Origin IGS: taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt .........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 aatcgtttgcttttaagatgttaataatgttgctaaatgctttgtctgatttatcggaaaaccgccgtctttttatccttcttcccaaacccacgagggttttcccgaaaagggtcgaggttttttgccgaaaccctcgtgggttttgatggaaagggctgtacgataataaccatgtta Mask Tandem Repeat Region ================================================ taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Find is-nt database================================================ Query_seq: TF1294:TF1296|TF1294:TF1296:conserved hypothetical protein:possible DNA-binding protein, histone-like family:->->:1378392..1378571 180 taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1294:TF1296|TF1294:TF1296:conserved hypothetical protein:possible DNA-binding protein, histone-like family:->->:1378392..1378571 180 taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1294:TF1296|TF1294:TF1296:conserved hypothetical protein:possible DNA-binding protein, histone-like family:->->:1378392..1378571 180 taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 5 End: 127 .... M V I I V Q P F P S K P T R V S A K N L D P F R E N P R G F G K K D K K T A V F R ..................................................... Protein_Len: 31 Strand: + Start: 87 End: 179 ...................................................................................... M G L G R R I K R R R F S D K S D K A F S N I I N I L K A N D . Protein_Len: 43 Strand: - Start: 35 End: 163 .................................. F G R P N R C F V E V R K P F V R T P K P L L I F L R R N E S L D S L A N L L M I L M ................. Protein_Len: 38 Strand: - Start: 15 End: 128 .............. R V A R E M L V W S P K P L F G R G K E P F G E H T Q S S P Y F S P P K G M .................................................... Protein_Len: 48 Strand: - Start: 1 End: 144 L M T I I T C G K G D F G V L T E A F F R S G K R S F G R P N P F F S L F V A T K R Y I L C L M .................................... taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt 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================================================ taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -11.9 Tail_Score: -4.25104 Start: 38 End: 91 Full_Region: atccttcttcccaaa cccacgagggttttcccgaaaag ggtcgagg ttttttgccgaaaccctcgtggg ttttgatggaaaggg .....................................cccacgagggttttcccgaaaagggtcgaggttttttgccgaaaccctcgtggg......................................................................................... Find igs database================================================ Query_seq: TF1294:TF1296|TF1294:TF1296:conserved hypothetical protein:possible DNA-binding protein, histone-like family:->->:1378392..1378571 180 taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: tfor_TF1294_TF1296|conserved hypothetical protein:possible DNA-binding protein, histone-like family|POSITIVE:POSITIVE|[1378392,1378571]|180 HSP 1 e-value: 8.0E-98 bit: 357.0 Len: 180 Query Start:1 Query End:180 Subject Strand: POSITIVE Subject Start: 1 Subject End: 180 taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt taacatggttattatcgtacagccctttccatcaaaacccacgagggtttcggcaaaaaacctcgacccttttcgggaaaaccctcgtgggtttgggaagaaggataaaaagacggcggttttccgataaatcagacaaagcatttagcaacattattaacatcttaaaagcaaacgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACAUGGUUAUUAUCGUACAGCCCUUUCCAUCAAAACCCACGAGGGUUUCGGCAAAAAACCUCGACCCUUUUCGGGAAAACCCUCGUGGGUUUGGGAAGAAGGAUAAAAAGACGGCGGUUUUCCGAUAAAUCAGACAAAGCAUUUAGCAACAUUAUUAACAUCUUAAAAGCAAACGAUU .............(((((...((.(((((((....(((((((((((((((.((.......))....(((.....))).)))))))))))))))))))))).(((((.....((...(((....))).....)).......((.....))............)))))....))..))))). (-49.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGUUUGCUUUUAAGAUGUUAAUAAUGUUGCUAAAUGCUUUGUCUGAUUUAUCGGAAAACCGCCGUCUUUUUAUCCUUCUUCCCAAACCCACGAGGGUUUUCCCGAAAAGGGUCGAGGUUUUUUGCCGAAACCCUCGUGGGUUUUGAUGGAAAGGGCUGUACGAUAAUAACCAUGUUA .(((((..(((((.((((((...........((.....))....(((((....))))).......))))))....(((.((.....((((((((((((((((.(((.....)))....(((.....))).)))))))))))))))).)).))).)))))...)))))............. (-55.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 416 89 41 122 60 tfor:TF2435|5end_DNA_repair_protein_radC_2614352..2614582_POSITIVE 409 89 41 61 5 tfor:TF0092|5end_outer_membrane_protein_98889..99119_POSITIVE 359 90 42 75 27 tfor:TF1559|5end_glycosyltransferase_1665879..1666109_POSITIVE 353 118 71 185 140 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 347 52 13 193 153 tfor:TF2781|5end_hypothetical_protein_2965822..2966052_POSITIVE 343 120 75 73 40 tfor:TF0634|5end_hypothetical_protein_668120..668350_POSITIVE 340 120 74 184 148 tfor:TF1841|5end_hypothetical_protein_1991936..1992166_POSITIVE 340 78 42 81 39 tfor:TF1030|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_1088229..1088459_POSITIVE 338 86 41 210 167 tfor:TF2344|5end_ATP/GTP_binding_protein_2507422..2507652_POSITIVE 338 97 52 129 75 tfor:TF1866|5end_conserved_hypothetical_protein;_possible_transposase_2022272..2022502_POSITIVE 334 78 32 191 132 tfor:TF0402|5end_conserved_hypothetical_protein_422107..422337_POSITIVE 331 90 43 134 77 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 331 95 51 60 20 tfor:TF0815|5end_conserved_hypothetical_protein_873199..873429_POSITIVE 330 104 62 145 103 tfor:TF1763|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_1900406..1900636_POSITIVE 328 100 51 49 8 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 326 81 41 53 9 tfor:TF1230|5end_hypothetical_protein_1314905..1315135_POSITIVE 326 90 41 199 150 tfor:TF0510|5end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,_vorA_536142..536372_POSITIVE 325 126 81 40 4 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 325 78 38 221 176 tfor:TF2048|5end_conserved_hypothetical_protein_2210643..2210873_POSITIVE 325 99 52 113 63 tfor:TF0750|5end_conserved_hypothetical_protein_797776..798006_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 90 41 52 3 tfor:TF1294|3end_conserved_hypothetical_protein_1378331..1378481_POSITIVE 359 90 42 75 27 tfor:TF1558|3end_possible_heme_biosynthesis_protein_1665959..1666109_POSITIVE 341 100 51 62 7 tfor:TF2434|3end_conserved_hypothetical_protein_2614363..2614513_POSITIVE 334 78 46 40 3 tfor:TF1029|3end_conserved_hypothetical_protein;_possible_phytoene_dehydrogenase_1088268..1088418_POSITIVE 334 78 32 132 73 tfor:TF0400|3end_conserved_hypothetical_protein_422128..422278_POSITIVE 331 90 43 137 80 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 328 100 51 49 8 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 325 99 52 88 38 tfor:TF0749|3end_protease_II_797831..797981_POSITIVE 321 96 60 126 76 tfor:TF1612|3end_conserved_hypothetical_protein_1729866..1730016_POSITIVE 320 88 41 91 40 tfor:TF3133|3end_conserved_hypothetical_protein_3369913..3370063_POSITIVE 319 119 73 144 93 tfor:TF2092|3end_ribonuclease_III_2261823..2261973_POSITIVE 313 75 36 148 109 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE 311 54 19 43 9 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 311 120 71 59 15 tfor:TF0489|3end_D-xylose-proton_symporter_513069..513219_POSITIVE 309 71 38 47 12 tfor:TF3110|3end_conserved_hypothetical_protein_with_helicase_domain_3346636..3346786_POSITIVE 308 99 64 146 102 tfor:TF1218|3end_hypothetical_protein_1304383..1304533_POSITIVE 307 94 51 70 20 tfor:TF1655|3end_long-chain-fatty-acid-CoA_ligase_1771068..1771218_POSITIVE 306 78 38 143 100 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 302 54 16 126 84 tfor:TF0350|3end_hypothetical_protein_371101..371251_POSITIVE 300 52 11 86 44 tfor:TF0605|3end_conserved_hypothetical_protein_636883..637033_POSITIVE