Origin IGS: gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg .........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 cggtatatccttttagaaatgaaacagcatagcccttttggttgttgcgctatcgagataaaaaacagccttgtatctgtctttcatctcttggccttgcgtttcttactctgtcaatgagtagcgagtagaaaagaagtgagccacgaaagtctgatataaaactttcgtggctcacctcaattcttgaatgctattttctccttcggttttattttgccgatggagtgggggatagc Mask Tandem Repeat Region ================================================ gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Find is-nt database================================================ Query_seq: PG1189:PG1190|PG1189:PG1190:hypothetical protein:glycerate dehydrogenase:->->:1272013..1272251 239 gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1189:PG1190|PG1189:PG1190:hypothetical protein:glycerate dehydrogenase:->->:1272013..1272251 239 gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1189:PG1190|PG1189:PG1190:hypothetical protein:glycerate dehydrogenase:->->:1272013..1272251 239 gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 56 End: 187 ....................................................... M E V S H E S F I S D F R G S L L F Y S L L I D R V R N A R P R D E R Q I Q G C F L S R .................................................... Protein_Len: 37 Strand: - Start: 123 End: 233 .......................................................................................................................... Q C L L F R L A L L H F V S V L S N K I E I A C C G F P S H Q K M E L L M ...... gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg 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================================================ gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -14.9 Tail_Score: -3.15961 Start: 54 End: 109 Full_Region: aatgagtagcgagta gaaaagaagtgagccacgaaagtct gatata aaactttcgtggctcacctcaattc ttgaatgctattttc .....................................................gaaaagaagtgagccacgaaagtctgatataaaactttcgtggctcacctcaattc.................................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -22.2 Tail_Score: -4.4767 Start: 59 End: 104 Full_Region: TAGCATTCAAGAATT GAGGTGAGCCACGAAAGTTT TATATC AGACTTTCGTGGCTCACTTC TTTTCTACTCGCTAC ..........................................................GAGGTGAGCCACGAAAGTTTTATATCAGACTTTCGTGGCTCACTTC....................................................................................................................................... Find igs database================================================ Query_seq: PG1189:PG1190|PG1189:PG1190:hypothetical protein:glycerate dehydrogenase:->->:1272013..1272251 239 gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Intra-Species Hit: Count: 1 Min: 1 Max: 239 Len: 239 Subject: NC_002950_PG1189_PG1190|hypothetical protein:glycerate dehydrogenase|POSITIVE:POSITIVE|[1272013,1272251]|239 HSP 1 e-value: 1.0E-133 bit: 474.0 Len: 239 Query Start:1 Query End:239 Subject Strand: POSITIVE Subject Start: 1 Subject End: 239 gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg gctatcccccactccatcggcaaaataaaaccgaaggagaaaatagcattcaagaattgaggtgagccacgaaagttttatatcagactttcgtggctcacttcttttctactcgctactcattgacagagtaagaaacgcaaggccaagagatgaaagacagatacaaggctgttttttatctcgatagcgcaacaaccaaaagggctatgctgtttcatttctaaaaggatataccg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUAUCCCCCACUCCAUCGGCAAAAUAAAACCGAAGGAGAAAAUAGCAUUCAAGAAUUGAGGUGAGCCACGAAAGUUUUAUAUCAGACUUUCGUGGCUCACUUCUUUUCUACUCGCUACUCAUUGACAGAGUAAGAAACGCAAGGCCAAGAGAUGAAAGACAGAUACAAGGCUGUUUUUUAUCUCGAUAGCGCAACAACCAAAAGGGCUAUGCUGUUUCAUUUCUAAAAGGAUAUACCG ..(((((....((((.((((..........)))).))))....((((.....((((..((((((((((((((((((((......))))))))))))))))))))..))))....)))).........((((...((((((((.((((..((((((((((((((........))))))))))))))....(.....).........)))).))).)))))..))))....)))))..... (-89.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUAUAUCCUUUUAGAAAUGAAACAGCAUAGCCCUUUUGGUUGUUGCGCUAUCGAGAUAAAAAACAGCCUUGUAUCUGUCUUUCAUCUCUUGGCCUUGCGUUUCUUACUCUGUCAAUGAGUAGCGAGUAGAAAAGAAGUGAGCCACGAAAGUCUGAUAUAAAACUUUCGUGGCUCACCUCAAUUCUUGAAUGCUAUUUUCUCCUUCGGUUUUAUUUUGCCGAUGGAGUGGGGGAUAGC .....(((((((.((((...(((((.(((..(((....((((......))))..(((((.(((.((((........)))).))).)))))..)))..))))))))....)))).....((((((((...((((..((.(((((((((((((((.(......).))))))))))))))).))..))))....)))))))).((((.(((((........))))).))))..))))))).. (-82.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 105 61 168 131 NC_002950:PG1079|5end_enoyl-CoA_hydratase/isomerase_family_protein_1146549..1146779_POSITIVE 313 110 61 226 184 NC_002950:PG0323|5end_hypothetical_protein_357388..357618_NEGATIVE 311 159 115 205 161 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 310 230 181 185 141 NC_002950:PG1920|5end_ribosomal_protein_L30_2016483..2016713_NEGATIVE 308 125 90 200 156 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 297 47 4 69 9 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 293 214 171 73 26 NC_002950:PG0063|5end_outer_membrane_efflux_protein_77056..77286_NEGATIVE 292 47 4 69 9 NC_002950:PG0499|5end_hypothetical_protein_538709..538939_POSITIVE 289 130 83 172 128 NC_002950:PG1035|5end_hypothetical_protein_1096875..1097105_POSITIVE 288 216 171 76 21 NC_002950:PG1859|5end_glycerate_kinase_family_protein_1958334..1958564_NEGATIVE 283 208 161 67 30 NC_002950:PG0343|5end_methionine_gamma-lyase_378362..378592_NEGATIVE 282 220 171 212 161 NC_002950:PG1601|5end_biotin--acetyl-CoA-carboxylase_ligase_1681792..1682022_NEGATIVE 280 48 2 85 26 NC_002950:PG1787|5end_hypothetical_protein_1875908..1876138_NEGATIVE 279 159 114 166 128 NC_002950:PG0026|5end_hypothetical_protein_29234..29464_POSITIVE 277 46 1 81 30 NC_002950:PG1159|5end_cobalamin_biosynthesis_protein_CbiB_1238967..1239197_NEGATIVE 277 183 144 218 168 NC_002950:PG0809|5end_hypothetical_protein_872014..872244_NEGATIVE 275 156 112 156 101 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 272 225 189 50 15 NC_002950:PG0685|5end_ABC_transporter,_ATP-binding_protein_740116..740346_POSITIVE 269 117 84 216 177 NC_002950:PG0138|5end_malonyl_CoA-acyl_carrier_protein_transacylase_160673..160903_POSITIVE 267 120 74 148 108 NC_002950:PG1154|5end_hypothetical_protein_1235825..1236055_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 395 118 73 47 1 NC_002950:PG1189|3end_hypothetical_protein_1271952..1272102_POSITIVE 336 105 61 64 27 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 329 96 53 69 27 NC_002950:PG1678|3end_hypothetical_protein_1763755..1763905_NEGATIVE 317 215 172 146 100 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 309 147 103 120 70 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 307 225 188 91 52 NC_002950:PG2073|3end_hypothetical_protein_2174219..2174369_NEGATIVE 307 225 188 91 52 NC_002950:PG1669|3end_hypothetical_protein_1755411..1755561_NEGATIVE 307 225 188 91 52 NC_002950:PG1264|3end_hypothetical_protein_1344740..1344890_NEGATIVE 307 225 188 91 52 NC_002950:PG0103|3end_hypothetical_protein_121525..121675_POSITIVE 302 157 111 116 75 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 296 163 122 57 10 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 293 214 171 55 8 NC_002950:PG0064|3end_heavy_metal_efflux_pump,_CzcA_family_77074..77224_NEGATIVE 287 126 82 147 90 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 279 159 114 48 10 NC_002950:PG0025|3end_fumarylacetoacetate_hydrolase_family_protein_29196..29346_POSITIVE 278 80 32 93 44 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 277 46 1 67 16 NC_002950:PG1160|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_1238981..1239131_NEGATIVE 269 164 126 148 100 NC_002950:PG0814|3end_hypothetical_protein_875904..876054_NEGATIVE 269 117 84 101 62 NC_002950:PG0137|3end_aminoacyl-histidine_dipeptidase_160638..160788_POSITIVE 267 169 129 50 3 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE 266 47 1 119 79 NC_002950:PG2004|3end_hypothetical_protein_2093135..2093285_NEGATIVE