCGUGAAGCCAUUUGGAUUAGCAGGUUCUGUUGAACGGGAUUGAGGGAAGAUGAGAAGAGGCUAUCUGUGCACAACACACAAAGACAGCCUCUUCCCAAAAGAAAACCCUACAUCUGCAACUUA ((((((...(((..((((.......)))).))).)))))).....(((((.(((((((.(((.((......)).))).))))))).)))))..........((....))....((((((((((.....))))....((((....((.(((((((((.((((((.......)))..))).))))))))).))........))))..))))))...... (-59.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 69 27 147 111 tfor:TF0198|5end_transposase_related_sequence_221054..221284_POSITIVE 361 44 1 139 92 tfor:TF1632|5end_conserved_hypothetical_protein_1743860..1744090_POSITIVE 353 60 12 211 160 tfor:TF1950|5end_conserved_hypothetical_protein;_possible_transporter_2099828..2100058_POSITIVE 346 70 21 59 17 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 340 79 31 138 89 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 331 89 47 62 13 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 321 159 111 120 80 tfor:TF1323|5end_metallo-beta-lactamase_superfamily_protein_1402650..1402880_POSITIVE 319 88 51 50 9 tfor:TF2598|5end_conserved_hypothetical_protein_2771032..2771262_POSITIVE 315 47 1 155 108 tfor:TF0081|5end_pantothenate_kinase_87464..87694_POSITIVE 311 79 32 80 21 tfor:TF2492|5end_NifU-related_protein_2666683..2666913_POSITIVE 308 59 17 176 124 tfor:TF1696|5end_conserved_hypothetical_protein_1816893..1817123_POSITIVE 307 68 22 57 7 tfor:TF1819|5end_cation_efflux_system_AcrB/AcrD/AcrF_family;_ABC_transporter,_ATP-binding/permease_component_1958681..1958911_POSITIVE 306 90 41 73 20 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 306 70 29 142 101 tfor:TF2754|5end_hypothetical_protein_2940446..2940676_POSITIVE 306 80 32 97 49 tfor:TF1656|5end_possible_2-methylthioadenine_synthetase_1771115..1771345_POSITIVE 305 60 15 54 3 tfor:TF1019|5end_N-acetylmuramoyl-L-alanine_amidase_1075367..1075597_POSITIVE 302 88 46 140 93 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 301 96 57 146 98 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 300 65 23 223 172 tfor:TF2389|5end_conserved_hypothetical_protein_2558795..2559025_POSITIVE 299 129 87 179 130 tfor:TF2655|5end_DNA_topoisomerase_I_2824543..2824773_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 470 70 27 61 18 tfor:TF0383|3end_alkyl_hydroperoxide_reductase,_subunit_C_406056..406206_POSITIVE 470 70 27 145 102 tfor:TF0384|3end_conserved_hypothetical_protein_406140..406290_POSITIVE 387 69 27 50 14 tfor:TF0196|3end_conserved_hypothetical_protein_221037..221187_POSITIVE 360 50 3 95 54 tfor:TF1868|3end_conserved_hypothetical_protein;_possible_transposase_2023043..2023193_POSITIVE 358 80 34 126 82 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 346 70 21 59 17 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 340 79 31 139 90 tfor:TF1947|3end_conserved_hypothetical_protein_2096023..2096173_POSITIVE 331 89 47 120 71 tfor:TF2158|3end_conserved_hypothetical_protein_2334584..2334734_POSITIVE 311 94 54 55 1 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 311 79 32 72 13 tfor:TF2490|3end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2666755..2666905_POSITIVE 307 58 19 142 97 tfor:TF2578|3end_30S_ribosomal_protein_S11_2747164..2747314_POSITIVE 306 90 41 77 24 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 306 70 29 64 23 tfor:TF2753|3end_zinc_protease_2940448..2940598_POSITIVE 302 72 35 51 6 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 301 96 57 69 21 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 300 98 55 121 78 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 299 129 87 115 66 tfor:TF2654|3end_arginyl-tRNA_synthetase_2824559..2824709_POSITIVE 299 119 72 57 16 tfor:TF1259|3end_hypothetical_protein_1345204..1345354_POSITIVE 298 70 25 88 33 tfor:TF0002|3end_hypothetical_protein_647..797_POSITIVE 293 69 25 139 96 tfor:TF2047|3end_hypothetical_protein_2210298..2210448_POSITIVE