Origin IGS: taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa .........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 ttatatcaattacttgaagtaccacattccgaatatgtacccaaaatgccgttttcgggtacacgtctcaaggatatgtacccattttgtctcttttgggtacatattcaaggtatatcactatgcacgactcactccgccaaagtcattatataccttatcagtggcaaatataaggaataggaatcaattataccccttttcgggggtattta Mask Tandem Repeat Region ================================================ taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Find is-nt database================================================ Query_seq: TF1543:TF1544|TF1543:TF1544:conserved hypothetical protein:possible transcriptional regulator:->->:1650835..1651049 215 taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1543:TF1544|TF1543:TF1544:conserved hypothetical protein:possible transcriptional regulator:->->:1650835..1651049 215 taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1543:TF1544|TF1543:TF1544:conserved hypothetical protein:possible transcriptional regulator:->->:1650835..1651049 215 taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 105 End: 203 ........................................................................................................ M N M Y P K E T K W V H I L E T C T R K R H F G Y I F G M W Y F K ............ Protein_Len: 33 Strand: + Start: 109 End: 207 ............................................................................................................ M C T Q K R Q N G Y I S L R R V P E N G I L G T Y S E C G T S S N ........ Protein_Len: 47 Strand: - Start: 43 End: 183 .......................................... I Q W Q Y P I Y H S Q R L S D H M T I Y R S Y T G L L S L I P V Y G Q S T Y G F V A N Q T C M ................................ Protein_Len: 45 Strand: - Start: 36 End: 170 ................................... E K Y K G S I L Y I I V K A S H T T C L S I G Q I H V W F L C F P Y M D K L R T G S F P M ............................................. Protein_Len: 60 Strand: - Start: 2 End: 211 . R N R I N A V S L T Y L S K P P T L R A Y H Y V K F I Y G F S V F H T C I R S V H V R F R C K P Y M N P I H Y K L Y N M .... taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa 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================================================ taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -4.6 Tail_Score: -2.72049 Start: 110 End: 141 Full_Region: GTGATATACCTTGAA TATGTACCCA AAAGAGACAAAA TGGGTACATA TCCTTGAGACGTGTA .............................................................................................................TATGTACCCAAAAGAGACAAAATGGGTACATA.......................................................................... TransTerm Strand: + Conf: 43 HP_score: -2.8 Tail_Score: -2.90392 Start: 112 End: 139 Full_Region: GATATACCTTGAATA TGTACCCA AAAGAGACAAAA TGGGTACA TATCCTTGAGACGTG ...............................................................................................................TGTACCCAAAAGAGACAAAATGGGTACA............................................................................ TransTerm Strand: - Conf: 44 HP_score: -2.8 Tail_Score: -3.05819 Start: 112 End: 139 Full_Region: cacgtctcaaggata tgtaccca ttttgtctcttt tgggtaca tattcaaggtatatc ...............................................................................................................tgtacccattttgtctcttttgggtaca............................................................................ TransTerm Strand: - Conf: 71 HP_score: -4.5 Tail_Score: -4.78933 Start: 132 End: 160 Full_Region: ccaaaatgccgtttt cgggtacacgtct caa ggatatgtaccca ttttgtctcttttgg ...................................................................................................................................cgggtacacgtctcaaggatatgtaccca....................................................... TransTerm Strand: + Conf: 74 HP_score: -9.3 Tail_Score: -3.05521 Start: 153 End: 180 Full_Region: CATATCCTTGAGACG TGTACCCGAAA ACGGCA TTTTGGGTACA TATTCGGAATGTGGT ........................................................................................................................................................TGTACCCGAAAACGGCATTTTGGGTACA................................... Find igs database================================================ Query_seq: TF1543:TF1544|TF1543:TF1544:conserved hypothetical protein:possible transcriptional regulator:->->:1650835..1651049 215 taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Intra-Species Hit: Count: 1 Min: 1 Max: 215 Len: 215 Subject: tfor_TF1543_TF1544|conserved hypothetical protein:possible transcriptional regulator|POSITIVE:POSITIVE|[1650835,1651049]|215 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 215 Query Start:1 Query End:215 Subject Strand: POSITIVE Subject Start: 1 Subject End: 215 taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa taaatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaagtaattgatataa Inter-species Hit: Count: 1 Min: 3 Max: 203 Len: 201 Subject: NC_002950_PG0856_PG0857|hypothetical protein:transcriptional regulator, putative|POSITIVE:POSITIVE|[917236,917458]|223 HSP 1 e-value: 3.0E-79 bit: 295.0 Len: 201 Query Start:3 Query End:203 Subject Strand: POSITIVE Subject Start: 10 Subject End: 210 ..aatacccccgaaaaggggtataattgattcctattccttatatttgccactgataaggtatataatgactttggcggagtgagtcgtgcatagtgatataccttgaatatgtacccaaaagagacaaaatgggtacatatccttgagacgtgtacccgaaaacggcattttgggtacatattcggaatgtggtacttcaag............ ..aatatccccgaaaaggggtataatacatttatattccttatatttgccactgataaggtatataatgactttctcggagtgagccgtgcatagtgatatgccttgaatatgtacccaaaagagacaaaatgggtacatatccttgggacgtgtacccgaaaacggcatttggggtacatattcggaatatggaacttcaag............ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACCCCCGAAAAGGGGUAUAAUUGAUUCCUAUUCCUUAUAUUUGCCACUGAUAAGGUAUAUAAUGACUUUGGCGGAGUGAGUCGUGCAUAGUGAUAUACCUUGAAUAUGUACCCAAAAGAGACAAAAUGGGUACAUAUCCUUGAGACGUGUACCCGAAAACGGCAUUUUGGGUACAUAUUCGGAAUGUGGUACUUCAAG .(((((((......)))))))..((((..((((((((.................(((((((((.(((((((.........)))))))........)))))))))((((((((((((((((.........((((((((..((.....))..)))))))).........)))))))))))))))))))))).))....)))). (-70.87) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGAAGUACCACAUUCCGAAUAUGUACCCAAAAUGCCGUUUUCGGGUACACGUCUCAAGGAUAUGUACCCAUUUUGUCUCUUUUGGGUACAUAUUCAAGGUAUAUCACUAUGCACGACUCACUCCGCCAAAGUCAUUAUAUACCUUAUCAGUGGCAAAUAUAAGGAAUAGGAAUCAAUUAUACCCCUUUUCGGGGGUAUU ((((.....((((.....((((((((((((((((..........(((((((..((.....))..)))))))..........)))))))))))))))).((((((((.(((.((..((........)).)).)))....)))))))).....))))......))))...............((((((((....)))))))). (-62.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 382 168 121 110 55 tfor:TF1143|5end_ABC_transporter,_ATP-binding/permease_component_1221704..1221934_POSITIVE 336 199 155 206 168 tfor:TF2037|5end_conserved_hypothetical_protein;_possible_anaerobic_ribonucleoside-triphosphate_reductase_2196754..2196984_POSITIVE 327 179 133 61 5 tfor:TF1471|5end_conserved_hypothetical_protein_1564608..1564838_POSITIVE 326 176 135 134 98 tfor:TF2617|5end_conserved_hypothetical_protein_2793812..2794042_POSITIVE 326 179 132 76 28 tfor:TF0005|5end_possible_beta-lactamase_600..830_POSITIVE 321 189 142 142 86 tfor:TF1260|5end_chaperone_protein_DnaJ_1345325..1345555_POSITIVE 318 88 47 170 133 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 317 189 141 67 16 tfor:TF1146|5end_2-dehydropantoate_2-reductase_1227162..1227392_POSITIVE 311 189 141 53 8 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 310 112 71 56 12 tfor:TF1160|5end_MutT/nudix_family_protein_1240305..1240535_POSITIVE 307 175 137 229 188 tfor:TF2247|5end_transfer_region-related_protein,_TraA_2421463..2421693_POSITIVE 307 175 137 54 13 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 306 191 151 116 73 tfor:TF0278|5end_conserved_hypothetical_protein_305570..305800_POSITIVE 303 170 129 231 190 tfor:TF1951|5end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2100792..2101022_POSITIVE 301 178 148 83 44 tfor:TF0371|5end_beta-mannosidase_precursor_386763..386993_POSITIVE 300 118 73 214 161 tfor:TF2372|5end_acyl-(acyl-carrier-protein)-UDP-N-acetylglucosami_ne_acyltransferase_2537558..2537788_POSITIVE 299 192 155 228 197 tfor:TF2500|5end_ABC_transporter,_ATP-binding_protein_2674449..2674679_POSITIVE 298 178 137 196 155 tfor:TF2593|5end_amino_acid_transport_protein_2762882..2763112_POSITIVE 298 195 160 102 66 tfor:TF1861|5end_conserved_hypothetical_protein;_possible_membrane_protein_2017220..2017450_POSITIVE 296 87 45 101 54 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 186 144 129 92 tfor:TF1774|3end_arylsulfatase_precursor_1912939..1913089_POSITIVE 326 176 135 134 98 tfor:TF2616|3end_outer_membrane_protein,_TonB_dependent_receptor_2793892..2794042_POSITIVE 319 89 43 116 60 tfor:TF1740|3end_hypothetical_protein_1869192..1869342_POSITIVE 311 189 141 53 8 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 309 172 131 141 100 tfor:TF1950|3end_conserved_hypothetical_protein;_possible_transporter_2100780..2100930_POSITIVE 306 191 151 113 70 tfor:TF0277|3end_outer_membrane_protein_305647..305797_POSITIVE 299 196 156 43 2 tfor:TF0141|3end_exodeoxyribonuclease_VII,_large_subunit_149830..149980_POSITIVE 296 87 45 101 54 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 296 199 151 143 93 tfor:TF0959|3end_periplasmic_protease_1008540..1008690_POSITIVE 293 160 117 129 80 tfor:TF0899|3end_hypothetical_protein_946159..946309_POSITIVE 292 178 141 144 110 tfor:TF0294|3end_possible_translation_factor_321902..322052_POSITIVE 289 177 131 63 7 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 287 189 148 138 101 tfor:TF0998|3end_[acyl-carrier-protein]_S-malonyltransferase_1052977..1053127_POSITIVE 287 190 141 148 99 tfor:TF0022|3end_two-component_system_sensor_histidine_kinase_19522..19672_POSITIVE 286 103 64 72 24 tfor:TF1738|3end_outer_membrane_protein_1866946..1867096_POSITIVE 285 114 75 41 3 tfor:TF1188|3end_conserved_hypothetical_protein_1270634..1270784_POSITIVE 282 195 166 133 103 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 282 189 141 140 80 tfor:TF2782|3end_conserved_hypothetical_protein_2967356..2967506_POSITIVE 281 178 145 41 9 tfor:TF2592|3end_conserved_hypothetical_protein_2762807..2762957_POSITIVE 281 178 134 53 13 tfor:TF1354|3end_TonB_protein_1435216..1435366_POSITIVE