Origin IGS: aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaaatgacatattcattttcgatctttaacgatcagcaaaaacgtcgggcattagtgctgctcagtttcttccacatttttatcatcgccgccagtaactatctcgtgcagattccctttgaagtgcatgtgccgttgacgttctttggcgcacaggaagacttc .........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 gaagtcttcctgtgcgccaaagaacgtcaacggcacatgcacttcaaagggaatctgcacgagatagttactggcggcgatgataaaaatgtggaagaaactgagcagcactaatgcccgacgtttttgctgatcgttaaagatcgaaaatgaatatgtcatttgaaattacctttttagtttaaattggggttagggaacccagttcgtgatttcgcaaaaaatgcatcttagaggcattgtaacataatcaggtaaaattattttctccctttcaataaaaaaacttaaaaaatttaaaattttttgtaagaaaatcagaggtaactccgtctaatgcacatacgtgaaaatcgtaaggttttcacgtacaaagcacttttctataaataacaaatctcacaatctctaaaggagtttatt Mask Tandem Repeat Region ================================================ aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaaatgacatattcattttcgatctttaacgatcagcaaaaacgtcgggcattagtgctgctcagtttcttccacatttttatcatcgccgccagtaactatctcgtgcagattccctttgaagtgcatgtgccgttgacgttctttggcgcacaggaagacttc Find is-nt database================================================ Query_seq: AA00949:AA00950|AA00949:AA00950:hypothetical protein:conserved hypothetical protein:->->:656639..657061 423 aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaaatgacatattcattttcgatctttaacgatcagcaaaaacgtcgggcattagtgctgctcagtttcttccacatttttatcatcgccgccagtaactatctcgtgcagattccctttgaagtgcatgtgccgttgacgttctttggcgcacaggaagacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00949:AA00950|AA00949:AA00950:hypothetical protein:conserved hypothetical protein:->->:656639..657061 423 aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaaatgacatattcattttcgatctttaacgatcagcaaaaacgtcgggcattagtgctgctcagtttcttccacatttttatcatcgccgccagtaactatctcgtgcagattccctttgaagtgcatgtgccgttgacgttctttggcgcacaggaagacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00949:AA00950|AA00949:AA00950:hypothetical protein:conserved hypothetical protein:->->:656639..657061 423 aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaaatgacatattcattttcgatctttaacgatcagcaaaaacgtcgggcattagtgctgctcagtttcttccacatttttatcatcgccgccagtaactatctcgtgcagattccctttgaagtgcatgtgccgttgacgttctttggcgcacaggaagacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 7 Min: 262 Max: 423 Len: 162 Subject: UniRef90_Q65VA5 Cluster: Hypothetical protein; n=1; Mannheimia succiniciproducens MBEL55E|Rep: Hypothetical protein - Mannheimia succiniciproducens (strain MBEL55E) HSP 1 e-value: 9.0E-16 bit: 84.7 Len: 162 Query Start:262 Query End:423 Subject Strand: null Subject Start: 1 Subject End: 54 ..................................................................................................................................................................................................................................................................... M T Y S F S I F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T F F G A Q E D F ..................................................................................................................................................................................................................................................................... M K T S L S I F N D Q Q K R R A L I L I S L F H I L I I A A S N Y L V Q V P F E I H L P F T A L G A K E N F Subject: UniRef90_Q9CJV2 Cluster: Hypothetical protein PM1889; n=1; Pasteurella multocida|Rep: Hypothetical protein PM1889 - Pasteurella multocida HSP 1 e-value: 3.0E-15 bit: 83.2 Len: 162 Query Start:262 Query End:423 Subject Strand: null Subject Start: 1 Subject End: 54 ..................................................................................................................................................................................................................................................................... M T Y S F S I F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T F F G A Q E D F ..................................................................................................................................................................................................................................................................... M K N T F S I F N D Q Q T R R A L I L L S F F H I L I I A A S N Y L V Q I P F E I T L P L S Q L G T R E D F Subject: UniRef90_Q0I211 Cluster: Hypothetical protein; n=2; Histophilus somni|Rep: Hypothetical protein - Haemophilus somnus (strain 129Pt) (Histophilus somni (strain 129Pt)) HSP 1 e-value: 2.0E-14 bit: 80.1 Len: 147 Query Start:277 Query End:423 Subject Strand: null Subject Start: 6 Subject End: 54 .................................................................................................................................................................................................................................................................................... S I F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T F F G A Q E D F .................................................................................................................................................................................................................................................................................... S I F N D Q Q K K R A L I I L S F F H I F I I T A S N Y L V Q I P F E I T I P L T T L G F A E N F Subject: UniRef90_Q3EFB4 Cluster: Conserved hypothetical HI0862 precursor; n=1; Actinobacillus succinogenes 130Z|Rep: Conserved hypothetical HI0862 precursor - Actinobacillus succinogenes 130Z HSP 1 e-value: 1.0E-13 bit: 77.4 Len: 162 Query Start:262 Query End:423 Subject Strand: null Subject Start: 1 Subject End: 54 ..................................................................................................................................................................................................................................................................... M T Y S F S I F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T F F G A Q E D F ..................................................................................................................................................................................................................................................................... M T R N S T I I T H K Q K R N A L I L L T F F H I F I I A A S N Y L V Q I P F E I R L P L T A L G A A E D F Subject: UniRef90_P44908 Cluster: Hypothetical protein HI0862; n=4; Haemophilus influenzae|Rep: Hypothetical protein HI0862 - Haemophilus influenzae HSP 1 e-value: 3.0E-13 bit: 76.3 Len: 162 Query Start:262 Query End:423 Subject Strand: null Subject Start: 1 Subject End: 54 ..................................................................................................................................................................................................................................................................... M T Y S F S I F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T F F G A Q E D F ..................................................................................................................................................................................................................................................................... M K L T S P I F N D Q Q K R R A I I W L S F F H I F I I A A S N Y F V Q I P F E I T L K L T A L G A A N D F Subject: UniRef90_A3N3W7 Cluster: Hypothetical protein; n=1; Actinobacillus pleuropneumoniae L20|Rep: Hypothetical protein - Actinobacillus pleuropneumoniae serotype 5b (strain L20) HSP 1 e-value: 6.0E-9 bit: 62.0 Len: 117 Query Start:283 Query End:399 Subject Strand: null Subject Start: 7 Subject End: 45 .......................................................................................................................................................................................................................................................................................... F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T ........................ .......................................................................................................................................................................................................................................................................................... F S D A Q K R R S L I L L S L F H I F I I A I S N Y L V Q I T F E V K I P F T ........................ Subject: UniRef90_Q7VP52 Cluster: Hypothetical protein; n=1; Haemophilus ducreyi|Rep: Hypothetical protein - Haemophilus ducreyi HSP 1 e-value: 9.0E-8 bit: 58.2 Len: 117 Query Start:283 Query End:399 Subject Strand: null Subject Start: 7 Subject End: 45 .......................................................................................................................................................................................................................................................................................... F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T ........................ .......................................................................................................................................................................................................................................................................................... F S D A Q K R R S L I L L S S F H I F I I S L S N Y L V Q I T F E I K F P F T ........................ aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 103 End: 228 ...................................................................................................... M I F L Q K I L N F L S F F I E R E K I I L P D Y V T M P L R C I F C E I T N W V P ................................................................................................................................................................................................... Protein_Len: 54 Strand: + Start: 262 End: 423 ..................................................................................................................................................................................................................................................................... M T Y S F S I F N D Q Q K R R A L V L L S F F H I F I I A A S N Y L V Q I P F E V H V P L T F F G A Q E D F Protein_Len: 34 Strand: - Start: 313 End: 414 ........................................................................................................................................................................................................................................................................................................................ H Q E T E E V N K D D G G T V I E H L N G K F H M H R Q R E K A C M ......... aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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================================================ aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.1 Tail_Score: -3.10558 Start: 55 End: 69 Full_Region: GAAAAGTGCTTTGTA CGTGA AAACC TTACG ATTTTCACGTATGTG ......................................................CGTGAAAACCTTACG.................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 83 HP_score: -2.2 Tail_Score: -5.7946 Start: 123 End: 137 Full_Region: TTTCTTACAAAAAAT TTTAAA TTT TTTAAG TTTTTTTATTGAAAG ..........................................................................................................................TTTAAATTTTTTAAG.............................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 73 HP_score: -4.2 Tail_Score: -5.02074 Start: 185 End: 199 Full_Region: CTGATTATGTTACAA TGCCTC TAA GATGCA TTTTTTGCGAAATCA ........................................................................................................................................................................................TGCCTCTAAGATGCA................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: AA00949:AA00950|AA00949:AA00950:hypothetical protein:conserved hypothetical protein:->->:656639..657061 423 aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaattttaaattttttaagtttttttattgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 261 Len: 261 Subject: aact_AA00949_AA00950|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[656639,657061]|423 HSP 1 e-value: 3.0E-62 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaa.............................................................................................................................................................................................................................................................................................................. aataaactcctttagagattgtgagatttgttatttatagaaaagtgctttgtacgtgaaaaccttacgattttcacgtatgtgcattagacggagttacctctgattttcttacaaaaaa.............................................................................................................................................................................................................................................................................................................. HSP 2 e-value: 8.0E-60 bit: 232.0 Len: 117 Query Start:145 Query End:261 Subject Strand: POSITIVE Subject Start: 145 Subject End: 261 ................................................................................................................................................attgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaa.................................................................................................................................................................. ................................................................................................................................................attgaaagggagaaaataattttacctgattatgttacaatgcctctaagatgcattttttgcgaaatcacgaactgggttccctaaccccaatttaaactaaaaaggtaatttcaa.................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAACUCCUUUAGAGAUUGUGAGAUUUGUUAUUUAUAGAAAAGUGCUUUGUACGUGAAAACCUUACGAUUUUCACGUAUGUGCAUUAGACGGAGUUACCUCUGAUUUUCUUACAAAAAAUUUUAAAUUUUUUAAGUUUUUUUAUUGAAAGGGAGAAAAUAAUUUUACCUGAUUAUGUUACAAUGCCUCUAAGAUGCAUUUUUUGCGAAAUCACGAACUGGGUUCCCUAACCCCAAUUUAAACUAAAAAGGUAAUUUCAA ......((((((((((((((..((((((((..((((..((((((((((..((((((((((((.(....).)))))))))))).)))))...(((((....)))))..)))))......))))..))))))))...))))))).......))))))).........((((((((((.(((...(((((.((...)).)))))....))).)))).......(((((....)))))...............))))))...... (-56.91) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAAUUACCUUUUUAGUUUAAAUUGGGGUUAGGGAACCCAGUUCGUGAUUUCGCAAAAAAUGCAUCUUAGAGGCAUUGUAACAUAAUCAGGUAAAAUUAUUUUCUCCCUUUCAAUAAAAAAACUUAAAAAAUUUAAAAUUUUUUGUAAGAAAAUCAGAGGUAACUCCGUCUAAUGCACAUACGUGAAAAUCGUAAGGUUUUCACGUACAAAGCACUUUUCUAUAAAUAACAAAUCUCACAAUCUCUAAAGGAGUUUAUU ......((((((..((((((..(((((((.........))))))).(((....)))....(((((.((...)).)))))..))).)))..)))))).........((((......((((((((..((((.....))))..)))))))).((((((..(((((.....)).)))..(((...((((((((((((....))))))))))))....))).))))))............................))))...... (-52.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 227 182 201 152 aact:AA02939|5end_phosphoserine_phosphatase_2056881..2057111_POSITIVE 292 239 197 190 140 aact:AA01384|5end_hypothetical_protein_935320..935550_POSITIVE 284 227 183 82 35 aact:AA01634|5end_hypothetical_protein_1104324..1104554_POSITIVE 278 230 181 204 168 aact:AA01568|5end_dipeptide_transport_system_ATP-binding_protein_1056037..1056267_POSITIVE 277 106 63 40 1 aact:AA02677|5end_formate_dehydrogenase,_beta_subunit_1864102..1864332_POSITIVE 268 242 207 78 43 aact:AA02937|5end_conserved_hypothetical_protein_2056379..2056609_POSITIVE 265 95 56 171 137 aact:AA03000|5end_uracil-DNA_glycosylase_(UDG)_2095076..2095306_POSITIVE 259 117 75 199 150 aact:AA01845|5end_gamma-glutamyltranspeptidase_precursor_1239841..1240071_POSITIVE 257 229 181 93 30 aact:AA01240|5end_30S_ribosomal_protein_S11_844875..845105_POSITIVE 256 106 62 212 155 aact:AA02511|5end_transmembrane_protein_1742047..1742277_POSITIVE 256 227 182 52 14 aact:AA02330|5end_UDP-N-acetylglucosamine_enolpyruvyl_transferase_1589933..1590163_POSITIVE 254 228 182 64 14 aact:AA02954|5end_penicillin_tolerance_protein;_hydroxymethylbutenyl_pyrophosphate_reductase_2065610..2065840_POSITIVE 253 105 61 139 93 aact:AA01262|5end_hydrolase_859576..859806_POSITIVE 252 89 42 97 49 aact:AA02399|5end_30S_ribosomal_protein_S21_1650900..1651130_POSITIVE 250 229 182 78 21 aact:AA01566|5end_conserved_hypothetical_protein_1051811..1052041_POSITIVE 250 229 182 78 21 aact:AA01261|5end_conserved_hypothetical_protein_856443..856673_POSITIVE 250 229 185 209 164 aact:AA00930|5end_pantothenate_kinase_640275..640505_POSITIVE 248 225 187 74 29 aact:AA02755|5end_hypothetical_protein_1929303..1929533_POSITIVE 248 105 64 225 174 aact:AA02267|5end_conserved_hypothetical_protein_1545416..1545646_POSITIVE 244 84 48 137 100 aact:AA01925|5end_conserved_hypothetical_protein_1299961..1300191_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 106 65 35 4 aact:AA02676|3end_formate_dehydrogenase_alpha_subunit_1864177..1864327_POSITIVE 265 95 56 146 112 aact:AA02999|3end_conserved_hypothetical_protein_2095131..2095281_POSITIVE 262 236 197 151 106 aact:AA01383|3end_DNA_processing_chain_A_935366..935516_POSITIVE 259 117 75 108 59 aact:AA01843|3end_sensor_protein;_probable_two-component_system_sensor_histidine_kinase_1239830..1239980_POSITIVE 257 229 181 74 11 aact:AA01239|3end_30S_ribosomal_protein_S13_844936..845086_POSITIVE 254 228 182 61 11 aact:AA02952|3end_lipoprotein_signal_peptidase_2065687..2065837_POSITIVE 250 229 185 148 103 aact:AA00929|3end_DNA_gyrase_subunit_B_640294..640444_POSITIVE 248 225 187 49 4 aact:AA02754|3end_conserved_hypothetical_protein_1929358..1929508_POSITIVE 248 105 64 151 100 aact:AA02266|3end_exodeoxyribonuclease_V_beta_chain_1545422..1545572_POSITIVE 242 228 182 100 47 aact:AA02303|3end_ATP-dependent_DNA_helicase_1574854..1575004_POSITIVE 242 102 67 78 41 aact:AA02040|3end_hypothetical_protein_(possible_transposase_fragment)_1388434..1388584_POSITIVE 240 229 185 78 27 aact:AA00881|3end_hypothetical_protein_613485..613635_POSITIVE 235 225 187 150 108 aact:AA00087|3end_possible_hydrolase_(alpha/beta_fold_family)_66022..66172_POSITIVE 234 101 62 150 103 aact:AA01969|3end_hypothetical_protein_1332165..1332315_POSITIVE 233 222 185 105 72 aact:AA01626|3end_N_utilization_substance_protein_B_1100946..1101096_POSITIVE 233 80 32 62 11 aact:AA01439|3end_probable_ferredoxin_(fdx-2)_966498..966648_POSITIVE 231 88 44 47 3 aact:AA00949|3end_hypothetical_protein_656578..656728_POSITIVE 229 85 44 63 26 aact:AA02801|3end_myo-inositol_catabolism_protein_1969073..1969223_POSITIVE 228 221 188 112 72 aact:AA02858|3end_conserved_hypothetical_protein_2006068..2006218_POSITIVE 226 95 55 112 71 aact:AA00886|3end_hypothetical_protein_616855..617005_POSITIVE