Origin IGS: taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgttgtttatagcggtgacaaagctacaaaaatataaagacaaaaaaaagccgatggaagaaatccaccggccttttcggttatggtcttacgattgatta Mask Tandem Repeat Region ================================================ taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Find is-nt database================================================ Query_seq: TF1331:TF1332|TF1331:TF1332:outer membrane protein:cytochrome c-type synthesis protein (cytochrome c biogenesis protein); ABC transporter, permease:->->:1410995..1411096 102 taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1331:TF1332|TF1331:TF1332:outer membrane protein:cytochrome c-type synthesis protein (cytochrome c biogenesis protein); ABC transporter, permease:->->:1410995..1411096 102 taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1331:TF1332|TF1331:TF1332:outer membrane protein:cytochrome c-type synthesis protein (cytochrome c biogenesis protein); ABC transporter, permease:->->:1410995..1411096 102 taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M N R K T I T E K A G G F L P S A F F C L Y I F V A L S P L .......... Protein_Len: 32 Strand: - Start: 7 End: 102 ...... D Y S W L R F P R H I E E M P K K K D K Y K Q L K T V A I F L M taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat 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================================================ taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 62 HP_score: -2.5 Tail_Score: -4.60808 Start: 20 End: 63 Full_Region: CAATCGTAAGACCAT AACCGAAAAGGCCGGTGGA TTTCT TCCATCGGCTTTTTTTTGTC TTTATATTTTTGTAG ...................AACCGAAAAGGCCGGTGGATTTCTTCCATCGGCTTTTTTTTGTC....................................... TransTerm Strand: + Conf: 61 HP_score: -5.1 Tail_Score: -3.88932 Start: 22 End: 61 Full_Region: ATCGTAAGACCATAA CCGAAAAGGCCGGTGGA TTTCT TCCATCGGCTTTTTTTTG TCTTTATATTTTTGT .....................CCGAAAAGGCCGGTGGATTTCTTCCATCGGCTTTTTTTTG......................................... TransTerm Strand: - Conf: 67 HP_score: -5.6 Tail_Score: -4.33151 Start: 29 End: 53 Full_Region: ataaagacaaaaaaa agccgatgga agaaa tccaccggcc ttttcggttatggtc ............................agccgatggaagaaatccaccggcc................................................. TransTerm Strand: - Conf: 71 HP_score: -9.1 Tail_Score: -3.19168 Start: 30 End: 52 Full_Region: taaagacaaaaaaaa gccgatgga agaaa tccaccggc cttttcggttatggt .............................gccgatggaagaaatccaccggc.................................................. Find igs database================================================ Query_seq: TF1331:TF1332|TF1331:TF1332:outer membrane protein:cytochrome c-type synthesis protein (cytochrome c biogenesis protein); ABC transporter, permease:->->:1410995..1411096 102 taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Intra-Species Hit: Count: 1 Min: 1 Max: 102 Len: 102 Subject: tfor_TF1331_TF1332|outer membrane protein:cytochrome c-type synthesis protein (cytochrome c biogenesis protein); ABC transporter, permease|POSITIVE:POSITIVE|[1410995,1411096]|102 HSP 1 e-value: 3.0E-37 bit: 155.0 Len: 102 Query Start:1 Query End:102 Subject Strand: POSITIVE Subject Start: 1 Subject End: 102 taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcnnnnnnnngtctttatatttttgtagctttgtcaccgctataaacaacat taatcaatcgtaagaccataaccgaaaaggccggtggatttcttccatcggcttttttttgtctttatatttttgtagctttgtcaccgctataaacaacat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAAUCGUAAGACCAUAACCGAAAAGGCCGGUGGAUUUCUUCCAUCGGCUUUUUUUUGUCUUUAUAUUUUUGUAGCUUUGUCACCGCUAUAAACAACAU ...........(((((.......(((((((((((((((.....)))))))))))))))..)))))......((((((((.........))))))))...... (-30.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUUGUUUAUAGCGGUGACAAAGCUACAAAAAUAUAAAGACAAAAAAAAGCCGAUGGAAGAAAUCCACCGGCCUUUUCGGUUAUGGUCUUACGAUUGAUUA (((((.(((.(((((....)...)))).))))))))...(((...((((.((((.((((.....)))).)))).))))..))).(((((........))))) (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 59 15 163 118 tfor:TF3033|5end_S1_RNA_binding_domain_protein,_S1_ribosomal_protein_3256786..3257016_POSITIVE 345 53 16 127 88 tfor:TF2231|5end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_2400307..2400537_POSITIVE 318 63 26 203 168 tfor:TF0691|5end_conserved_hypothetical_protein_735611..735841_POSITIVE 316 78 31 190 139 tfor:TF2569|5end_50S_ribosomal_protein_L6_2741622..2741852_POSITIVE 316 63 23 174 129 tfor:TF0992|5end_hypothetical_protein_1048251..1048481_POSITIVE 309 64 21 221 185 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 307 52 16 204 166 tfor:TF2454|5end_D-alanyl-D-alanine_dipeptidase_2631259..2631489_POSITIVE 304 60 16 106 45 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 303 53 13 198 138 tfor:TF0464|5end_precorrin_methylase_480211..480441_POSITIVE 301 66 23 84 43 tfor:TF1002|5end_replicative_DNA_helicase_1056620..1056850_POSITIVE 297 63 22 190 148 tfor:TF2937|5end_translation_elongation_factor_Tu_3139238..3139468_POSITIVE 296 69 22 79 31 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 296 52 17 45 9 tfor:TF1907|5end_ADP-heptose:LPS_heptosyltransferase_II_2061579..2061809_POSITIVE 295 80 32 231 181 tfor:TF2099|5end_D-tyrosyl-tRNA(Tyr)_deacylase_2272896..2273126_POSITIVE 295 63 22 169 124 tfor:TF1063|5end_possible_amidase_enhancer_precursor;_sporulation-related_protein_1132671..1132901_POSITIVE 288 54 11 188 146 tfor:TF1304|5end_conserved_hypothetical_protein_1385008..1385238_POSITIVE 286 55 23 228 195 tfor:TF3109|5end_hypothetical_protein_3341998..3342228_POSITIVE 286 52 22 56 21 tfor:TF1933|5end_methionyl-tRNA_synthetase_2079675..2079905_POSITIVE 285 62 22 79 32 tfor:TF0461|5end_ATP:cob(I)alamin_adenosyltransferase_476990..477220_POSITIVE 283 51 15 165 135 tfor:TF3121|5end_nicotinate_phosphoribosyltransferase_3354815..3355045_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 59 15 135 90 tfor:TF3032|3end_thiamin_biosynthesis_protein_3256838..3256988_POSITIVE 389 57 12 66 26 tfor:TF1331|3end_outer_membrane_protein_1410934..1411084_POSITIVE 345 53 16 134 95 tfor:TF2230|3end_CTn_excision_protein_2400394..2400544_POSITIVE 309 64 21 132 96 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 296 69 22 52 4 tfor:TF2950|3end_chloromuconate_cycloisomerase_3158549..3158699_POSITIVE 291 60 22 89 51 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 286 52 22 56 21 tfor:TF1932|3end_pigmentation_and_extracellular_proteinase_regulator_2079755..2079905_POSITIVE 285 62 22 79 32 tfor:TF0460|3end_hypothetical_protein_477070..477220_POSITIVE 284 53 16 44 7 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 283 51 15 45 15 tfor:TF3120|3end_HD_superfamily_hydrolase_3354775..3354925_POSITIVE 282 68 28 91 51 tfor:TF0592|3end_epimerase/reductase_626451..626601_POSITIVE 278 60 14 66 19 tfor:TF0985|3end_fructose-bisphosphate_aldolase_1042973..1043123_POSITIVE 278 63 23 135 79 tfor:TF0207|3end_conserved_hypothetical_protein_233505..233655_POSITIVE 275 61 22 95 50 tfor:TF2907|3end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3103681..3103831_POSITIVE 272 79 35 66 10 tfor:TF1466|3end_DNA_gyrase_modulator_1557084..1557234_POSITIVE 270 79 31 58 18 tfor:TF1283|3end_hypothetical_protein_1367747..1367897_POSITIVE 268 54 13 137 98 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 266 51 22 139 112 tfor:TF1062|3end_glycosyltransferase_1132739..1132889_POSITIVE 262 57 18 148 97 tfor:TF0228|3end_probable_integral_outer_membrane_protein_254809..254959_POSITIVE 260 66 21 45 2 tfor:TF1548|3end_thiophene_and_furan_oxidation_protein_1653987..1654137_POSITIVE