Origin IGS: tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgatcatcggaattgtattcgagcccctgactgcgatctgggcagaggaggtgtctcgtatcaaattactatgcagacagtcgcccttttgagggctgacactgtctgcacagatcggggtaagaataattcggagtctatattcagagatatactaatgtacttttcta Mask Tandem Repeat Region ================================================ tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Find is-nt database================================================ Query_seq: PG1019:PG1020|PG1019:PG1020:lipoprotein, putative:hypothetical protein:->->:1080537..1080707 171 tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1019:PG1020|PG1019:PG1020:lipoprotein, putative:hypothetical protein:->->:1080537..1080707 171 tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1019:PG1020|PG1019:PG1020:lipoprotein, putative:hypothetical protein:->->:1080537..1080707 171 tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 12 End: 107 ........... M S I S L N I D S E L F L P R S V Q T V S A L K R A T V C I V I ................................................................ Protein_Len: 50 Strand: + Start: 20 End: 169 ................... M S E Y R L R I I L T P I C A D S V S P Q K G D C L H S N L I R D T S S A Q I A V R G S N T I P M I .. Protein_Len: 30 Strand: - Start: 82 End: 171 ................................................................................. F P S Q R C L L K I R S V E E A W I A T L P E F V I G I I M Protein_Len: 51 Strand: - Start: 2 End: 154 . S F Y M L I D R F I S E S N N K G R D T C V T D A R L L A V T Q M T I Q Y S V G G R G L D C D P A R M ................. tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac 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================================================ tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -10.3 Tail_Score: -2.96695 Start: 58 End: 102 Full_Region: TATTCTTACCCCGAT CTGTGCAGACAGTGTCAGCCCT CAAA AGGGCGACTGTCTGCATAG TAATTTGATACGAGA .........................................................CTGTGCAGACAGTGTCAGCCCTCAAAAGGGCGACTGTCTGCATAG..................................................................... Find igs database================================================ Query_seq: PG1019:PG1020|PG1019:PG1020:lipoprotein, putative:hypothetical protein:->->:1080537..1080707 171 tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Intra-Species Hit: Count: 1 Min: 1 Max: 171 Len: 171 Subject: NC_002950_PG1019_PG1020|lipoprotein, putative:hypothetical protein|POSITIVE:POSITIVE|[1080537,1080707]|171 HSP 1 e-value: 2.0E-92 bit: 339.0 Len: 171 Query Start:1 Query End:171 Subject Strand: POSITIVE Subject Start: 1 Subject End: 171 tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac tagaaaagtacattagtatatctctgaatatagactccgaattattcttaccccgatctgtgcagacagtgtcagccctcaaaagggcgactgtctgcatagtaatttgatacgagacacctcctctgcccagatcgcagtcaggggctcgaatacaattccgatgatcac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAGUACAUUAGUAUAUCUCUGAAUAUAGACUCCGAAUUAUUCUUACCCCGAUCUGUGCAGACAGUGUCAGCCCUCAAAAGGGCGACUGUCUGCAUAGUAAUUUGAUACGAGACACCUCCUCUGCCCAGAUCGCAGUCAGGGGCUCGAAUACAAUUCCGAUGAUCAC ((((.(.((((....)))).).))))......(((((.(((((..........(((.(((((((((((((....(((((....))))).)))))))))))))....)))...((((...(((...((((.......))))..)))..)))).....))))).)).).)).. (-52.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAUCAUCGGAAUUGUAUUCGAGCCCCUGACUGCGAUCUGGGCAGAGGAGGUGUCUCGUAUCAAAUUACUAUGCAGACAGUCGCCCUUUUGAGGGCUGACACUGUCUGCACAGAUCGGGGUAAGAAUAAUUCGGAGUCUAUAUUCAGAGAUAUACUAAUGUACUUUUCUA ..(((..((.(((((((..((..(((((.......((((((.(((((...((((((..(((......))).............(((((....))))).)))))).))))).)))))))))))..))))))))).))))).......(((((..(((....)))..))))). (-57.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 97 54 201 158 NC_002950:PG1952|5end_DedA_family_protein_2042870..2043100_POSITIVE 363 152 114 57 20 NC_002950:PG0671|5end_iron_compound_ABC_transporter,_permease_protein_721888..722118_POSITIVE 360 98 56 228 165 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 358 99 53 72 9 NC_002950:PG2130|5end_hypothetical_protein_2235567..2235797_POSITIVE 354 170 126 77 28 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 354 99 54 66 2 NC_002950:PG0553|5end_extracellular_protease,_putative_611189..611419_NEGATIVE 348 157 113 90 31 NC_002950:PG1356|5end_hypothetical_protein_1435849..1436079_NEGATIVE 344 139 91 226 183 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 342 95 57 156 114 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 341 167 125 61 13 NC_002950:PG1875|5end_hemolysin_1970621..1970851_NEGATIVE 333 100 57 192 152 NC_002950:PG1411|5end_potassium_uptake_protein_TrkA,_putative_1495166..1495396_NEGATIVE 329 170 122 57 3 NC_002950:PG1849|5end_DNA_repair_protein_RecN_1949034..1949264_NEGATIVE 327 163 124 52 2 NC_002950:PG1128|5end_exodeoxyribonuclease_VII_large_subunit_1203737..1203967_POSITIVE 326 147 119 224 195 NC_002950:PG2108|5end_thiazole_synthase_2217450..2217680_NEGATIVE 325 148 109 52 4 NC_002950:PG1750|5end_alpha-1,3/4-fucosidase,_putative_1835323..1835553_POSITIVE 324 167 122 177 131 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 322 100 51 91 25 NC_002950:PG0691|5end_NifU-related_protein_747469..747699_NEGATIVE 322 99 51 63 23 NC_002950:PG0434|5end_hypothetical_protein_472513..472743_NEGATIVE 322 156 113 224 175 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 320 166 128 225 174 NC_002950:PG0072|5end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_87147..87377_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 170 122 66 16 NC_002950:PG0545|3end_hypothetical_protein_600228..600378_POSITIVE 363 152 114 60 23 NC_002950:PG0670|3end_lipoprotein,_putative_721971..722121_POSITIVE 357 100 58 57 11 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 351 90 52 40 5 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 349 140 91 68 18 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 348 126 81 47 10 NC_002950:PG1809|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_1905491..1905641_NEGATIVE 345 102 72 33 1 NC_002950:PG1019|3end_lipoprotein,_putative_1080476..1080626_POSITIVE 342 97 52 131 86 NC_002950:PG1315|3end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_1395618..1395768_NEGATIVE 341 167 125 49 1 NC_002950:PG1876|3end_hypothetical_protein_1970633..1970783_NEGATIVE 340 80 35 151 87 NC_002950:PG0985|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1047516..1047666_POSITIVE 338 98 57 91 51 NC_002950:PG2077|3end_hypothetical_protein_2177005..2177155_NEGATIVE 327 156 112 125 70 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE 324 167 122 140 94 NC_002950:PG1043|3end_ferrous_iron_transport_protein_B_1110675..1110825_NEGATIVE 324 99 52 148 95 NC_002950:PG0384|3end_MutS2_family_protein_418697..418847_POSITIVE 320 166 128 132 81 NC_002950:PG0073|3end_orotidine_5'-monophosphate_decarboxylase_87240..87390_NEGATIVE 314 165 123 142 111 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE 313 163 122 143 91 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 311 170 121 51 1 NC_002950:PG0621|3end_hypothetical_protein_676020..676170_POSITIVE 310 99 51 140 85 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 308 151 113 59 4 NC_002950:PG1966|3end_hypothetical_protein_2056118..2056268_NEGATIVE