Origin IGS: cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag .........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 ctctttcgtattgattattgtcaatgccttatatggtttcattttcgcacaatgagagatcgtttttttgtgcaaaggtgtggtttctccttctcgagatatgtcatctttaattccattatttcgtcttaggaaccgaacaaaggtagaatttttaaggagaaggataaatgaaaaaaccgttaaaaacatgaaagtaggagataagtgtgagaatgagtgcgcctgatctttgtgatcggcgcactcttttcgttgtttggtcctatggacagtctattggtatccggatcgtattcggg Mask Tandem Repeat Region ================================================ cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Find is-nt database================================================ Query_seq: PG1276:PG1277|PG1276:PG1277:DNA-binding protein, histone-like family:UDP-glucose-6 dehydrogenase, putative:->->:1353592..1353893 302 cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1276:PG1277|PG1276:PG1277:DNA-binding protein, histone-like family:UDP-glucose-6 dehydrogenase, putative:->->:1353592..1353893 302 cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1276:PG1277|PG1276:PG1277:DNA-binding protein, histone-like family:UDP-glucose-6 dehydrogenase, putative:->->:1353592..1353893 302 cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 28 End: 117 ........................... M S I G P N N E K S A P I T K I R R T H S H T Y L L L S C F ......................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 56 End: 145 ....................................................... M R R S Q R S G A L I L T L I S Y F H V F N G F F I Y P S P ............................................................................................................................................................. Protein_Len: 60 Strand: + Start: 111 End: 302 .............................................................................................................. M F L T V F S F I L L L K N S T F V R F L R R N N G I K D D I S R E G E T T P L H K K T I S H C A K M K P Y K A L T I I Protein_Len: 31 Strand: - Start: 193 End: 285 ................................................................................................................................................................................................ L H C I E L L L F W V K A C F F S R E N H S F S V M Y P M S M ................. Protein_Len: 40 Strand: - Start: 174 End: 293 ............................................................................................................................................................................. S S I I S N F I V Y R S F S F G C R Q V F F R D R M T R F H F W I L C Q C Y D M ......... Protein_Len: 56 Strand: - Start: 77 End: 244 ............................................................................ A C E N E C K D G V K M N K V T K E N I R R R L F E V K T R N R L R F L P I L S S M D R S P S V V G K C L F V M .......................................................... Protein_Len: 33 Strand: - Start: 1 End: 99 G F V I R I G I S Q G Y S W V V F L T R R D C L D P A S M R V S M ........................................................................................................................................................................................................... cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag 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================================================ cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -11.8 Tail_Score: -3.34501 Start: 53 End: 86 Full_Region: GACCAAACAACGAAA AGAGTGCGCCGATC ACAAA GATCAGGCGCACTCA TTCTCACACTTATCT ....................................................AGAGTGCGCCGATCACAAAGATCAGGCGCACTCA........................................................................................................................................................................................................................ TransTerm Strand: + Conf: 95 HP_score: -15.3 Tail_Score: -2.60219 Start: 54 End: 85 Full_Region: ACCAAACAACGAAAA GAGTGCGCCGATC ACAAA GATCAGGCGCACTC ATTCTCACACTTATC .....................................................GAGTGCGCCGATCACAAAGATCAGGCGCACTC......................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -15.3 Tail_Score: -4.63107 Start: 54 End: 85 Full_Region: gataagtgtgagaat gagtgcgcctgatc tttgt gatcggcgcactc ttttcgttgtttggt .....................................................gagtgcgcctgatctttgtgatcggcgcactc......................................................................................................................................................................................................................... TransTerm Strand: + Conf: 81 HP_score: -12.1 Tail_Score: -2.83747 Start: 56 End: 83 Full_Region: CAAACAACGAAAAGA GTGCGCCGATC ACAAA GATCAGGCGCAC TCATTCTCACACTTA .......................................................GTGCGCCGATCACAAAGATCAGGCGCAC........................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG1276:PG1277|PG1276:PG1277:DNA-binding protein, histone-like family:UDP-glucose-6 dehydrogenase, putative:->->:1353592..1353893 302 cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: NC_002950_PG1276_PG1277|DNA-binding protein, histone-like family:UDP-glucose-6 dehydrogenase, putative|POSITIVE:POSITIVE|[1353592,1353893]|302 HSP 1 e-value: 1.0E-158 bit: 557.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacnnnnnnncgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag cccgaatacgatccggataccaatagactgtccataggaccaaacaacgaaaagagtgcgccgatcacaaagatcaggcgcactcattctcacacttatctcctactttcatgtttttaacggttttttcatttatccttctccttaaaaattctacctttgttcggttcctaagacgaaataatggaattaaagatgacatatctcgagaaggagaaaccacacctttgcacaaaaaaacgatctctcattgtgcgaaaatgaaaccatataaggcattgacaataatcaatacgaaagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGAAUACGAUCCGGAUACCAAUAGACUGUCCAUAGGACCAAACAACGAAAAGAGUGCGCCGAUCACAAAGAUCAGGCGCACUCAUUCUCACACUUAUCUCCUACUUUCAUGUUUUUAACGGUUUUUUCAUUUAUCCUUCUCCUUAAAAAUUCUACCUUUGUUCGGUUCCUAAGACGAAAUAAUGGAAUUAAAGAUGACAUAUCUCGAGAAGGAGAAACCACACCUUUGCACAAAAAAACGAUCUCUCAUUGUGCGAAAAUGAAACCAUAUAAGGCAUUGACAAUAAUCAAUACGAAAGAG .(((.........)))............((((..(((((.........((.(((((((((((((((.....)))).))))))))).)).)).........))))).....(((((((....((((((........((((((((......(((((((......((((..........))))....)))))))..(((((...))))).))))))))...........(((((((((...............)))))))))...))))))....))))))).))))..........(....).. (-70.63) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUUCGUAUUGAUUAUUGUCAAUGCCUUAUAUGGUUUCAUUUUCGCACAAUGAGAGAUCGUUUUUUUGUGCAAAGGUGUGGUUUCUCCUUCUCGAGAUAUGUCAUCUUUAAUUCCAUUAUUUCGUCUUAGGAACCGAACAAAGGUAGAAUUUUUAAGGAGAAGGAUAAAUGAAAAAACCGUUAAAAACAUGAAAGUAGGAGAUAAGUGUGAGAAUGAGUGCGCCUGAUCUUUGUGAUCGGCGCACUCUUUUCGUUGUUUGGUCCUAUGGACAGUCUAUUGGUAUCCGGAUCGUAUUCGGG .......((((..((.((((((.(((......(((((((((((((.((((((.((((.....)))).)))))).))))))..((((.((((((((((((((((..((.....))..)).))))))..((((((((((.......))).....))))))))))))))).))))....)))))))......)))....((((((..((((..((((((.(((((((((.((((.....)))))))))))))))))))...)))).)))))).))))))..))..))))((((((...)))))). (-87.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 80 31 124 81 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 338 100 51 109 59 NC_002950:PG0807|5end_NusB_family_protein_864724..864954_NEGATIVE 317 79 37 64 23 NC_002950:PG0303|5end_ferredoxin_338651..338881_POSITIVE 306 80 31 126 81 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 304 90 57 131 94 NC_002950:PG0068|5end_hypothetical_protein_81748..81978_POSITIVE 303 90 44 95 42 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 303 93 53 61 9 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 302 49 2 74 27 NC_002950:PG1555|5end_hypothetical_protein_1636011..1636241_POSITIVE 301 67 28 195 154 NC_002950:PG1249|5end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase,_putative_1327161..1327391_NEGATIVE 300 50 2 57 1 NC_002950:PG1407|5end_nitroimidazole_resistance_protein,_putative_1491648..1491878_NEGATIVE 300 260 212 100 44 NC_002950:PG0525|5end_CTP_synthetase_568999..569229_POSITIVE 295 96 51 224 159 NC_002950:PG2167|5end_immunoreactive_53_kDa_antigen_PG123_2273543..2273773_NEGATIVE 292 42 16 226 201 NC_002950:PG1000|5end_hypothetical_protein_1057594..1057824_POSITIVE 290 179 136 118 72 NC_002950:PG1459|5end_hypothetical_protein_1539769..1539999_NEGATIVE 290 85 51 229 188 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 288 100 59 66 25 NC_002950:PG1465|5end_hypothetical_protein_1541982..1542212_POSITIVE 287 81 56 150 120 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 285 86 41 225 169 NC_002950:PG0317|5end_peptidase,_M49_family_352431..352661_NEGATIVE 283 69 22 129 74 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 281 100 54 49 2 NC_002950:PG1330|5end_large_conductance_mechanosensitive_channel_protein_1409666..1409896_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 425 85 51 37 3 NC_002950:PG0566|3end_DNA-binding_protein,_histone-like_family_622935..623085_NEGATIVE 419 85 41 58 12 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE 415 85 54 37 6 NC_002950:PG1276|3end_DNA-binding_protein,_histone-like_family_1353531..1353681_POSITIVE 333 198 151 89 33 NC_002950:PG1085|3end_hypothetical_protein_1153531..1153681_POSITIVE 317 79 37 54 13 NC_002950:PG0302|3end_hypothetical_protein_338721..338871_POSITIVE 303 90 44 73 20 NC_002950:PG1944|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2031755..2031905_POSITIVE 303 93 53 64 12 NC_002950:PG1380|3end_ABC_transporter,_ATP-binding_protein_1460705..1460855_POSITIVE 303 91 51 58 14 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 296 90 41 134 77 NC_002950:PG1251|3end_hypothetical_protein_1328212..1328362_POSITIVE 293 91 59 79 43 NC_002950:PG0193|3end_cationic_outer_membrane_protein_OmpH_230720..230870_POSITIVE 287 81 56 146 116 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE 283 69 22 136 81 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 279 96 54 130 78 NC_002950:PG1317|3end_hypothetical_protein_1396744..1396894_NEGATIVE 275 249 202 131 92 NC_002950:PG0800|3end_hypothetical_protein_854719..854869_NEGATIVE 273 250 207 112 73 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 267 80 31 67 3 NC_002950:PG0311|3end_glycosyl_transferase,_group_2_family_protein_345559..345709_NEGATIVE 266 111 74 143 104 NC_002950:PG0472|3end_iron-sulfur_cluster_binding_protein,_putative_514414..514564_POSITIVE 264 80 36 96 64 NC_002950:PG1324|3end_Holliday_junction_resolvase_1402862..1403012_NEGATIVE 263 50 2 74 33 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 262 60 12 60 13 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE