Origin IGS: taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagtcatcagattgcaatgtcgagtttgcaaatcgcggcaaaagtaatcaaaaaaagataaacataacgtactgaagtgatattttttgttaaacattacagacagatggttcggcccccaaacaatgccttttttttttcgccccaacaaaaagagagattcgtaagattta Mask Tandem Repeat Region ================================================ taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Find is-nt database================================================ Query_seq: TF0436:TF0437|TF0436:TF0437:conserved hyothetical protein:conserved hypothetical protein:->->:460889..461062 174 taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0436:TF0437|TF0436:TF0437:conserved hyothetical protein:conserved hypothetical protein:->->:460889..461062 174 taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0436:TF0437|TF0436:TF0437:conserved hyothetical protein:conserved hypothetical protein:->->:460889..461062 174 taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Predict ORF larger than 30AA ================================================ Protein_Len: 50 Strand: + Start: 23 End: 172 ...................... M L G R K K K G I V W G P N H L S V M F N K K Y H F S T L C L S F F D Y F C R D L Q T R H C N L M T .. Protein_Len: 32 Strand: - Start: 2 End: 97 . F R V F R E K Q Q P S F F F A N N P P R V M Q R Y H K V F F I M ............................................................................. taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt 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================================================ taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0436:TF0437|TF0436:TF0437:conserved hyothetical protein:conserved hypothetical protein:->->:460889..461062 174 taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: tfor_TF0436_TF0437|conserved hyothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[460889,461062]|174 HSP 1 e-value: 8.0E-64 bit: 244.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 taaatcttacgaatctctctttttgttggggcgnnnnnnnnnnggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatcnnnnnnngattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt taaatcttacgaatctctctttttgttggggcgaaaaaaaaaaggcattgtttgggggccgaaccatctgtctgtaatgtttaacaaaaaatatcacttcagtacgttatgtttatctttttttgattacttttgccgcgatttgcaaactcgacattgcaatctgatgacttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCUUACGAAUCUCUCUUUUUGUUGGGGCGAAAAAAAAAAGGCAUUGUUUGGGGGCCGAACCAUCUGUCUGUAAUGUUUAACAAAAAAUAUCACUUCAGUACGUUAUGUUUAUCUUUUUUUGAUUACUUUUGCCGCGAUUUGCAAACUCGACAUUGCAAUCUGAUGACUUU ............(((.........((((.((((((((((((((((....((((((...))))))...(((...((.((((((......)))))).))..))).............)))))))))......))))))).))))((((((........))))))...)))...... (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUCAUCAGAUUGCAAUGUCGAGUUUGCAAAUCGCGGCAAAAGUAAUCAAAAAAAGAUAAACAUAACGUACUGAAGUGAUAUUUUUUGUUAAACAUUACAGACAGAUGGUUCGGCCCCCAAACAAUGCCUUUUUUUUUUCGCCCCAACAAAAAGAGAGAUUCGUAAGAUUUA .(((((....((((((..(((((.(.........).)))))...)))))).................(((..(((((....((((((((((........))))).))))).)))))..............((((((((((..........))))))))))...)))..))))). (-25.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 86 43 63 18 tfor:TF1929|5end_conserved_hypothetical_protein_2076049..2076279_POSITIVE 342 70 25 203 151 tfor:TF2666|5end_hypothetical_protein_2841818..2842048_POSITIVE 335 88 44 82 26 tfor:TF2762|5end_conserved_hypothetical_protein_2945857..2946087_POSITIVE 321 70 27 130 81 tfor:TF1580|5end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1687187..1687417_POSITIVE 311 70 25 49 3 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 310 76 31 105 42 tfor:TF2640|5end_hypothetical_protein_2809106..2809336_POSITIVE 308 60 14 60 16 tfor:TF1320|5end_beta-galactosidase_1398414..1398644_POSITIVE 301 59 11 181 126 tfor:TF2745|5end_hypothetical_protein_2927562..2927792_POSITIVE 298 67 30 52 6 tfor:TF1415|5end_outer_membrane_protein,_TonB_dependent_receptor_1494268..1494498_POSITIVE 298 163 131 217 185 tfor:TF0794|5end_hypothetical_protein_851380..851610_POSITIVE 294 162 133 229 197 tfor:TF2822|5end_arginine_repressor_3011793..3012023_POSITIVE 292 160 116 190 144 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 291 82 42 68 24 tfor:TF2193|5end_outer_membrane_protein,_TonB_dependent_receptor_2368432..2368662_POSITIVE 290 70 28 75 29 tfor:TF1578|5end_hypothetical_protein_1686187..1686417_POSITIVE 288 70 28 59 13 tfor:TF1588|5end_hypothetical_protein_1702268..1702498_POSITIVE 285 82 41 180 138 tfor:TF0517|5end_TPR-repeat-containing_protein_540621..540851_POSITIVE 284 61 24 139 103 tfor:TF2791|5end_GTP-binding_protein_TypA_2975298..2975528_POSITIVE 284 82 54 160 133 tfor:TF2051|5end_hypothetical_protein_2215183..2215413_POSITIVE 283 159 120 155 112 tfor:TF1928|5end_conserved_hypothetical_protein_2075529..2075759_POSITIVE 283 70 26 219 167 tfor:TF1812|5end_tryptophan_synthase,_beta_chain_1952696..1952926_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 86 43 58 13 tfor:TF1928|3end_conserved_hypothetical_protein_2076124..2076274_POSITIVE 335 88 44 70 14 tfor:TF2761|3end_thioredoxin_2945925..2946075_POSITIVE 321 70 27 137 88 tfor:TF1579|3end_hypothetical_protein_1687274..1687424_POSITIVE 302 81 45 128 94 tfor:TF0877|3end_ISPg2-related_(PGIS2-related)_transposase_931817..931967_POSITIVE 298 163 131 48 16 tfor:TF0793|3end_conserved_hypothetical_protein;_possible_AAA_superfamily_ATPase_851291..851441_POSITIVE 288 70 25 63 11 tfor:TF2666|3end_hypothetical_protein_2842263..2842413_POSITIVE 283 64 21 81 41 tfor:TF3046|3end_hypothetical_protein_3275192..3275342_POSITIVE 283 159 120 148 105 tfor:TF1927|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075602..2075752_POSITIVE 281 65 30 125 93 tfor:TF2507|3end_ATP-dependent_DNA_helicase_2686365..2686515_POSITIVE 281 63 25 144 111 tfor:TF0468|3end_hypothetical_protein_487188..487338_POSITIVE 281 156 114 86 23 tfor:TF0410|3end_8-amino-7-oxononanoate_synthase_428869..429019_POSITIVE 280 160 125 48 5 tfor:TF0804|3end_possible_phosphatidylglycerophosphate_synthase_862899..863049_POSITIVE 278 68 21 72 16 tfor:TF2006|3end_uracil_permease_2158642..2158792_POSITIVE 275 170 126 143 104 tfor:TF1571|3end_conserved_hypothetical_protein_1681032..1681182_POSITIVE 274 79 43 147 87 tfor:TF0982|3end_conserved_hypothetical_protein_1039474..1039624_POSITIVE 273 170 135 151 118 tfor:TF2833|3end_lipid_A_disaccharide_synthase_3025183..3025333_POSITIVE 273 170 124 149 101 tfor:TF2529|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_2711496..2711646_POSITIVE 272 147 104 150 96 tfor:TF2974|3end_conserved_hypothetical_protein;_possible_hydrolase_3182439..3182589_POSITIVE 271 100 51 102 60 tfor:TF3098|3end_conserved_hypothetical_protein_3330535..3330685_POSITIVE 271 169 135 56 21 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE