Origin IGS: agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttatagtaccacttttaggtactattgtcaatgttttttatatactgatgacggtttttccaaactctaagaattatgttaaatctaaacctatcgacaaagcgttttttttaatatagaattgttaattatatggaaaggctttgagccttaggagggagact Mask Tandem Repeat Region ================================================ agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Find is-nt database================================================ Query_seq: TDE2212:TDE2213|TDE2212:TDE2213:galactokinase:hypothetical protein:<-->:2252772..2252939 168 agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2212:TDE2213|TDE2212:TDE2213:galactokinase:hypothetical protein:<-->:2252772..2252939 168 agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2212:TDE2213|TDE2212:TDE2213:galactokinase:hypothetical protein:<-->:2252772..2252939 168 agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 49 End: 162 ................................................ I L F F A K D I P K S K V Y N K S N P F V T M L I Y F V N V I T G L L P V M ...... agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 133 End: 162 ....................................................................................................................................ATTGACAATAGTACCTAAAAGTGGTACTAT...... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 43 End: 72 ..........................................ATCGACAAAGCGTTTTTTTTAATATAGAAT................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2212:TDE2213|TDE2212:TDE2213:galactokinase:hypothetical protein:<-->:2252772..2252939 168 agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_002967_TDE2212_TDE2213|galactokinase:hypothetical protein|NEGATIVE:POSITIVE|[2252772,2252939]|168 HSP 1 e-value: 2.0E-76 bit: 285.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 agtctccctcctaaggctcaaagcctttccatataattaacaattctatattnnnnnnnncgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta agtctccctcctaaggctcaaagcctttccatataattaacaattctatattaaaaaaaacgctttgtcgataggtttagatttaacataattcttagagtttggaaaaaccgtcatcagtatataaaaaacattgacaatagtacctaaaagtggtactataaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCUCCCUCCUAAGGCUCAAAGCCUUUCCAUAUAAUUAACAAUUCUAUAUUAAAAAAAACGCUUUGUCGAUAGGUUUAGAUUUAACAUAAUUCUUAGAGUUUGGAAAAACCGUCAUCAGUAUAUAAAAAACAUUGACAAUAGUACCUAAAAGUGGUACUAUAAAUUA .(((........(((((.....)))))..................................(((.((.((.....(((((((((.............))))))))).....)).))..)))..............))).((((((((.......))))))))...... (-25.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAUAGUACCACUUUUAGGUACUAUUGUCAAUGUUUUUUAUAUACUGAUGACGGUUUUUCCAAACUCUAAGAAUUAUGUUAAAUCUAAACCUAUCGACAAAGCGUUUUUUUUAAUAUAGAAUUGUUAAUUAUAUGGAAAGGCUUUGAGCCUUAGGAGGGAGACU ......((((((((.......)))))))).((((..((.........))...))))....(((((...((((.....((((((((((...((((((........)).))))..))))))))))..................(((((.....))))).))))))))).. (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 50 1 141 92 NC_002967:TDE2212|5end_galactokinase_2252681..2252911_NEGATIVE 267 50 4 213 158 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 266 29 1 206 165 NC_002967:TDE0004|5end_hypothetical_protein_4243..4473_POSITIVE 256 40 4 38 2 NC_002967:TDE1731|5end_hypothetical_protein_1786935..1787165_NEGATIVE 251 27 2 67 39 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 232 160 122 77 43 NC_002967:TDE1663|5end_OmpA_family_protein_1717319..1717549_POSITIVE 231 34 5 220 187 NC_002967:TDE1973|5end_CvpA_family_protein_1987706..1987936_NEGATIVE 228 48 2 60 5 NC_002967:TDE2712|5end_hypothetical_protein_2769008..2769238_POSITIVE 220 28 1 219 186 NC_002967:TDE2583|5end_hypothetical_protein_2616322..2616552_POSITIVE 220 31 13 58 41 NC_002967:TDE2061|5end_hypothetical_protein_2087792..2088022_NEGATIVE 218 34 1 36 3 NC_002967:TDE0832|5end_hypothetical_protein_852549..852779_POSITIVE 218 47 2 106 62 NC_002967:TDE0690|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_726898..727128_POSITIVE 217 106 61 85 44 NC_002967:TDE2430|5end_bacteriocin_ABC_transporter,_bacteriocin-binding_protein,_putative_2459173..2459403_NEGATIVE 217 32 1 231 193 NC_002967:TDE1919|5end_hypothetical_protein_1939890..1940120_NEGATIVE 215 33 4 133 111 NC_002967:TDE1157|5end_phage_terminase,_large_subunit,_putative_1193293..1193523_NEGATIVE 214 35 1 192 159 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 213 32 3 133 101 NC_002967:TDE2205|5end_enoate_reductase,_putative_2244755..2244985_NEGATIVE 212 43 5 54 15 NC_002967:TDE2538|5end_hypothetical_protein_2563785..2564015_POSITIVE 212 50 2 109 59 NC_002967:TDE0958|5end_patatin_family_protein_981040..981270_POSITIVE 210 32 1 79 40 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 118 72 63 19 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 238 32 1 51 12 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 236 30 1 85 53 NC_002967:TDE1691|3end_hypothetical_protein_1747407..1747557_NEGATIVE 230 115 72 141 100 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 228 34 2 74 41 NC_002967:TDE2329|3end_hypothetical_protein_2366347..2366497_NEGATIVE 225 28 1 134 108 NC_002967:TDE1500|3end_hypothetical_protein_1546763..1546913_NEGATIVE 221 18 1 144 124 NC_002967:TDE0003|3end_hypothetical_protein_4282..4432_POSITIVE 220 31 13 48 31 NC_002967:TDE2062|3end_hypothetical_protein_2087802..2087952_NEGATIVE 218 47 2 100 56 NC_002967:TDE0689|3end_5-methylthioribose_kinase_726972..727122_POSITIVE 217 106 61 88 47 NC_002967:TDE2431|3end_bacteriocin_ABC_transporter,_ATP-binding/permease_protein,_putative_2459170..2459320_NEGATIVE 212 43 5 47 8 NC_002967:TDE2537|3end_hypothetical_protein_2563858..2564008_POSITIVE 212 50 2 64 14 NC_002967:TDE0957|3end_glycerophosphoryl_diester_phosphodiesterase_family_protein_981075..981225_POSITIVE 211 47 3 135 85 NC_002967:TDE0475|3end_ABC_transporter,_ATP-binding_protein_531153..531303_NEGATIVE 210 32 1 66 27 NC_002967:TDE1145|3end_hypothetical_protein_1182868..1183018_NEGATIVE 209 98 57 94 59 NC_002967:TDE0438|3end_queuine_tRNA-ribosyltransferase_493672..493822_NEGATIVE 207 30 1 69 38 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 206 30 4 40 7 NC_002967:TDE1406|3end_hypothetical_protein_1448677..1448827_NEGATIVE 204 40 1 54 9 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE 204 45 1 57 24 NC_002967:TDE0154|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_176208..176358_NEGATIVE 203 113 73 58 9 NC_002967:TDE2566|3end_hypothetical_protein_2591332..2591482_NEGATIVE