📄 meme.crp0.oops
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********************************************************************************MEME - Motif discovery tool********************************************************************************MEME version 3.5.4 (Release date: 3.5.4)For further information on how to interpret these results or to geta copy of the MEME software please access http://meme.nbcr.net.This file may be used as input to the MAST algorithm for searchingsequence databases for matches to groups of motifs. MAST is availablefor interactive use and downloading at http://meme.nbcr.net.****************************************************************************************************************************************************************REFERENCE********************************************************************************If you use this program in your research, please cite:Timothy L. Bailey and Charles Elkan,"Fitting a mixture model by expectation maximization to discovermotifs in biopolymers", Proceedings of the Second InternationalConference on Intelligent Systems for Molecular Biology, pp. 28-36,AAAI Press, Menlo Park, California, 1994.****************************************************************************************************************************************************************TRAINING SET********************************************************************************DATAFILE= /mnt/hgfs/linuxshare/meme_3.5.4/scripts/../tests/crp0.sALPHABET= ACGTSequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ce1cg 1.0000 105 ara 1.0000 105 bglr1 1.0000 105 crp 1.0000 105 cya 1.0000 105 deop2 1.0000 105 gale 1.0000 105 ilv 1.0000 105 lac 1.0000 105 male 1.0000 105 malk 1.0000 105 malt 1.0000 105 ompa 1.0000 105 tnaa 1.0000 105 uxu1 1.0000 105 pbr322 1.0000 105 trn9cat 1.0000 105 tdc 1.0000 105 ****************************************************************************************************************************************************************COMMAND LINE SUMMARY********************************************************************************This information can also be useful in the event you wish to report aproblem with the MEME software.command: meme /mnt/hgfs/linuxshare/meme_3.5.4/scripts/../tests/crp0.s -mod oops -dna -revcomp -nostatus -nmotifs 2 -minw 8 model: mod= oops nmotifs= 2 evt= infobject function= E-value of product of p-valueswidth: minw= 8 maxw= 50 minic= 0.00width: wg= 11 ws= 1 endgaps= yesnsites: minsites= 18 maxsites= 18 wnsites= 0.8theta: prob= 1 spmap= uni spfuzz= 0.5em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05data: n= 1890 N= 18strands: + -sample: seed= 0 seqfrac= 1Letter frequencies in dataset:A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from dataset with add-one prior applied):A 0.304 C 0.196 G 0.196 T 0.304 ****************************************************************************************************************************************************************MOTIF 1 width = 15 sites = 18 llr = 169 E-value = 3.4e-006********************************************************************************-------------------------------------------------------------------------------- Motif 1 Description--------------------------------------------------------------------------------Simplified A 1::9:1231::1829pos.-specific C 111144321317:81probability G 8:9:232241212::matrix T 19:14143378211: bits 2.4 2.1 * 1.9 * 1.6 * Information 1.4 *** *content 1.2 **** **(13.5 bits) 0.9 **** * *** 0.7 ***** ****** 0.5 ****** ****** 0.2 ****** ******* 0.0 ---------------Multilevel GTGATCTAGTTCACAconsensus CGCTTC sequence G ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value--------------------------------------------------------------------------------Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------------lac - 12 1.53e-06 TGCCTAATGA GTGAGCTAACTCACA TTAATTGCGTompa + 52 2.44e-06 TTTCATATGC CTGACGGAGTTCACA CTTGTAAGTTara - 58 2.72e-06 ATAGCAAAGT GTGACGCCGTGCAAA TAATCAATGTtnaa + 75 3.77e-06 CCGAACGATT GTGATTCGATTCACA TTTAAACAATmalk + 65 5.16e-06 AAGGAATTTC GTGATGTTGCTTGCA AAAATCGTGGcya - 53 5.16e-06 GGTCTAAAAC GTGATCAATTTAACA CCTTGCTGATpbr322 - 56 5.73e-06 TTACGCATCT GTGCGGTATTTCACA CCGCATATGGbglr1 - 79 9.29e-06 TGATAAAAAT ATGACCATGCTCACA GTTATTAACTdeop2 - 10 1.02e-05 TCACTGTAAT GCGATCTGGTTCAAA TAATTCACT malt + 45 1.12e-05 ATTTGGAATT GTGACACAGTGCAAA TTCAGACACAce1cg + 65 1.12e-05 GACTGTTTTT TTGATCGTTTTCACA AAAATGGAAGcrp - 66 1.35e-05 GCACGGTAAT GTGACGTCCTTTGCA TACATGCAGTuxu1 + 21 1.62e-05 TGAAATTGTT GTGATGTGGTTAACC CAATTAGAATmale - 17 1.62e-05 GTCGCTTTGT GTGATCTCTGTTACA GAATTGGCGGtdc + 82 1.77e-05 AAGTTAATTT GTGAGTGGTCGCACA TATCCTGTT gale + 55 5.66e-05 TTTATTCCAT GTCACACTTTTCGCA TCTTTGTTATilv + 43 1.54e-04 AGTACAAAAC GTGATCAACCCCTCA ATTTTCCCTTtrn9cat + 40 2.28e-04 ATAAATCCTG GTGTCCCTGTTGATA CCGGGAAGCC---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 block diagrams--------------------------------------------------------------------------------SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM------------- ---------------- -------------lac 1.5e-06 11_[-1]_79ompa 2.4e-06 51_[+1]_39ara 2.7e-06 57_[-1]_33tnaa 3.8e-06 74_[+1]_16malk 5.2e-06 64_[+1]_26cya 5.2e-06 52_[-1]_38pbr322 5.7e-06 55_[-1]_35bglr1 9.3e-06 78_[-1]_12deop2 1e-05 9_[-1]_81malt 1.1e-05 44_[+1]_46ce1cg 1.1e-05 64_[+1]_26crp 1.3e-05 65_[-1]_25uxu1 1.6e-05 20_[+1]_70male 1.6e-05 16_[-1]_74tdc 1.8e-05 81_[+1]_9gale 5.7e-05 54_[+1]_36ilv 0.00015 42_[+1]_48trn9cat 0.00023 39_[+1]_51---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 in BLOCKS format--------------------------------------------------------------------------------BL MOTIF 1 width=15 seqs=18lac ( 12) GTGAGCTAACTCACA 1 ompa ( 52) CTGACGGAGTTCACA 1 ara ( 58) GTGACGCCGTGCAAA 1 tnaa ( 75) GTGATTCGATTCACA 1 malk ( 65) GTGATGTTGCTTGCA 1 cya ( 53) GTGATCAATTTAACA 1 pbr322 ( 56) GTGCGGTATTTCACA 1 bglr1 ( 79) ATGACCATGCTCACA 1 deop2 ( 10) GCGATCTGGTTCAAA 1 malt ( 45) GTGACACAGTGCAAA 1 ce1cg ( 65) TTGATCGTTTTCACA 1 crp ( 66) GTGACGTCCTTTGCA 1 uxu1 ( 21) GTGATGTGGTTAACC 1 male ( 17) GTGATCTCTGTTACA 1 tdc ( 82) GTGAGTGGTCGCACA 1 gale ( 55) GTCACACTTTTCGCA 1 ilv ( 43) GTGATCAACCCCTCA 1 trn9cat ( 40) GTGTCCCTGTTGATA 1 //---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix--------------------------------------------------------------------------------log-odds matrix: alength= 4 w= 15 n= 1638 bayes= 6.49185 E= 3.4e-006 -245 -182 209 -245 -1081 -182 -1081 163 -1081 -182 227 -1081 155 -182 -1081 -245 -1081 99 -23 55 -145 118 77 -145 -87 50 -23 35 13 -23 18 -13 -145 -82 118 13 -1081 50 -182 113 -1081 -182 -23 135 -145 177 -182 -87 135 -1081 -23 -245 -87 199 -1081 -245 163 -182 -1081 -1081 ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 position-specific probability matrix--------------------------------------------------------------------------------letter-probability matrix: alength= 4 w= 15 nsites= 18 E= 3.4e-006 0.055556 0.055556 0.833333 0.055556 0.000000 0.055556 0.000000 0.944444 0.000000 0.055556 0.944444 0.000000 0.888889 0.055556 0.000000 0.055556 0.000000 0.388889 0.166667 0.444444 0.111111 0.444444 0.333333 0.111111 0.166667 0.277778 0.166667 0.388889 0.333333 0.166667 0.222222 0.277778 0.111111 0.111111 0.444444 0.333333 0.000000 0.277778 0.055556 0.666667 0.000000 0.055556 0.166667 0.777778 0.111111 0.666667 0.055556 0.166667 0.777778 0.000000 0.166667 0.055556 0.166667 0.777778 0.000000 0.055556 0.944444 0.055556 0.000000 0.000000 --------------------------------------------------------------------------------⌨️ 快捷键说明
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