Origin IGS: caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc .........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 gacggaaatcggtcaaaaaaacacttgatataagaaggaactcttatttttgttccaaaaccgcatcgcttgtgagaaagaagctctccatattcttcataggcttggcctcccttgtcgtgctgatcatcggtattatgccccatcatcatcacaacaaaggtatggcatgtctcatggcaaaacattgtcatgagaacgcccctgcggacaaagagcacactcatagcgaaccgacctgcgtagccaaaaccttctacctgtccggtgcggaacttcgactcaagcacagatattctctctgcgaagagtgccacgatccccatcacatccatgtattccctattctctttgccgtagccgatctattg Mask Tandem Repeat Region ================================================ caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc Find is-nt database================================================ Query_seq: PG0068:PG0069|PG0068:PG0069:hypothetical protein:hypothetical protein:-><-:82140..82510 371 caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0068:PG0069|PG0068:PG0069:hypothetical protein:hypothetical protein:-><-:82140..82510 371 caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0068:PG0069|PG0068:PG0069:hypothetical protein:hypothetical protein:-><-:82140..82510 371 caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 233 End: 325 ........................................................................................................................................................................................................................................ M I P M I S T T R E A K P M K N M E S F F L T S D A V L E Q K .............................................. Protein_Len: 60 Strand: + Start: 7 End: 369 ...... M G Y G K E N R E Y M D V M G I V A L F A E R I S V L E S K F R T G Q V E G F G Y A G R F A M S V L F V R R G V L M T M .. Protein_Len: 48 Strand: - Start: 179 End: 322 .................................................................................................................................................................................. S L T K G H S M G Y R Q Q S S S P A Y Y R H D A R C P L G L R H L I H L A E K E C A I R N Q F M ................................................. Protein_Len: 33 Strand: - Start: 129 End: 227 ................................................................................................................................ A P R N A I L T S K T R L P T R M V I N Q W S V H W V K T T I I M ................................................................................................................................................ Protein_Len: 30 Strand: - Start: 15 End: 104 .............. P L S F L S Y M S T I P I T A S K A S L I D T S S D F N R M ........................................................................................................................................................................................................................................................................... Protein_Len: 44 Strand: - Start: 2 End: 133 . I S R S R C L S Y P I C P H S P S R P V R R L S F I Q A Q T S T G C R V P L L N Q S R M .............................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 1 End: 342 A P A N E H C H K A M L C A M G K N H H H H P M I G I I L V V L S A L G I F F I S L K K R V L S A T K S C F Y S N R R M ............................. caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc 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================================================ caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -3.1 Tail_Score: -3.06831 Start: 67 End: 85 Full_Region: ATCGTGGCACTCTTC GCAGAGA GAATA TCTGTGC TTGAGTCGAAGTTCC ..................................................................GCAGAGAGAATATCTGTGC.............................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PG0068:PG0069|PG0068:PG0069:hypothetical protein:hypothetical protein:-><-:82140..82510 371 caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtgtttttttgaccgatttccgtc Intra-Species Hit: Count: 1 Min: 1 Max: 350 Len: 350 Subject: NC_002950_PG0068_PG0069|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[82140,82510]|371 HSP 1 e-value: 0.0 bit: 694.0 Len: 350 Query Start:1 Query End:350 Subject Strand: POSITIVE Subject Start: 1 Subject End: 350 caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtg..................... caatagatcggctacggcaaagagaatagggaatacatggatgtgatggggatcgtggcactcttcgcagagagaatatctgtgcttgagtcgaagttccgcaccggacaggtagaaggttttggctacgcaggtcggttcgctatgagtgtgctctttgtccgcaggggcgttctcatgacaatgttttgccatgagacatgccatacctttgttgtgatgatgatggggcataataccgatgatcagcacgacaagggaggccaagcctatgaagaatatggagagcttctttctcacaagcgatgcggttttggaacaaaaataagagttccttcttatatcaagtg..................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUAGAUCGGCUACGGCAAAGAGAAUAGGGAAUACAUGGAUGUGAUGGGGAUCGUGGCACUCUUCGCAGAGAGAAUAUCUGUGCUUGAGUCGAAGUUCCGCACCGGACAGGUAGAAGGUUUUGGCUACGCAGGUCGGUUCGCUAUGAGUGUGCUCUUUGUCCGCAGGGGCGUUCUCAUGACAAUGUUUUGCCAUGAGACAUGCCAUACCUUUGUUGUGAUGAUGAUGGGGCAUAAUACCGAUGAUCAGCACGACAAGGGAGGCCAAGCCUAUGAAGAAUAUGGAGAGCUUCUUUCUCACAAGCGAUGCGGUUUUGGAACAAAAAUAAGAGUUCCUUCUUAUAUCAAGUG (..((..((.((....))...))...))..)..(((...(((((((..((((.(...(.((((...(((.(((.....))).)))..)))))...((((((.(((((((..((((..........))))....)))...(((((.((((.(.((((((..(...((.((((..(((((((.(((....))).)))))))...(((...(((((((((((.((((.((.((........)).)).)))).))))))))))).)))...)))).))......)..))))))..)...))))..)))))..))))..))))))..........).))))..)))))))..))) (-115.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACUUGAUAUAAGAAGGAACUCUUAUUUUUGUUCCAAAACCGCAUCGCUUGUGAGAAAGAAGCUCUCCAUAUUCUUCAUAGGCUUGGCCUCCCUUGUCGUGCUGAUCAUCGGUAUUAUGCCCCAUCAUCAUCACAACAAAGGUAUGGCAUGUCUCAUGGCAAAACAUUGUCAUGAGAACGCCCCUGCGGACAAAGAGCACACUCAUAGCGAACCGACCUGCGUAGCCAAAACCUUCUACCUGUCCGGUGCGGAACUUCGACUCAAGCACAGAUAUUCUCUCUGCGAAGAGUGCCACGAUCCCCAUCACAUCCAUGUAUUCCCUAUUCUCUUUGCCGUAGCCGAUCUAUUG ..(((((...(((..(((((..........)))))....((((.(((((.(((((......(((((......(((.((..(((...(((.((.((((.(((.((((....(((.....))).....)))).))).)))).))...)))...(((((((((((....)))))))))))..)))..)).)))...)))))...))))))))))((((..(.(.((((..........))))).)..))))))))..)))....)))))...((((...((..(.((((((((......((....(((.......)))...))......)))))))).).))...)))).... (-94.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 439 170 121 187 129 NC_002950:PG1485|5end_conjugative_transposon_protein_TraC_1560370..1560600_NEGATIVE 437 138 91 203 138 NC_002950:PG1488|5end_hypothetical_protein_1561747..1561977_POSITIVE 435 177 132 60 6 NC_002950:PG0317|5end_peptidase,_M49_family_352431..352661_NEGATIVE 400 169 122 170 122 NC_002950:PG1556|5end_hypothetical_protein_1636595..1636825_POSITIVE 385 170 121 222 167 NC_002950:PG1097|5end_Mur_ligase_domain_protein/alanine_racemase_1162957..1163187_POSITIVE 384 177 133 188 141 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 384 270 229 65 15 NC_002950:PG0308|5end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343175..343405_POSITIVE 381 172 135 224 175 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 380 169 124 54 5 NC_002950:PG1664|5end_ABC_transporter,_permease_protein,_putative_1745813..1746043_POSITIVE 380 177 133 52 11 NC_002950:PG1428|5end_riboflavin_synthase_subunit_beta_1515022..1515252_NEGATIVE 379 148 101 184 123 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 376 150 101 210 161 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 376 198 162 191 151 NC_002950:PG0053|5end_hypothetical_protein_65086..65316_NEGATIVE 374 148 103 52 6 NC_002950:PG1622|5end_DNA_topoisomerase_IV_subunit_A_1704114..1704344_NEGATIVE 373 269 226 58 15 NC_002950:PG0924|5end_5'-nucleotidase,_lipoprotein_e(P4)_family_983668..983898_NEGATIVE 372 176 131 154 109 NC_002950:PG0125|5end_hypothetical_protein_146786..147016_NEGATIVE 371 174 133 52 2 NC_002950:PG0129|5end_mannosyltransferase_150585..150815_POSITIVE 369 269 228 103 67 NC_002950:PG0569|5end_hypothetical_protein_626223..626453_NEGATIVE 368 180 132 71 27 NC_002950:PG2143|5end_GTP-binding_protein_EngA_2248547..2248777_POSITIVE 365 196 153 54 10 NC_002950:PG0512|5end_guanylate_kinase_551914..552144_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 452 170 121 116 48 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 404 48 5 72 22 NC_002950:PG1493|3end_hypothetical_protein_1569538..1569688_POSITIVE 395 170 121 59 4 NC_002950:PG0945|3end_ABC_transporter,_permease_protein,_putative_1005104..1005254_NEGATIVE 394 168 124 69 17 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 382 140 96 109 62 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 380 177 133 71 30 NC_002950:PG1429|3end_hypothetical_protein_1515003..1515153_NEGATIVE 376 151 111 151 110 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 373 269 226 61 18 NC_002950:PG0925|3end_thymidine_kinase_983665..983815_NEGATIVE 368 168 124 145 89 NC_002950:PG1789|3end_peptidyl-dipeptidase_Dcp_1877417..1877567_NEGATIVE 364 129 82 84 36 NC_002950:PG1342|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1423681..1423831_POSITIVE 360 175 133 150 109 NC_002950:PG0584|3end_cell_division_protein_FtsZ_643320..643470_POSITIVE 359 127 81 71 18 NC_002950:PG0052|3end_sensor_histidine_kinase_64686..64836_POSITIVE 358 140 96 54 2 NC_002950:PG0228|3end_DdaH_family_protein_264024..264174_NEGATIVE 357 170 121 58 9 NC_002950:PG2027|3end_hypothetical_protein_2126098..2126248_POSITIVE 355 138 96 130 81 NC_002950:PG1364|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1444388..1444538_NEGATIVE 355 144 103 126 82 NC_002950:PG1323|3end_PhoH_family_protein_1402844..1402994_POSITIVE 353 179 131 82 32 NC_002950:PG2102|3end_immunoreactive_61_kDa_antigen_PG91_2211424..2211574_NEGATIVE 352 170 124 140 89 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 351 100 52 55 8 NC_002950:PG1614|3end_succinate_dehydrogenase_1693800..1693950_NEGATIVE 351 243 204 151 115 NC_002950:PG0250|3end_hypothetical_protein_283905..284055_NEGATIVE