Origin IGS: tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca .........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 tgaatcgttggttaggttgttgagttgttgaattgttgagttgttgaattgtttgctgaaaaccgaaaactaaataaccattgacaatttgggaaaaagccctgaaagggcgcgttaattcagcccaatgcgcagcgttgggagaaaaaagcaaccccacatcggagggctgtaagcctgaattaatgttggtgtaattgttgaactgttgatttgttgaattgttgatttgttgaattgtttgattgttgaattgtttaagcaactaaacaactaaacatctaaacaactcaacatccgaaggactgaaaactaaaaaaaaa Mask Tandem Repeat Region ================================================ tttttttttagttttcagtccttcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctaaccaacgattca Find is-nt database================================================ Query_seq: TF1174:TF1175|TF1174:TF1175:ABC transporter, permease component:membrane-fusion protein:->->:1257957..1258279 323 tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1174:TF1175|TF1174:TF1175:ABC transporter, permease component:membrane-fusion protein:->->:1257957..1258279 323 tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1174:TF1175|TF1174:TF1175:ABC transporter, permease component:membrane-fusion protein:->->:1257957..1258279 323 tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 51 End: 206 .................................................. M F S C L N N S T I K Q F N K S T I Q Q I N S S T I T P T L I Q A Y S P P M W G C F F L P T L R I G L N ..................................................................................................................... Protein_Len: 35 Strand: + Start: 205 End: 309 ............................................................................................................................................................................................................ M N A P F Q G F F P N C Q W L F S F R F S A N N S T T Q Q F N N S T T .............. Protein_Len: 60 Strand: + Start: 59 End: 322 .......................................................... M L K Q F N N Q T I Q Q I N N S T N Q Q F N N Y T N I N S G L Q P S D V G L L F S P N A A H W A E L T R P F R A F S Q I . Protein_Len: 38 Strand: - Start: 130 End: 243 ................................................................................................................................. V L M L E P K C G E S T P N S K E G L A A C Q A S N V R G K L A K E W I T M ................................................................................ tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca 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================================================ tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -9.1 Tail_Score: -4.60255 Start: 213 End: 225 Full_Region: GGGCTGAATTAACGC GCCCT TTC AGGGC TTTTTCCCAAATTGT ....................................................................................................................................................................................................................GCCCTTTCAGGGC.................................................................................................. Find igs database================================================ Query_seq: TF1174:TF1175|TF1174:TF1175:ABC transporter, permease component:membrane-fusion protein:->->:1257957..1258279 323 tttttttttagttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgcttaaacaattcaacaatcaaacaattcaacaaatcaacaattcaacaaatcaacagttcaacaattacaccaacattaattcaggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcagcaaacaattcaacaactcaacaattcaacaactcaacaacctaaccaacgattca Intra-Species Hit: Count: 2 Min: 10 Max: 268 Len: 259 Subject: tfor_TF1174_TF1175|ABC transporter, permease component:membrane-fusion protein|POSITIVE:POSITIVE|[1257957,1258279]|323 HSP 1 e-value: 2.0E-63 bit: 244.0 Len: 123 Query Start:146 Query End:268 Subject Strand: POSITIVE Subject Start: 146 Subject End: 268 .................................................................................................................................................ggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcag....................................................... .................................................................................................................................................ggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttcggttttcag....................................................... HSP 2 e-value: 6.0E-23 bit: 109.0 Len: 55 Query Start:10 Query End:64 Subject Strand: POSITIVE Subject Start: 10 Subject End: 64 .........agttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgctt................................................................................................................................................................................................................................................................... .........agttttcagtccttcggatgttgagttgtttagatgtttagttgtttagttgctt................................................................................................................................................................................................................................................................... Subject: tfor_TF1172_TF1173|ABC transporter, permease component:ABC transporter, permease component|POSITIVE:POSITIVE|[1255274,1255583]|310 HSP 1 e-value: 5.0E-39 bit: 163.0 Len: 114 Query Start:146 Query End:259 Subject Strand: POSITIVE Subject Start: 87 Subject End: 199 .................................................................................................................................................ggcttacagccctccgatgtggggttgcttttttctcccaacgctgcgcattgggctgaattaacgcgccctttcagggctttttcccaaattgtcaatggttatttagttttc................................................................ .................................................................................................................................................ggcttacagccctctgacgtggggttgctttt-tctcccaacgctgtgcattgggctgaattaacatgccctttcagggctttttctcaaattgtcaatggttatttagttttc................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUCAGUCCUUCGGAUGUUGAGUUGUUUAGAUGUUUAGUUGUUUAGUUGCUUAAACAAUUCAACAAUCAAACAAUUCAACAAAUCAACAAUUCAACAAAUCAACAGUUCAACAAUUACACCAACAUUAAUUCAGGCUUACAGCCCUCCGAUGUGGGGUUGCUUUUUUCUCCCAACGCUGCGCAUUGGGCUGAAUUAACGCGCCCUUUCAGGGCUUUUUCCCAAAUUGUCAAUGGUUAUUUAGUUUUCGGUUUUCAG .............((((((((((((((((((.((((((.((((((((((....)))))))))).))).))))))))))))))))............(((((((.(((.(((..((((((.........(((((((((.....(((((((.......))))))).........(((((.((...)).))))))))))))))...((((.....)))).........)))))).))).))))))).))))))))....... (-64.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAAAACCGAAAACUAAAUAACCAUUGACAAUUUGGGAAAAAGCCCUGAAAGGGCGCGUUAAUUCAGCCCAAUGCGCAGCGUUGGGAGAAAAAAGCAACCCCACAUCGGAGGGCUGUAAGCCUGAAUUAAUGUUGGUGUAAUUGUUGAACUGUUGAUUUGUUGAAUUGUUGAUUUGUUGAAUUGUUUGAUUGUUGAAUUGUUUAAGCAACUAAACAACUAAACAUCUAAACAACUCAACAUCCGAAGGACUGAAAACU .......((...............((..((((((..(.(((..((((.....)))).(((((((((((((((((((...))))))))........(((.((((......).))).)))....)))))))))))........................))).)..))))))..)).((((((.(((((((..((((...(((((((......)))))))...))))..))))))).))))))......)).......... (-71.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 848 220 171 192 144 tfor:TF1183|5end_hypothetical_protein_1268391..1268621_POSITIVE 827 217 171 190 140 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 798 217 172 219 169 tfor:TF2478|5end_hypothetical_protein_2655375..2655605_POSITIVE 797 217 172 78 33 tfor:TF0821|5end_hypothetical_protein_879879..880109_POSITIVE 795 220 171 196 148 tfor:TF1186|5end_hypothetical_protein_1269568..1269798_POSITIVE 795 220 171 202 154 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 775 219 171 125 68 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 775 219 171 118 61 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 768 217 171 116 71 tfor:TF2191|5end_hypothetical_protein_2365934..2366164_POSITIVE 768 217 171 78 33 tfor:TF0822|5end_hypothetical_protein_880487..880717_POSITIVE 759 217 172 216 170 tfor:TF1184|5end_hypothetical_protein_1269004..1269234_POSITIVE 731 220 171 179 130 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 691 190 141 224 175 tfor:TF0823|5end_conserved_hypothetical_protein_880660..880890_POSITIVE 688 180 134 68 22 tfor:TF0679|5end_hypothetical_protein_721155..721385_POSITIVE 632 190 141 223 173 tfor:TF1187|5end_hypothetical_protein_1269625..1269855_POSITIVE 629 180 134 60 13 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 623 180 131 184 136 tfor:TF2036|5end_possible_pyruvate_formate-lyase_activating_enzyme_2196302..2196532_POSITIVE 616 180 134 64 16 tfor:TF1716|5end_hypothetical_protein_1837442..1837672_POSITIVE 595 217 171 64 8 tfor:TF0678|5end_hypothetical_protein_721103..721333_POSITIVE 541 220 171 126 72 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 797 217 172 61 16 tfor:TF0820|3end_hypothetical_protein_879942..880092_POSITIVE 795 220 171 111 63 tfor:TF1185|3end_hypothetical_protein_1269563..1269713_POSITIVE 766 217 172 82 37 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 759 217 172 70 24 tfor:TF1182|3end_hypothetical_protein_1268938..1269088_POSITIVE 656 210 162 139 92 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 629 180 134 129 82 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 541 220 171 56 2 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 462 180 134 136 88 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 456 176 131 132 85 tfor:TF1274|3end_hypothetical_protein_1357895..1358045_POSITIVE 439 175 134 128 80 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 439 161 134 149 122 tfor:TF0678|3end_hypothetical_protein_721335..721485_POSITIVE 405 241 205 43 1 tfor:TF1848|3end_conserved_hypothetical_protein_1997944..1998094_POSITIVE 391 174 133 53 9 tfor:TF2702|3end_hypothetical_protein_2876136..2876286_POSITIVE 388 54 11 92 50 tfor:TF1170|3end_conserved_hypothetical_protein_1252799..1252949_POSITIVE 368 216 173 54 1 tfor:TF3003|3end_hypothetical_protein_3220629..3220779_POSITIVE 363 190 150 43 1 tfor:TF2755|3end_hypothetical_protein_2941053..2941203_POSITIVE 362 193 151 140 85 tfor:TF2848|3end_cobalamin_biosynthesis_protein_3037389..3037539_POSITIVE 362 218 172 103 54 tfor:TF0911|3end_transposase_954297..954447_POSITIVE 358 217 173 150 103 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 352 220 179 54 2 tfor:TF2490|3end_4-hydroxyphenylacetate-3-hydroxylase/4-hydroxybut_yryl_dehydratase_2666755..2666905_POSITIVE