Locus 4233

Sequence ID	3R_DroMel_CAF1
Location	11,374,003 – 11,374,180
Length	177
Max. P	0.999319

overview

Window 6

Location	11,374,003 – 11,374,114
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.87
Mean single sequence MFE	-30.80
Consensus MFE	-24.14
Energy contribution	-23.78
Covariance contribution	-0.36
Combinations/Pair	1.18
Mean z-score	-3.46
Structure conservation index	0.78
SVM decision value	3.10
SVM RNA-class probability	0.998427
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11374003 111 + 27905053
UAAAUGUAAAGAG-------AACGAUUUAGCCGGCCGGCGAAAAAACAUACAGUU-UUUCUCUC-UGUUCGGAAUUUGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUCCGGAUGA
.............-------..........(((..(((.((((((((.....)))-))).)).)-))..))).(((((((((((((((((...........))))))))))))))))).. ( -33.80)
>DroSec_CAF1 121624 112 + 1
UAAACAUAAAGAG-------AAUGUGUUAACCGGCCGGCGAAAAAACAUACCGUUUUUUCUCUC-AGUUCGAAAUUCGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUUCGCAUAU
..........(((-------(.........((....)).((((((((.....))))))))))))-...........((((((((((((((...........))))))))))))))..... ( -27.50)
>DroSim_CAF1 112656 112 + 1
UAAACAUAAAGAG-------AAUGUGUUAGCCGGCCGGCGAAAAAACAUACCGUUUUUUCUCUC-UGUUCGGAAUUCGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUUCGCAUAU
.........((((-------(........(((....)))((((((((.....))))))))))))-)..........((((((((((((((...........))))))))))))))..... ( -32.60)
>DroEre_CAF1 109202 118 + 1
UAAACACGAAGAGAAUAGAGAAUGAGUUAGCCGGCCGGCGAAAA-AUAUUU-AUUUUUUCUCUCGCGUUCGGAAUUCAGAGCUUUCGAAACAAAUAAAUCAUUUUGAAAGCUCUGCAUGU
..(((.(((.((((...((((((((((..(((....))).....-..))))-))))))))))))).))).......((((((((((((((...........))))))))))))))..... ( -34.90)
>DroYak_CAF1 111732 111 + 1
UAAACAUGAAGAG-------AAUGAGUUAGCCGGCCGGCAAAAA-AUAUUU-AUUUUUUCUCUCGCAUUCGGAAUAUAGAGCUUUCAAAAUAAAUAAAUCAUUUCGAAAGCUUUGCAUGU
...(((((....(-------((((.....(((....)))(((((-((....-)))))))......)))))......((((((((((.((((.........)))).))))))))))))))) ( -25.20)
>consensus
UAAACAUAAAGAG_______AAUGAGUUAGCCGGCCGGCGAAAAAACAUAC_GUUUUUUCUCUC_CGUUCGGAAUUCGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUUCGCAUGU
..........(((................(((....)))((((((((.....)))))))).)))............((((((((((((((...........))))))))))))))..... (-24.14 = -23.78 +  -0.36)

alignment

secondary structure

dotplot

Window 7

Location	11,374,003 – 11,374,114
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.87
Mean single sequence MFE	-33.22
Consensus MFE	-26.34
Energy contribution	-26.06
Covariance contribution	-0.28
Combinations/Pair	1.20
Mean z-score	-4.08
Structure conservation index	0.79
SVM decision value	3.51
SVM RNA-class probability	0.999319
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11374003 111 - 27905053
UCAUCCGGAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCAAAUUCCGAACA-GAGAGAAA-AACUGUAUGUUUUUUCGCCGGCCGGCUAAAUCGUU-------CUCUUUACAUUUA
......(((((((((((((..(.....)..)))))))))))))...........(-((((((((-(((.....))))....(((....))).......))-------))))))....... ( -35.40)
>DroSec_CAF1 121624 112 - 1
AUAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCGAAUUUCGAACU-GAGAGAAAAAACGGUAUGUUUUUUCGCCGGCCGGUUAACACAUU-------CUCUUUAUGUUUA
.....((.(((((((((((..(.....)..))))))))))).))......((((.-(((((((....((((..((......))..))))((....)).))-------)))))...)))). ( -30.90)
>DroSim_CAF1 112656 112 - 1
AUAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCGAAUUCCGAACA-GAGAGAAAAAACGGUAUGUUUUUUCGCCGGCCGGCUAACACAUU-------CUCUUUAUGUUUA
.....((.(((((((((((..(.....)..))))))))))).))......(((((-((((((((((((.....))))))))(((....)))........)-------)))....))))). ( -34.00)
>DroEre_CAF1 109202 118 - 1
ACAUGCAGAGCUUUCAAAAUGAUUUAUUUGUUUCGAAAGCUCUGAAUUCCGAACGCGAGAGAAAAAAU-AAAUAU-UUUUCGCCGGCCGGCUAACUCAUUCUCUAUUCUCUUCGUGUUUA
.....((((((((((.(((..(.....)..))).))))))))))......((((((((((((((((((-....))-)))..(((....)))..............))))).)))))))). ( -37.30)
>DroYak_CAF1 111732 111 - 1
ACAUGCAAAGCUUUCGAAAUGAUUUAUUUAUUUUGAAAGCUCUAUAUUCCGAAUGCGAGAGAAAAAAU-AAAUAU-UUUUUGCCGGCCGGCUAACUCAUU-------CUCUUCAUGUUUA
(((((...((((((((((((((.....)))))))))))))).........(((((.(....(((((((-....))-)))))(((....)))...).))))-------)....)))))... ( -28.50)
>consensus
ACAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCGAAUUCCGAACA_GAGAGAAAAAAC_GUAUGUUUUUUCGCCGGCCGGCUAACUCAUU_______CUCUUUAUGUUUA
.....((.((((((((((((((.....)))))))))))))).))......((((..((((((((((((.....))))))))(((....))).................))))...)))). (-26.34 = -26.06 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	11,374,036 – 11,374,140
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.06
Mean single sequence MFE	-22.56
Consensus MFE	-16.22
Energy contribution	-15.34
Covariance contribution	-0.88
Combinations/Pair	1.29
Mean z-score	-2.39
Structure conservation index	0.72
SVM decision value	1.67
SVM RNA-class probability	0.970955
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11374036 104 + 27905053
AAAAAACAUACAGUU-UUUCUCUC-UGUUCGGAAUUUGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUCCGGAUGAAAAAAAA--------------ACUAGAAUAUCAAGCUUUG
...........((((-(((...((-(....)))(((((((((((((((((...........))))))))))))))))).....))))--------------)))................ ( -24.80)
>DroSec_CAF1 121657 119 + 1
AAAAAACAUACCGUUUUUUCUCUC-AGUUCGAAAUUCGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUUCGCAUAUAAAAAAAACUUUUAACGAUAAACUAGAAUAUCAAGCUUUG
(((((((.....))))))).....-((((.((.(((((((((((((((((...........))))))))))))).....(((((.....)))))...........)))).)).))))... ( -23.00)
>DroSim_CAF1 112689 119 + 1
AAAAAACAUACCGUUUUUUCUCUC-UGUUCGGAAUUCGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUUCGCAUAUAAAAAAAACUUUUAACGAUAAACUAGAAUAUCAAGCUUUG
............(((((((...((-(....)))...((((((((((((((...........)))))))))))))).......))))))).......((((........))))........ ( -21.30)
>DroEre_CAF1 109242 117 + 1
AAAA-AUAUUU-AUUUUUUCUCUCGCGUUCGGAAUUCAGAGCUUUCGAAACAAAUAAAUCAUUUUGAAAGCUCUGCAUGUUAGAC-AACUUUAGGCGAAAAACGGGAAUAUCAAGCUUUG
....-......-.....((((((((((((..(.((.((((((((((((((...........)))))))))))))).)).)..)))-..(....))))).....)))))............ ( -26.60)
>DroYak_CAF1 111765 116 + 1
AAAA-AUAUUU-AUUUUUUCUCUCGCAUUCGGAAUAUAGAGCUUUCAAAAUAAAUAAAUCAUUUCGAAAGCUUUGCAUGUUAAAA-AACUUGAAGC-AAAAACUAGAAUAUCGAGCUUUG
....-......-.........((((.((((......((((((((((.((((.........)))).))))))))))((.(((....-))).))....-........))))..))))..... ( -17.10)
>consensus
AAAAAACAUAC_GUUUUUUCUCUC_CGUUCGGAAUUCGGAGCUUUCAAAACAAAUAAAUCAUUUUGAAAGCUUCGCAUGUAAAAAAAACUUUAAACGAAAAACUAGAAUAUCAAGCUUUG
....................................((((((((((((((...........))))))))))))))............................................. (-16.22 = -15.34 +  -0.88)

alignment

secondary structure

dotplot

Window 9

Location	11,374,036 – 11,374,140
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.06
Mean single sequence MFE	-27.70
Consensus MFE	-15.26
Energy contribution	-15.82
Covariance contribution	0.56
Combinations/Pair	1.14
Mean z-score	-2.92
Structure conservation index	0.55
SVM decision value	1.90
SVM RNA-class probability	0.981809
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11374036 104 - 27905053
CAAAGCUUGAUAUUCUAGU--------------UUUUUUUUCAUCCGGAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCAAAUUCCGAACA-GAGAGAAA-AACUGUAUGUUUUUU
........(((((..((((--------------(((((((((....(((((((((((((..(.....)..)))))))))))))...(....)...-))))))))-))))).))))).... ( -31.60)
>DroSec_CAF1 121657 119 - 1
CAAAGCUUGAUAUUCUAGUUUAUCGUUAAAAGUUUUUUUUAUAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCGAAUUUCGAACU-GAGAGAAAAAACGGUAUGUUUUUU
.(((((..((((........)))).......((((((((......((.(((((((((((..(.....)..))))))))))).))..((((.....-)))))))))))).....))))).. ( -26.20)
>DroSim_CAF1 112689 119 - 1
CAAAGCUUGAUAUUCUAGUUUAUCGUUAAAAGUUUUUUUUAUAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCGAAUUCCGAACA-GAGAGAAAAAACGGUAUGUUUUUU
.(((((..((((........)))).......(((((((((.....((.(((((((((((..(.....)..))))))))))).))..(((......-)))))))))))).....))))).. ( -26.30)
>DroEre_CAF1 109242 117 - 1
CAAAGCUUGAUAUUCCCGUUUUUCGCCUAAAGUU-GUCUAACAUGCAGAGCUUUCAAAAUGAUUUAUUUGUUUCGAAAGCUCUGAAUUCCGAACGCGAGAGAAAAAAU-AAAUAU-UUUU
........((((((....((((((((.....(((-....)))...((((((((((.(((..(.....)..))).))))))))))..........))))))))......-.)))))-)... ( -27.60)
>DroYak_CAF1 111765 116 - 1
CAAAGCUCGAUAUUCUAGUUUUU-GCUUCAAGUU-UUUUAACAUGCAAAGCUUUCGAAAUGAUUUAUUUAUUUUGAAAGCUCUAUAUUCCGAAUGCGAGAGAAAAAAU-AAAUAU-UUUU
.....((((.(((((.....(((-((.....(((-....)))..)))))(((((((((((((.....)))))))))))))..........))))))))).........-......-.... ( -26.80)
>consensus
CAAAGCUUGAUAUUCUAGUUUAUCGCUAAAAGUUUUUUUUACAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGCUCCGAAUUCCGAACA_GAGAGAAAAAAC_GUAUGUUUUUU
..(((((.(.....).)))))........................((.((((((((((((((.....)))))))))))))).)).................(((((((.....))))))) (-15.26 = -15.82 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	11,374,074 – 11,374,180
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.30
Mean single sequence MFE	-19.88
Consensus MFE	-14.12
Energy contribution	-14.00
Covariance contribution	-0.12
Combinations/Pair	1.16
Mean z-score	-1.48
Structure conservation index	0.71
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11374074 106 - 27905053
UUUGCUUAACUAAUCGUUUUUCUCAAUGUAUUAUGUCAUCCAAAGCUUGAUAUUCUAGU--------------UUUUUUUUCAUCCGGAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGC
........((((((((((......)))).)))).))..(((((((((.(.....).)))--------------)))..........)))((((((((((..(.....)..)))))))))) ( -16.70)
>DroSec_CAF1 121696 120 - 1
UUUGCUUAACUAAACGGUUUUCUCAAUGUGUUAUGUCAUCCAAAGCUUGAUAUUCUAGUUUAUCGUUAAAAGUUUUUUUUAUAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGC
(((((..((((.((((((...((....((((((.((........)).))))))...))...))))))...))))..........)))))((((((((((..(.....)..)))))))))) ( -24.00)
>DroSim_CAF1 112728 120 - 1
UUUGCUUAACUAAACGUUUUUCUCAAUGUAUUAUGUCAUCCAAAGCUUGAUAUUCUAGUUUAUCGUUAAAAGUUUUUUUUAUAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGC
(((((..((((.((((.....((....((((((.((........)).))))))...)).....))))...))))..........)))))((((((((((..(.....)..)))))))))) ( -21.30)
>DroEre_CAF1 109280 119 - 1
UUUAUUCCACAAAUCUUUUUUCUCACUGUACUAUAUCAUUCAAAGCUUGAUAUUCCCGUUUUUCGCCUAAAGUU-GUCUAACAUGCAGAGCUUUCAAAAUGAUUUAUUUGUUUCGAAAGC
.........................(((((..((((((.........))))))....(((...((.(....).)-)...))).))))).((((((.(((..(.....)..))).)))))) ( -16.30)
>DroYak_CAF1 111803 118 - 1
UUUAUUCAAGAAAACUUUUUUCUCACUGCAUUAUAUCAUUCAAAGCUCGAUAUUCUAGUUUUU-GCUUCAAGUU-UUUUAACAUGCAAAGCUUUCGAAAUGAUUUAUUUAUUUUGAAAGC
........(((((.....)))))...(((((..........((((((.(.....).)))))).-.......(((-....))))))))..(((((((((((((.....))))))))))))) ( -21.10)
>consensus
UUUGCUUAACUAAACGUUUUUCUCAAUGUAUUAUGUCAUCCAAAGCUUGAUAUUCUAGUUUAUCGCUAAAAGUUUUUUUUACAUGCGAAGCUUUCAAAAUGAUUUAUUUGUUUUGAAAGC
................................((((((.........))))))....................................(((((((((((((.....))))))))))))) (-14.12 = -14.00 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:52 2006