Origin IGS: aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcaatcttattttcaaaaatttactgcaccacaccacacattttgcctgttcggtttcaccgttttaccgccatggacggcggtggttccattcttgcgatgttttgccgtgaggcaaaactcgaaactcaaaatcggacacagatgtccgattttgagtacctctccggcaaaatatgtgaac .........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 gttcacatattttgccggagaggtactcaaaatcggacatctgtgtccgattttgagtttcgagttttgcctcacggcaaaacatcgcaagaatggaaccaccgccgtccatggcggtaaaacggtgaaaccgaacaggcaaaatgtgtggtgtggtgcagtaaatttttgaaaataagattgacctgcactgtgttagccgctttagcggctcgaaaattttttgactaaaaaacggtatggatcttataaggtgccgcgtcagctggatagcatcctaaaccgtcctttccttcccatataccatttccccaaaataatgtataattggtctagcctaaaaatctaattcgatttttaggctagaccgtcgagtttttcataagtcttaaagacttatgaaaaacatcgcaaacagatttaggagggtttaatactt Mask Tandem Repeat Region ================================================ aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcaatcttattttcaaaaatttactgcaccacaccacacattttgcctgttcggtttcaccgttttaccgccatggacggcggtggttccattcttgcgatgttttgccgtgaggcaaaactcgaaactcaaaatcggacacagatgtccgattttgagtacctctccggcaaaatatgtgaac Find is-nt database================================================ Query_seq: TDE2514:TDE2515|TDE2514:TDE2515:serine/threonine protein phosphatase family protein:hypothetical protein:<-<-:2540623..2541061 439 aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcaatcttattttcaaaaatttactgcaccacaccacacattttgcctgttcggtttcaccgttttaccgccatggacggcggtggttccattcttgcgatgttttgccgtgaggcaaaactcgaaactcaaaatcggacacagatgtccgattttgagtacctctccggcaaaatatgtgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2514:TDE2515|TDE2514:TDE2515:serine/threonine protein phosphatase family protein:hypothetical protein:<-<-:2540623..2541061 439 aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcaatcttattttcaaaaatttactgcaccacaccacacattttgcctgttcggtttcaccgttttaccgccatggacggcggtggttccattcttgcgatgttttgccgtgaggcaaaactcgaaactcaaaatcggacacagatgtccgattttgagtacctctccggcaaaatatgtgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2514:TDE2515|TDE2514:TDE2515:serine/threonine protein phosphatase family protein:hypothetical protein:<-<-:2540623..2541061 439 aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcaatcttattttcaaaaatttactgcaccacaccacacattttgcctgttcggtttcaccgttttaccgccatggacggcggtggttccattcttgcgatgttttgccgtgaggcaaaactcgaaactcaaaatcggacacagatgtccgattttgagtacctctccggcaaaatatgtgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 280 Max: 438 Len: 159 Subject: UniRef90_Q73P53 Cluster: Hypothetical protein; n=1; Treponema denticola|Rep: Hypothetical protein - Treponema denticola HSP 1 e-value: 2.0E-19 bit: 97.1 Len: 159 Query Start:280 Query End:438 Subject Strand: null Subject Start: 11 Subject End: 63 ....................................................................................................................................................................................................................................................................................... F T Y F A G E V L K I G H L C P I L S F E F C L T A K H R K N G T T A V H G G K T V K P N R Q N V W C G A . ....................................................................................................................................................................................................................................................................................... F T H F A G E V L K I G R P C P I L S F E F C L S A K H R K N V T T A V R G G K A V K P N R Q N V F C G A . aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 249 End: 365 ........................................................................................................................................................................................................................................................ M Q V N L I F K N L L H H T T H F A C S V S P F Y R H G R R W F H S C D V L P .......................................................................... Protein_Len: 60 Strand: + Start: 169 End: 438 ........................................................................................................................................................................ M Q L T R H L I R S I P F F S Q K I F E P L K R L T Q C R S I L F S K I Y C T T P H I L P V R F H R F T A M D G G G S I . Protein_Len: 46 Strand: + Start: 302 End: 439 ............................................................................................................................................................................................................................................................................................................. M F G F T V L P P W T A V V P F L R C F A V R Q N S K L K I G H R C P I L S T S P A K Y V N Protein_Len: 37 Strand: - Start: 323 End: 433 .................................................................................................................................................................................................................................................................................................................................. R W P R R H N W E Q S T K G H P L V R F E F D S V S T R N Q T G R R C F M ...... Protein_Len: 46 Strand: - Start: 271 End: 408 .............................................................................................................................................................................................................................................................................. F N V A G C W V N Q R N P K V T K G G H V A T T G N K R H K A T L C F E F S L I P C L H G M ............................... Protein_Len: 41 Strand: - Start: 94 End: 216 ............................................................................................. I K L S S W N Y M I K P F H Y I P L F P R N L I S D L Q R P V K Y S G Y R K K T M ............................................................................................................................................................................................................................... aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc 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================================================ aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -6.7 Tail_Score: -4.76644 Start: 65 End: 116 Full_Region: tccccaaaataatgt ataattggtctagcctaaaaatc taattc gatttttaggctagaccgtcgag tttttcataagtctt ................................................................ataattggtctagcctaaaaatctaattcgatttttaggctagaccgtcgag................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -10.2 Tail_Score: -3.44902 Start: 66 End: 115 Full_Region: ccccaaaataatgta taattggtctagcctaaaaatc taattc gatttttaggctagaccgtcga gtttttcataagtct .................................................................taattggtctagcctaaaaatctaattcgatttttaggctagaccgtcga.................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -14.1 Tail_Score: -3.51545 Start: 69 End: 112 Full_Region: CTTATGAAAAACTCG ACGGTCTAGCCTAAAAATC GAATTA GATTTTTAGGCTAGACCAA TTATACATTATTTTG ....................................................................ACGGTCTAGCCTAAAAATCGAATTAGATTTTTAGGCTAGACCAA....................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -17.6 Tail_Score: -2.69842 Start: 70 End: 111 Full_Region: TTATGAAAAACTCGA CGGTCTAGCCTAAAAATC GAATTA GATTTTTAGGCTAGACCA ATTATACATTATTTT .....................................................................CGGTCTAGCCTAAAAATCGAATTAGATTTTTAGGCTAGACCA........................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 71 HP_score: -6.8 Tail_Score: -4.08767 Start: 307 End: 317 Full_Region: CACATTTTGCCTGTT CGGT TTC ACCG TTTTACCGCCATGGA ..................................................................................................................................................................................................................................................................................................................CGGTTTCACCG.......................................................................................................................... TransTerm Strand: - Conf: 75 HP_score: -10.4 Tail_Score: -3.10597 Start: 377 End: 420 Full_Region: acatattttgccgga gaggtactcaaaatcggaca tctg tgtccgattttgagtttcga gttttgcctcacggc ........................................................................................................................................................................................................................................................................................................................................................................................gaggtactcaaaatcggacatctgtgtccgattttgagtttcga................... TransTerm Strand: + Conf: 89 HP_score: -9.9 Tail_Score: -4.20531 Start: 390 End: 407 Full_Region: ACTCGAAACTCAAAA TCGGACA CAGA TGTCCGA TTTTGAGTACCTCTC .....................................................................................................................................................................................................................................................................................................................................................................................................TCGGACACAGATGTCCGA................................ Find igs database================================================ Query_seq: TDE2514:TDE2515|TDE2514:TDE2515:serine/threonine protein phosphatase family protein:hypothetical protein:<-<-:2540623..2541061 439 aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnc Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: NC_002967_TDE2514_TDE2515|serine/threonine protein phosphatase family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2540623,2541061]|439 HSP 1 e-value: 1.0E-144 bit: 511.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtca..................................................................................................................................................................................... aagtattaaaccctcctaaatctgtttgcgatgtttttcataagtctttaagacttatgaaaaactcgacggtctagcctaaaaatcgaattagatttttaggctagaccaattatacattattttggggaaatggtatatgggaaggaaaggacggtttaggatgctatccagctgacgcggcaccttataagatccataccgttttttagtcaaaaaattttcgagccgctaaagcggctaacacagtgcaggtca..................................................................................................................................................................................... HSP 2 e-value: 4.0E-9 bit: 63.9 Len: 40 Query Start:71 Query End:110 Subject Strand: NEGATIVE Subject Start: 71 Subject End: 110 ......................................................................ggtctagcctaaaaatcgaattagatttttaggctagacc......................................................................................................................................................................................................................................................................................................................................... ......................................................................ggtctagcctaaaaatctaattcgatttttaggctagacc......................................................................................................................................................................................................................................................................................................................................... HSP 3 e-value: 3.0E-7 bit: 58.0 Len: 33 Query Start:33 Query End:65 Subject Strand: NEGATIVE Subject Start: 33 Subject End: 65 ................................gtttttcataagtctttaagacttatgaaaaac...................................................................................................................................................................................................................................................................................................................................................................................... ................................gtttttcataagtcttaaagacttatgaaaaac...................................................................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUUAAACCCUCCUAAAUCUGUUUGCGAUGUUUUUCAUAAGUCUUUAAGACUUAUGAAAAACUCGACGGUCUAGCCUAAAAAUCGAAUUAGAUUUUUAGGCUAGACCAAUUAUACAUUAUUUUGGGGAAAUGGUAUAUGGGAAGGAAAGGACGGUUUAGGAUGCUAUCCAGCUGACGCGGCACCUUAUAAGAUCCAUACCGUUUUUUAGUCAAAAAAUUUUCGAGCCGCUAAAGCGGCUAACACAGUGCAGGUCA ..(((((...((.(((((.((((((((.(((.((((((((((((((.....)))))))))))))))))..(((((((((((((((((......)))))))))))))))))....................)))))).)).))))).))((((((((((...((((..(((...((((...)))).....)))..))))..))))))))))................((((((....)))))).....)))))...... (-91.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACCUGCACUGUGUUAGCCGCUUUAGCGGCUCGAAAAUUUUUUGACUAAAAAACGGUAUGGAUCUUAUAAGGUGCCGCGUCAGCUGGAUAGCAUCCUAAACCGUCCUUUCCUUCCCAUAUACCAUUUCCCCAAAAUAAUGUAUAAUUGGUCUAGCCUAAAAAUCUAAUUCGAUUUUUAGGCUAGACCGUCGAGUUUUUCAUAAGUCUUAAAGACUUAUGAAAAACAUCGCAAACAGAUUUAGGAGGGUUUAAUACUU .((((.(((((.....((((((....)))))).......(((((.....))))).................))))).).))).(((....)))....((((((.((((.((.......(((((.(((..........))))))))...(((((((((((((((((......)))))))))))))))))..(((((((((((((((((.....)))))))))))))).)))......))...)))).))))))...... (-85.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 849 110 61 201 152 NC_002967:TDE2514|5end_serine/threonine_protein_phosphatase_family_protein_2540532..2540762_NEGATIVE 438 68 25 157 113 NC_002967:TDE2505|5end_hypothetical_protein_2530125..2530355_POSITIVE 385 68 23 224 170 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 352 188 141 166 114 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 351 184 142 204 156 NC_002967:TDE1633|5end_citrate_lyase_acyl_carrier_protein_1682691..1682921_NEGATIVE 341 190 147 199 157 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 335 181 141 50 12 NC_002967:TDE2728|5end_hypothetical_protein_2785607..2785837_POSITIVE 335 68 22 230 176 NC_002967:TDE1852|5end_ABC_transporter,_ATP-binding_protein_1881866..1882096_NEGATIVE 321 240 196 136 87 NC_002967:TDE1832|5end_hypothetical_protein_1865921..1866151_NEGATIVE 321 240 196 136 87 NC_002967:TDE1796|5end_hypothetical_protein_1835515..1835745_NEGATIVE 309 187 141 105 55 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 303 187 147 114 61 NC_002967:TDE2134|5end_hypothetical_protein_2164447..2164677_POSITIVE 301 60 13 192 145 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 301 246 203 183 130 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 295 240 193 184 130 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 294 200 155 109 55 NC_002967:TDE1137|5end_hypothetical_protein_1166749..1166979_NEGATIVE 293 198 152 207 165 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 292 185 142 65 15 NC_002967:TDE1622|5end_hypothetical_protein_1670981..1671211_NEGATIVE 288 205 166 49 1 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 286 204 161 182 122 NC_002967:TDE2397|5end_hypothetical_protein_2425564..2425794_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 757 240 196 62 18 NC_002967:TDE2268|3end_hypothetical_protein_2304822..2304972_NEGATIVE 438 68 25 49 5 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 422 74 31 53 2 NC_002967:TDE2465|3end_hypothetical_protein_2489391..2489541_NEGATIVE 352 188 141 144 92 NC_002967:TDE1334|3end_hypothetical_protein_1370874..1371024_POSITIVE 351 184 142 110 62 NC_002967:TDE1634|3end_hypothetical_protein_1682785..1682935_NEGATIVE 342 68 29 130 80 NC_002967:TDE2464|3end_hypothetical_protein_2489369..2489519_POSITIVE 335 68 22 130 76 NC_002967:TDE1853|3end_hypothetical_protein_1881966..1882116_NEGATIVE 318 184 142 81 41 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 310 184 141 79 35 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 302 198 151 60 10 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 301 60 13 147 100 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 295 240 193 82 28 NC_002967:TDE0692|3end_hypothetical_protein_729920..730070_POSITIVE 285 203 173 108 74 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 283 180 132 117 72 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 283 152 118 104 70 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 276 185 152 72 40 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 275 190 142 98 36 NC_002967:TDE1004|3end_flagellar_filament_core_protein_1029276..1029426_NEGATIVE 274 169 127 89 52 NC_002967:TDE2097|3end_hypothetical_protein_2124478..2124628_NEGATIVE 274 187 142 60 17 NC_002967:TDE1255|3end_hypothetical_protein_1288977..1289127_NEGATIVE 270 80 34 125 67 NC_002967:TDE1491|3end_chemotaxis_protein_CheA_1537294..1537444_POSITIVE