Origin IGS: tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcttcgcttcaaaagaaaaccccgaaagtcagacaatgggctttcggggcttatttcgattttcagtacatgttgcttgttaatctccttccttttgggagggga Mask Tandem Repeat Region ================================================ tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Find is-nt database================================================ Query_seq: PG1677:PG1678|PG1677:PG1678:phosphoglycerate kinase:hypothetical protein:-><-:1763739..1763844 106 tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1677:PG1678|PG1677:PG1678:phosphoglycerate kinase:hypothetical protein:-><-:1763739..1763844 106 tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1677:PG1678|PG1677:PG1678:phosphoglycerate kinase:hypothetical protein:-><-:1763739..1763844 106 tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Predict ORF larger than 30AA ================================================ tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat 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================================================ tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -9.3 Tail_Score: -5.07652 Start: 57 End: 86 Full_Region: GAAAATCGAAATAAG CCCCGAAAGCC CATTGTCT GACTTTCGGGG TTTTCTTTTGAAGCG ........................................................CCCCGAAAGCCCATTGTCTGACTTTCGGGG.................... Find igs database================================================ Query_seq: PG1677:PG1678|PG1677:PG1678:phosphoglycerate kinase:hypothetical protein:-><-:1763739..1763844 106 tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: NC_002950_PG1677_PG1678|phosphoglycerate kinase:hypothetical protein|POSITIVE:NEGATIVE|[1763739,1763844]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat tcccctcccaaaaggaaggagattaacaagcaacatgtactgaaaatcgaaataagccccgaaagcccattgtctgactttcggggttttcttttgaagcgaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCCUCCCAAAAGGAAGGAGAUUAACAAGCAACAUGUACUGAAAAUCGAAAUAAGCCCCGAAAGCCCAUUGUCUGACUUUCGGGGUUUUCUUUUGAAGCGAAGAU ((.(((.((....)).))).)).......((..((.....))....((((((.((((((((((((..((.....)).))))))))))))..)))))).))...... (-28.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUCGCUUCAAAAGAAAACCCCGAAAGUCAGACAAUGGGCUUUCGGGGCUUAUUUCGAUUUUCAGUACAUGUUGCUUGUUAAUCUCCUUCCUUUUGGGAGGGGA ......(((..(((.((((.(((((((((((........)))))))))))....))))..)))..)))................(((((((((....))))))))) (-34.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 96 52 67 17 NC_002950:PG0572|5end_hypothetical_protein_627571..627801_NEGATIVE 320 83 46 229 187 NC_002950:PG0624|5end_hypothetical_protein_678078..678308_POSITIVE 318 90 47 179 144 NC_002950:PG0237|5end_uracil-DNA_glycosylase_274778..275008_POSITIVE 310 89 41 177 124 NC_002950:PG1079|5end_enoyl-CoA_hydratase/isomerase_family_protein_1146549..1146779_POSITIVE 306 96 55 82 36 NC_002950:PG1486|5end_conjugative_transposon_protein_TraA_1561166..1561396_NEGATIVE 304 89 48 59 16 NC_002950:PG1324|5end_Holliday_junction_resolvase_1403431..1403661_NEGATIVE 303 86 41 147 109 NC_002950:PG0287|5end_hypothetical_protein_320457..320687_POSITIVE 297 100 55 87 35 NC_002950:PG2050|5end_hypothetical_protein_2149434..2149664_NEGATIVE 295 100 55 180 134 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 288 85 47 231 192 NC_002950:PG1679|5end_hypothetical_protein_1763796..1764026_POSITIVE 286 99 55 195 153 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 284 87 46 70 29 NC_002950:PG1954|5end_NAD_dependent_epimerase/reductase-related_protein_2044513..2044743_POSITIVE 278 96 54 87 46 NC_002950:PG0961|5end_hypothetical_protein_1022272..1022502_NEGATIVE 273 77 31 61 10 NC_002950:PG0529|5end_carbamoyl-phosphate_synthase_small_subunit_574637..574867_POSITIVE 272 86 55 213 180 NC_002950:PG1100|5end_hypothetical_protein_1169012..1169242_NEGATIVE 271 100 68 32 1 NC_002950:PG0713|5end_anthranilate_synthase_component_II_767749..767979_NEGATIVE 268 100 56 191 151 NC_002950:PG1185|5end_hypothetical_protein_1267752..1267982_NEGATIVE 267 92 55 227 179 NC_002950:PG2179|5end_NADH-ubiquinone_oxidoreductase_2287806..2288036_NEGATIVE 267 97 54 66 24 NC_002950:PG0133|5end_hypothetical_protein_155764..155994_NEGATIVE 265 100 57 68 16 NC_002950:PG2086|5end_hypothetical_protein_2186571..2186801_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 96 55 62 15 NC_002950:PG0343|3end_methionine_gamma-lyase_377181..377331_NEGATIVE 410 96 53 64 22 NC_002950:PG1305|3end_glycine_dehydrogenase_1383671..1383821_NEGATIVE 352 97 54 44 2 NC_002950:PG1677|3end_phosphoglycerate_kinase_1763678..1763828_POSITIVE 325 100 57 42 1 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 318 90 47 145 110 NC_002950:PG0236|3end_hypothetical_protein_274824..274974_POSITIVE 317 90 53 62 23 NC_002950:PG1789|3end_peptidyl-dipeptidase_Dcp_1877417..1877567_NEGATIVE 317 89 48 54 6 NC_002950:PG0571|3end_aspartate-semialdehyde_dehydrogenase_627492..627642_POSITIVE 310 89 41 73 20 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 309 100 53 63 6 NC_002950:PG1788|3end_cysteine_peptidase,_putative_1877327..1877477_POSITIVE 309 100 53 123 64 NC_002950:PG0498|3end_S-ribosylhomocysteinase_538527..538677_POSITIVE 303 86 41 64 26 NC_002950:PG0286|3end_hypothetical_protein_320454..320604_POSITIVE 293 100 56 37 2 NC_002950:PG1875|3end_hemolysin_1969647..1969797_NEGATIVE 287 100 55 140 96 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 286 96 55 148 93 NC_002950:PG1672|3end_hypothetical_protein_1757884..1758034_POSITIVE 286 96 55 148 93 NC_002950:PG1267|3end_hypothetical_protein_1347213..1347363_POSITIVE 286 96 55 148 93 NC_002950:PG0100|3end_hypothetical_protein_119052..119202_NEGATIVE 284 87 46 66 25 NC_002950:PG1953|3end_YitT_family_protein_2044589..2044739_POSITIVE 277 85 46 135 97 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 277 97 61 60 23 NC_002950:PG1473|3end_conjugative_transposon_protein_TraQ_1549761..1549911_NEGATIVE 276 88 46 63 9 NC_002950:PG0005|3end_hypothetical_protein_3797..3947_NEGATIVE