Origin IGS: aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg .........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 ccgttgccgatatccggtttggggcctcatgggatcgtactgccgatcctatgaggctctttcttctttagtatgggcttagatcgagtgcgttatttccaagtttttacgatcgtacatctataaaaaggaacaatccggctcctcacgacaagcgaaatcgagcgaaaagaaggccaaagacggccataggataccacaggcagccgcaggatgcagttcgattcccgggtacaaagcggccgttctacctttgcatcgtcagcaaaaaggaacgaaagcaaggatggccatccgataacgacaaaccgaagtgccgacagtattatttcatcaatctattaaacaacaaaaattatt Mask Tandem Repeat Region ================================================ aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Find is-nt database================================================ Query_seq: PG2040:PG2041|PG2040:PG2041:DNA-binding protein, histone-like family:hypothetical protein:<-<-:2138965..2139324 360 aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2040:PG2041|PG2040:PG2041:DNA-binding protein, histone-like family:hypothetical protein:<-<-:2138965..2139324 360 aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2040:PG2041|PG2040:PG2041:DNA-binding protein, histone-like family:hypothetical protein:<-<-:2138965..2139324 360 aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 124 End: 237 ........................................................................................................................... M Y P G I E L H P A A A C G I L W P S L A F F S L D F A C R E E P D C S F L ........................................................................................................................... Protein_Len: 60 Strand: + Start: 23 End: 265 ...................... M D E I I L S A L R F V V I G W P S L L S F L F A D D A K V E R P L C T R E S N C I L R L P V V S Y G R L W P S F R S I ............................................................................................... Protein_Len: 60 Strand: - Start: 63 End: 278 .............................................................. R H L P L V A A K Y G P I S S C G A A A Q P I R H G D K A K K E S S K A Q R S S G S Q E K K Y I Y S R L F K S I V C E M .................................................................................. Protein_Len: 43 Strand: - Start: 19 End: 147 .................. Y I S S I I S D A S R N T T I P H G D K S E N R K A S S A F T S R G S Q V R S D F Q M ..................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 2 End: 238 . N D S P W G Q K R E K K S V I C L Y F P R K T G P F R V A D Q P Q R H Y G I A T K P R R K A R N R K D H P A P N N R K M .......................................................................................................................... aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg 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================================================ aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 67 HP_score: -2.5 Tail_Score: -4.89852 Start: 216 End: 231 Full_Region: TTTCGCTTGTCGTGA GGAGC CGGATT GTTCC TTTTTATAGATGTAC .......................................................................................................................................................................................................................GGAGCCGGATTGTTCC................................................................................................................................. TransTerm Strand: - Conf: 71 HP_score: -6.8 Tail_Score: -4.04806 Start: 298 End: 343 Full_Region: gttgccgatatccgg tttggggcctcatgggatcg tactgc cgatcctatgaggctctttc ttctttagtatgggc .........................................................................................................................................................................................................................................................................................................tttggggcctcatgggatcgtactgccgatcctatgaggctctttc................. Find igs database================================================ Query_seq: PG2040:PG2041|PG2040:PG2041:DNA-binding protein, histone-like family:hypothetical protein:<-<-:2138965..2139324 360 aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Intra-Species Hit: Count: 1 Min: 1 Max: 360 Len: 360 Subject: NC_002950_PG2040_PG2041|DNA-binding protein, histone-like family:hypothetical protein|NEGATIVE:NEGATIVE|[2138965,2139324]|360 HSP 1 e-value: 0.0 bit: 714.0 Len: 360 Query Start:1 Query End:360 Subject Strand: POSITIVE Subject Start: 1 Subject End: 360 aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg aataatttttgttgtttaatagattgatgaaataatactgtcggcacttcggtttgtcgttatcggatggccatccttgctttcgttcctttttgctgacgatgcaaaggtagaacggccgctttgtacccgggaatcgaactgcatcctgcggctgcctgtggtatcctatggccgtctttggccttcttttcgctcgatttcgcttgtcgtgaggagccggattgttcctttttatagatgtacgatcgtaaaaacttggaaataacgcactcgatctaagcccatactaaagaagaaagagcctcataggatcggcagtacgatcccatgaggccccaaaccggatatcggcaacgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUUUUUGUUGUUUAAUAGAUUGAUGAAAUAAUACUGUCGGCACUUCGGUUUGUCGUUAUCGGAUGGCCAUCCUUGCUUUCGUUCCUUUUUGCUGACGAUGCAAAGGUAGAACGGCCGCUUUGUACCCGGGAAUCGAACUGCAUCCUGCGGCUGCCUGUGGUAUCCUAUGGCCGUCUUUGGCCUUCUUUUCGCUCGAUUUCGCUUGUCGUGAGGAGCCGGAUUGUUCCUUUUUAUAGAUGUACGAUCGUAAAAACUUGGAAAUAACGCACUCGAUCUAAGCCCAUACUAAAGAAGAAAGAGCCUCAUAGGAUCGGCAGUACGAUCCCAUGAGGCCCCAAACCGGAUAUCGGCAACGG .........((((((((.((......)).)))))))).(((((..(.(((((((((..((((..((((((((((....((..((((((.(((((((.......)))))))..))))))..))...(((((((((.......((((.....))))...)))).)))))...)))))))))).))))(((((((..((((...(((((.....))))))))).(((((((((((((((((.(((.....))))))))))...))))..........))))))...........))))))).....(((((((.((((((......)))))).)))))))..))))))))))..))))).... (-108.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGUUGCCGAUAUCCGGUUUGGGGCCUCAUGGGAUCGUACUGCCGAUCCUAUGAGGCUCUUUCUUCUUUAGUAUGGGCUUAGAUCGAGUGCGUUAUUUCCAAGUUUUUACGAUCGUACAUCUAUAAAAAGGAACAAUCCGGCUCCUCACGACAAGCGAAAUCGAGCGAAAAGAAGGCCAAAGACGGCCAUAGGAUACCACAGGCAGCCGCAGGAUGCAGUUCGAUUCCCGGGUACAAAGCGGCCGUUCUACCUUUGCAUCGUCAGCAAAAAGGAACGAAAGCAAGGAUGGCCAUCCGAUAACGACAAACCGAAGUGCCGACAGUAUUAUUUCAUCAAUCUAUUAAACAACAAAAAUUAUU ..((((..((((..(((((((((((((((((((((((......))))))))))))))))......((((.(((((((....(((((((((((((..((((...((((...(((.....)))...)))).)))).....((((((((........((........))........((((......))))............))).)))))...)))))).))))))))))..)))))))).(((((((((.(((((((.......)))..))))..(....)..)))))))))............))))))).(((((.....)))))............))))...)))).......... (-107.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1012 90 41 181 132 NC_002950:PG2040|5end_DNA-binding_protein,_histone-like_family_2138874..2139104_NEGATIVE 436 359 311 183 129 NC_002950:PG1125|5end_hypothetical_protein_1201727..1201957_NEGATIVE 433 128 85 162 114 NC_002950:PG0090|5end_Dps_family_protein_105524..105754_POSITIVE 432 199 152 223 179 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 417 158 116 104 63 NC_002950:PG0997|5end_transcriptional_regulator,_putative_1056666..1056896_POSITIVE 415 159 113 71 22 NC_002950:PG1068|5end_hypothetical_protein_1134636..1134866_POSITIVE 408 160 117 44 1 NC_002950:PG0034|5end_thioredoxin_42549..42779_NEGATIVE 407 220 175 227 176 NC_002950:PG2066|5end_lipoprotein,_putative_2162116..2162346_POSITIVE 405 359 311 223 170 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 405 159 116 196 150 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 401 88 41 162 105 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 400 319 271 231 185 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 394 356 311 228 174 NC_002950:PG2000|5end_signal_peptidase-related_protein_2089468..2089698_NEGATIVE 393 88 43 65 20 NC_002950:PG1038|5end_ATP-dependent_DNA_helicase_UvrD/PcrA/Rep_Family_1102744..1102974_POSITIVE 393 217 171 211 157 NC_002950:PG0976|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1038326..1038556_POSITIVE 392 159 113 219 172 NC_002950:PG2100|5end_immunoreactive_63_kDa_antigen_PG102_2210191..2210421_NEGATIVE 392 360 311 225 169 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 391 149 110 62 24 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 391 198 152 229 163 NC_002950:PG1021|5end_hypothetical_protein_1083592..1083822_NEGATIVE 391 216 171 205 146 NC_002950:PG0580|5end_N-acetylglucosaminyl_transferase_637097..637327_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 199 152 122 78 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 407 220 175 136 85 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 406 220 171 144 85 NC_002950:PG1794|3end_DNA_polymerase_type_I_1888838..1888988_POSITIVE 403 189 142 88 37 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 397 184 141 137 97 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 395 209 164 51 7 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 393 88 43 65 20 NC_002950:PG1037|3end_hypothetical_protein_1102824..1102974_POSITIVE 392 159 113 132 85 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 389 144 103 50 10 NC_002950:PG1816|3end_NAD(P)H_dehydrogenase,_quinone_family,_putative_1911430..1911580_NEGATIVE 386 200 152 56 13 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 386 185 142 136 98 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 384 160 112 65 19 NC_002950:PG0211|3end_cobalamin_biosynthesis_protein_CbiG/precorrin-4_C11-methyltransferase_245966..246116_NEGATIVE 382 184 141 134 97 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 381 360 311 54 7 NC_002950:PG0884|3end_hypothetical_protein_947809..947959_POSITIVE 380 178 137 136 95 NC_002950:PG2073|3end_hypothetical_protein_2174219..2174369_NEGATIVE 380 178 137 136 95 NC_002950:PG1669|3end_hypothetical_protein_1755411..1755561_NEGATIVE 380 178 137 136 95 NC_002950:PG1264|3end_hypothetical_protein_1344740..1344890_NEGATIVE 380 134 94 63 4 NC_002950:PG0286|3end_hypothetical_protein_320454..320604_POSITIVE 380 178 137 136 95 NC_002950:PG0103|3end_hypothetical_protein_121525..121675_POSITIVE 379 159 118 135 100 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE