Origin IGS: aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga .........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 tctgtgcgcgaattcatttttaatttgtatttttgctatccataagagtacctgtgagcaaagtatagcagactatagcaaacagaacggttgccaaatcgttacctgaaaatcagccaatcgcacggaacgcccttagataaaggaatgtcgctttcctatccaaagttacggtaaatatatgtatatacaacaatcgcacttgtattcagtatatctctctgtagcaaacattgttcgtatgggatgcaaccaagaattgctgtacatttgttcggacagatcaagcgggagtagcagcctgcgctactcaagacaaattcaaatttgcagtcgaaatgacaatcgaacaattatatgcagcctatctggctcatcct Mask Tandem Repeat Region ================================================ aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Find is-nt database================================================ Query_seq: PG1106:PG1107|PG1106:PG1107:UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase:hypothetical protein:<-->:1178520..1178899 380 aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1106:PG1107|PG1106:PG1107:UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase:hypothetical protein:<-->:1178520..1178899 380 aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1106:PG1107|PG1106:PG1107:UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase:hypothetical protein:<-->:1178520..1178899 380 aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 81 End: 209 ................................................................................ M L L P L D L S E Q M Y S N S W L H P I R T M F A T E R Y T E Y K C D C C I Y I Y L P ........................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 28 End: 219 ........................... M F D C H F D C K F E F V L S S A G C Y S R L I C P N K C T A I L G C I P Y E Q C L L Q R D I L N T S A I V V Y T Y I Y ................................................................................................................................................................. Protein_Len: 31 Strand: + Start: 173 End: 265 ............................................................................................................................................................................ M Q V R L L Y I H I F T V T L D R K A T F L Y L R A F R A I G ................................................................................................................... Protein_Len: 35 Strand: - Start: 275 End: 379 .................................................................................................................................................................................................................................................................................. T V I Q C G N Q K S Y D A I S Q E C T S K H I A F I C I L F S N A C M . Protein_Len: 39 Strand: - Start: 87 End: 203 ...................................................................................... E R K I Q G F L H V A I R P Q M G Y S C H K S C L S I S F V L A I T T Y V Y M ................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 2 End: 241 . Q R S Y R L S S S G S S R D S C I Y L L E Q N C G M R V I N A V S L Y V S Y L H S Q Q I Y M Y K G Y S Q I P F R C E K M ........................................................................................................................................... Protein_Len: 49 Strand: - Start: 1 End: 147 P H A L Y A A Y L Q E I T M E V A F K F K D Q T A C A A V G A Q D T R V F T C C N K T A D W V F M ......................................................................................................................................................................................................................................... aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga 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================================================ aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 41 HP_score: -2.9 Tail_Score: -2.58999 Start: 66 End: 92 Full_Region: CAAATTTGAATTTGT CTTGAGTAGCG CAGGC TGCTACTCCCG CTTGATCTGTCCGAA .................................................................CTTGAGTAGCGCAGGCTGCTACTCCCG................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: PG1106:PG1107|PG1106:PG1107:UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase:hypothetical protein:<-->:1178520..1178899 380 aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Intra-Species Hit: Count: 1 Min: 1 Max: 380 Len: 380 Subject: NC_002950_PG1106_PG1107|UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase:hypothetical protein|NEGATIVE:POSITIVE|[1178520,1178899]|380 HSP 1 e-value: 0.0 bit: 753.0 Len: 380 Query Start:1 Query End:380 Subject Strand: POSITIVE Subject Start: 1 Subject End: 380 aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga aggatgagccagataggctgcatataattgttcgattgtcatttcgactgcaaatttgaatttgtcttgagtagcgcaggctgctactcccgcttgatctgtccgaacaaatgtacagcaattcttggttgcatcccatacgaacaatgtttgctacagagagatatactgaatacaagtgcgattgttgtatatacatatatttaccgtaactttggataggaaagcgacattcctttatctaagggcgttccgtgcgattggctgattttcaggtaacgatttggcaaccgttctgtttgctatagtctgctatactttgctcacaggtactcttatggatagcaaaaatacaaattaaaaatgaattcgcgcacaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAUGAGCCAGAUAGGCUGCAUAUAAUUGUUCGAUUGUCAUUUCGACUGCAAAUUUGAAUUUGUCUUGAGUAGCGCAGGCUGCUACUCCCGCUUGAUCUGUCCGAACAAAUGUACAGCAAUUCUUGGUUGCAUCCCAUACGAACAAUGUUUGCUACAGAGAGAUAUACUGAAUACAAGUGCGAUUGUUGUAUAUACAUAUAUUUACCGUAACUUUGGAUAGGAAAGCGACAUUCCUUUAUCUAAGGGCGUUCCGUGCGAUUGGCUGAUUUUCAGGUAACGAUUUGGCAACCGUUCUGUUUGCUAUAGUCUGCUAUACUUUGCUCACAGGUACUCUUAUGGAUAGCAAAAAUACAAAUUAAAAAUGAAUUCGCGCACAGA .((((((((((((...((((..((((.(((((((((.((((...((...((((((....))))))...((((((((.....)))))))).))..))))..)).))))))).))))))))...)).))))).))))).....((((.((((.((.(((((...(((.((((.......))))..))).))))))).)))).............(((((((((((((.......)))))..))))))))..)))).((((((.((.(((.....))).))..((((((((..(((((((((..(((((((....)))))....))..))))).......))))...)).......))))))..........))))))..... (-93.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUGUGCGCGAAUUCAUUUUUAAUUUGUAUUUUUGCUAUCCAUAAGAGUACCUGUGAGCAAAGUAUAGCAGACUAUAGCAAACAGAACGGUUGCCAAAUCGUUACCUGAAAAUCAGCCAAUCGCACGGAACGCCCUUAGAUAAAGGAAUGUCGCUUUCCUAUCCAAAGUUACGGUAAAUAUAUGUAUAUACAACAAUCGCACUUGUAUUCAGUAUAUCUCUCUGUAGCAAACAUUGUUCGUAUGGGAUGCAACCAAGAAUUGCUGUACAUUUGUUCGGACAGAUCAAGCGGGAGUAGCAGCCUGCGCUACUCAAGACAAAUUCAAAUUUGCAGUCGAAAUGACAAUCGAACAAUUAUAUGCAGCCUAUCUGGCUCAUCCU ..(((...(((..(((((((....(((((..((((..........(((((.((((((((((((((((((((......((......(((((((....)))))))..(((.....)))......))..((.....((((.....))))......((..((((((.(...(((((((...((((((....((((((.........))))))...))))))....))))))).(((...))).).)))))).))..)).....))))))))).)))))))..)))).....(((((........)))))..)))))..........))))..)))))..)))))))...))).))).....(((.((((.....)))))))... (-91.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1045 120 71 211 162 NC_002950:PG1106|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,_6-diaminopimelate--D-alanyl-D-alanyl_ligase_1178429..1178659_NEGATIVE 365 120 74 80 29 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 363 110 61 66 11 NC_002950:PG0578|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_634480..634710_POSITIVE 358 103 65 73 29 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 356 130 82 69 18 NC_002950:PG1354|5end_hydrolase,_carbon-nitrogen_family_1434765..1434995_NEGATIVE 355 298 251 190 143 NC_002950:PG1988|5end_hypothetical_protein_2078867..2079097_NEGATIVE 355 79 32 155 103 NC_002950:PG1898|5end_transporter,_putative_1997335..1997565_NEGATIVE 347 119 74 190 149 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 346 335 292 231 191 NC_002950:PG2218|5end_potassium_uptake_protein_TrkA_2331580..2331810_POSITIVE 346 103 63 71 22 NC_002950:PG1465|5end_hypothetical_protein_1541982..1542212_POSITIVE 346 329 286 67 23 NC_002950:PG0860|5end_transcriptional_regulator,_putative_918888..919118_POSITIVE 344 92 54 219 185 NC_002950:PG0003|5end_hypothetical_protein_2938..3168_NEGATIVE 342 267 221 182 126 NC_002950:PG1743|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_1828348..1828578_NEGATIVE 339 350 308 63 18 NC_002950:PG1890|5end_lipoprotein,_putative_1987565..1987795_POSITIVE 336 298 253 92 48 NC_002950:PG1760|5end_ABC_transporter,_ATP-binding_protein_1846507..1846737_POSITIVE 336 109 62 156 94 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 334 88 41 92 48 NC_002950:PG1580|5end_hypothetical_protein_1657499..1657729_POSITIVE 333 47 1 78 25 NC_002950:PG2162|5end_lipid_A_disaccharide_synthase_2268764..2268994_NEGATIVE 332 299 256 189 141 NC_002950:PG1081|5end_acetate_kinase_1149627..1149857_NEGATIVE 330 105 61 203 152 NC_002950:PG0359|5end_flavin_reductase_domain_protein_392851..393081_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 260 215 70 28 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 365 120 74 76 25 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 358 103 65 76 32 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 356 130 82 72 21 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 355 79 32 150 98 NC_002950:PG1899|3end_TonB-dependent_receptor,_putative_1997340..1997490_NEGATIVE 336 298 253 102 58 NC_002950:PG1759|3end_adhesion_protein,_putative_1846597..1846747_POSITIVE 336 109 62 149 87 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 334 88 41 81 37 NC_002950:PG1579|3end_ATPase,_MoxR_family_1657568..1657718_POSITIVE 334 106 74 150 122 NC_002950:PG0683|3end_ABC_transporter,_permease_protein,_putative_737701..737851_POSITIVE 332 299 256 143 95 NC_002950:PG1082|3end_phosphotransacetylase_1149673..1149823_NEGATIVE 329 276 232 147 95 NC_002950:PG0714|3end_copper_homeostasis_protein_CutC_767925..768075_NEGATIVE 325 119 74 74 30 NC_002950:PG1773|3end_PAP2_superfamily_protein_1861232..1861382_POSITIVE 324 120 77 50 2 NC_002950:PG1334|3end_band_7/Mec-2_family_protein_1415422..1415572_NEGATIVE 324 295 253 122 75 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 323 267 222 122 73 NC_002950:PG2159|3end_protoporphyrinogen_oxidase_2265874..2266024_POSITIVE 322 320 272 128 84 NC_002950:PG1232|3end_glutamate_dehydrogenase_1308274..1308424_NEGATIVE 321 107 62 52 3 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 314 330 282 148 93 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE 310 83 43 151 111 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 310 265 221 76 9 NC_002950:PG0093|3end_HlyD_family_secretion_protein_108643..108793_NEGATIVE