Locus 2303

Sequence ID	3R_DroMel_CAF1
Location	6,550,880 – 6,551,109
Length	229
Max. P	0.986783

overview

Window 2

Location	6,550,880 – 6,550,970
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-24.58
Consensus MFE	-23.38
Energy contribution	-23.42
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.21
Structure conservation index	0.95
SVM decision value	0.22
SVM RNA-class probability	0.639208
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6550880 90 + 27905053
UUUGGCUUCUCUGACAGACAGCCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGAC
((((((((((.....)))..(((........)))........))))))).......((((((....)))))).................. ( -24.30)
>DroSec_CAF1 27764 90 + 1
GUUGGCUUCUCUGACAGACAGUCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGAC
.((((((..((((((.....)))((.......)).)))....))))))........((((((....)))))).................. ( -23.80)
>DroSim_CAF1 27527 90 + 1
UUUGGCUUCUCUGACAGACAGCCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGAC
((((((((((.....)))..(((........)))........))))))).......((((((....)))))).................. ( -24.30)
>DroEre_CAF1 30785 90 + 1
UUUGGCUUCUUUGACAGACAGCCGUAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGAC
((((((((((((........(((........))).((.......)).))))))...((((((....)))))).....))))))....... ( -26.20)
>DroYak_CAF1 28993 90 + 1
UUUGGCUUCUCUGACAGACAGCCGUAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGAC
((((((((((.....)))..(((........)))........))))))).......((((((....)))))).................. ( -24.30)
>consensus
UUUGGCUUCUCUGACAGACAGCCGCAUUAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGAC
((((((((((.....)))..(((........)))........))))))).......((((((....)))))).................. (-23.38 = -23.42 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	6,550,907 – 6,551,001
Length	94
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	91.49
Mean single sequence MFE	-29.68
Consensus MFE	-24.20
Energy contribution	-24.48
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-2.75
Structure conservation index	0.82
SVM decision value	1.01
SVM RNA-class probability	0.899502
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6550907 94 + 27905053
UAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUG
.....(((((((((((((((((.......((((((....)))))).........(((........)))..))))))))....)))))..)))). ( -31.10)
>DroSec_CAF1 27791 94 + 1
UAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUG
.....(((((((((((((((((.......((((((....)))))).........(((........)))..))))))))....)))))..)))). ( -31.10)
>DroSim_CAF1 27554 94 + 1
UAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUG
.....(((((((((((((((((.......((((((....)))))).........(((........)))..))))))))....)))))..)))). ( -31.10)
>DroEre_CAF1 30812 94 + 1
UAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUG
.....(((((((((((((((((.......((((((....)))))).........(((........)))..))))))))....)))))..)))). ( -31.10)
>DroYak_CAF1 29020 94 + 1
UAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUG
.....(((((((((((((((((.......((((((....)))))).........(((........)))..))))))))....)))))..)))). ( -31.10)
>DroAna_CAF1 33317 76 + 1
------------------CGAAAGAAAAAGGGCUCAUUUGGGCUCACUCAGAUAGACAUUGACCAGUCCAUUUGGCCAUGUCAAUUUAUCUGCG
------------------(....).....((((((....))))))...(((((((((((.(.((((.....))))).)))))....)))))).. ( -22.60)
>consensus
UAAAGGCAGGAACUUGGCCAAAAGAAAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUG
....(((.........)))...(((....((((((....))))))....((((.(((((.(.((((.....))))).)))))))))..)))... (-24.20 = -24.48 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	6,550,907 – 6,551,001
Length	94
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	91.49
Mean single sequence MFE	-25.45
Consensus MFE	-21.58
Energy contribution	-22.30
Covariance contribution	0.72
Combinations/Pair	1.08
Mean z-score	-1.86
Structure conservation index	0.85
SVM decision value	0.50
SVM RNA-class probability	0.761844
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6550907 94 - 27905053
CACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUUUCUUUUGGCCAAGUUCCUGCCUUUA
..(((.....)))((.(((((((((((((........)))))...(((.((((.(....).))))...))).)))))))).))........... ( -27.20)
>DroSec_CAF1 27791 94 - 1
CACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUUUCUUUUGGCCAAGUUCCUGCCUUUA
..(((.....)))((.(((((((((((((........)))))...(((.((((.(....).))))...))).)))))))).))........... ( -27.20)
>DroSim_CAF1 27554 94 - 1
CACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUUUCUUUUGGCCAAGUUCCUGCCUUUA
..(((.....)))((.(((((((((((((........)))))...(((.((((.(....).))))...))).)))))))).))........... ( -27.20)
>DroEre_CAF1 30812 94 - 1
CACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUUUCUUUUGGCCAAGUUCCUGCCUUUA
..(((.....)))((.(((((((((((((........)))))...(((.((((.(....).))))...))).)))))))).))........... ( -27.20)
>DroYak_CAF1 29020 94 - 1
CACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUUUCUUUUGGCCAAGUUCCUGCCUUUA
..(((.....)))((.(((((((((((((........)))))...(((.((((.(....).))))...))).)))))))).))........... ( -27.20)
>DroAna_CAF1 33317 76 - 1
CGCAGAUAAAUUGACAUGGCCAAAUGGACUGGUCAAUGUCUAUCUGAGUGAGCCCAAAUGAGCCCUUUUUCUUUCG------------------
..((((((....((((((((((.......))))).)))))))))))((.(.((.(....).)))))..........------------------ ( -16.70)
>consensus
CACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUUUCUUUUGGCCAAGUUCCUGCCUUUA
..(((.....)))...(((((((((((((........)))))...(((.((((.(....).))))...))).)))))))).............. (-21.58 = -22.30 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	6,550,932 – 6,551,034
Length	102
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	96.87
Mean single sequence MFE	-30.99
Consensus MFE	-25.44
Energy contribution	-25.19
Covariance contribution	-0.25
Combinations/Pair	1.13
Mean z-score	-2.39
Structure conservation index	0.82
SVM decision value	0.64
SVM RNA-class probability	0.807804
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6550932 102 + 27905053
AAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUGUU-UGCCCCAUCGAUCUGGUCAUUACAUUUGAAG
....((((((....)))))).(((((........(((((((((.((..(((.....(((.....)))....-.)))..)).)).)))))))......))))). ( -31.64)
>DroSec_CAF1 27816 102 + 1
AAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUGUU-UGCCCCAUCGAUCUGGCCAUUACAUUUGAAG
....((((((....)))))).(((((((.(((((.(.((((.....))))).)))))))).....((((..-.(((..........)))...))))..)))). ( -28.70)
>DroSim_CAF1 27579 102 + 1
AAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUGUU-UGGCCCAUCGAUCUGGCCAUUACAUUUGAAG
....((((((....)))))).(((((((.(((((.(.((((.....))))).)))))))).....((((..-(((((.........))))).))))..)))). ( -33.50)
>DroEre_CAF1 30837 102 + 1
AAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUGUU-UGCCCCAUCGAUCUGGCCAUUACAUUUGAAG
....((((((....)))))).(((((((.(((((.(.((((.....))))).)))))))).....((((..-.(((..........)))...))))..)))). ( -28.70)
>DroYak_CAF1 29045 102 + 1
AAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUGUU-UGCCCCAUCGAUCUGGCCAUUACAUUUGAAG
....((((((....)))))).(((((((.(((((.(.((((.....))))).)))))))).....((((..-.(((..........)))...))))..)))). ( -28.70)
>DroAna_CAF1 33324 103 + 1
AAAAGGGCUCAUUUGGGCUCACUCAGAUAGACAUUGACCAGUCCAUUUGGCCAUGUCAAUUUAUCUGCGUUUUGGCCCAUCGAUCUGGCCAUUACAUCUGAAG
....((((((....))))))..((((((.(((((.(.((((.....))))).)))))...........((..(((((.........)))))..)))))))).. ( -34.70)
>consensus
AAAAGGGCUCAUUUGGGCCCAUUCAGCUAGACAUUGACCAGUCCAUUUGGCCAUGUCAGUUUAUCUGUGUU_UGCCCCAUCGAUCUGGCCAUUACAUUUGAAG
....((((((....)))))).(((((...(((........)))....((((((.(((........................))).))))))......))))). (-25.44 = -25.19 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	6,550,932 – 6,551,034
Length	102
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	96.87
Mean single sequence MFE	-30.05
Consensus MFE	-25.25
Energy contribution	-25.33
Covariance contribution	0.09
Combinations/Pair	1.10
Mean z-score	-1.99
Structure conservation index	0.84
SVM decision value	0.54
SVM RNA-class probability	0.773723
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6550932 102 - 27905053
CUUCAAAUGUAAUGACCAGAUCGAUGGGGCA-AACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUU
.((((...(((.(((((((.((.((..(((.-....(((.....))).....)))..)).))))))))).)).)....)))).((((.(....).)))).... ( -30.10)
>DroSec_CAF1 27816 102 - 1
CUUCAAAUGUAAUGGCCAGAUCGAUGGGGCA-AACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUU
.((((...(((.(((((((.((.((..(((.-....(((.....))).....)))..)).))))))))).)).)....)))).((((.(....).)))).... ( -29.50)
>DroSim_CAF1 27579 102 - 1
CUUCAAAUGUAAUGGCCAGAUCGAUGGGCCA-AACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUU
.((((...(((.(((((((.((.((.(((((-....(((.....)))...)))))..)).))))))))).)).)....)))).((((.(....).)))).... ( -30.40)
>DroEre_CAF1 30837 102 - 1
CUUCAAAUGUAAUGGCCAGAUCGAUGGGGCA-AACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUU
.((((...(((.(((((((.((.((..(((.-....(((.....))).....)))..)).))))))))).)).)....)))).((((.(....).)))).... ( -29.50)
>DroYak_CAF1 29045 102 - 1
CUUCAAAUGUAAUGGCCAGAUCGAUGGGGCA-AACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUU
.((((...(((.(((((((.((.((..(((.-....(((.....))).....)))..)).))))))))).)).)....)))).((((.(....).)))).... ( -29.50)
>DroAna_CAF1 33324 103 - 1
CUUCAGAUGUAAUGGCCAGAUCGAUGGGCCAAAACGCAGAUAAAUUGACAUGGCCAAAUGGACUGGUCAAUGUCUAUCUGAGUGAGCCCAAAUGAGCCCUUUU
.............(((((......(((((....((.((((((....((((((((((.......))))).))))))))))).))..)))))..)).)))..... ( -31.30)
>consensus
CUUCAAAUGUAAUGGCCAGAUCGAUGGGGCA_AACACAGAUAAACUGACAUGGCCAAAUGGACUGGUCAAUGUCUAGCUGAAUGGGCCCAAAUGAGCCCUUUU
.((((...(((.(((((((.((.((..(((......(((.....))).....)))..)).))))))))).)).)....)))).((((.(....).)))).... (-25.25 = -25.33 +   0.09)

alignment

secondary structure

dotplot

Window 7

Location	6,551,001 – 6,551,109
Length	108
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	92.49
Mean single sequence MFE	-33.32
Consensus MFE	-27.18
Energy contribution	-26.70
Covariance contribution	-0.48
Combinations/Pair	1.21
Mean z-score	-2.33
Structure conservation index	0.82
SVM decision value	2.05
SVM RNA-class probability	0.986783
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6551001 108 + 27905053
UUUGCCCCAUCGAUCUGGUCAUUACAUUUGAAGUGUUAUGGCUUGGACAUCAGCACGUAACAUGGGUUCUUUUUGGCCAACUUCGACUUCGGAUAUGGUUAUCUGCCU---
.........((((..((((((...........(((((((((((........))).))))))))..........))))))...))))...((((((....))))))...--- ( -27.10)
>DroSec_CAF1 27885 108 + 1
UUUGCCCCAUCGAUCUGGCCAUUACAUUUGAAGUGUUAUGGCUUGGACAUCAGCACGUAACACGGGUUCUUUUUGGCCAACUUCGACUUGGGCUAUGGCUAUCUGCCU---
...((((..((((..((((((...........(((((((((((........))).))))))))..........))))))...))))...))))...(((.....))).--- ( -39.20)
>DroSim_CAF1 27648 108 + 1
UUUGGCCCAUCGAUCUGGCCAUUACAUUUGAAGUGUUAUGGCUUGGACAUCAGCACGUAACACGGGUUCUUUUUGGCCAACUUCGACUUGGGCUAUAGCUAUCUGCCU---
..(((((((((((..((((((...........(((((((((((........))).))))))))..........))))))...))))..)))))))..((.....))..--- ( -39.20)
>DroEre_CAF1 30906 102 + 1
UUUGCCCCAUCGAUCUGGCCAUUACAUUUGAAGUGUUAUGGCUUGGACAUCAGCACGUAACACGGGUUCUUUUUGGCCAACUUCGAC------UAUGGCUAUCUGUCU---
...(((...((((..((((((...........(((((((((((........))).))))))))..........))))))...)))).------...))).........--- ( -31.20)
>DroYak_CAF1 29114 111 + 1
UUUGCCCCAUCGAUCUGGCCAUUACAUUUGAAGUGUUAUGGCUUGGACAUCAGCACGUAACACGGGUUCUUUUUGGCAAACUUCGGCAUCGGGUAUGGCUAUCUGUCUAUC
..(((((..((((....((((...........(((((((((((........))).))))))))..........)))).....))))....))))).(((.....))).... ( -29.90)
>consensus
UUUGCCCCAUCGAUCUGGCCAUUACAUUUGAAGUGUUAUGGCUUGGACAUCAGCACGUAACACGGGUUCUUUUUGGCCAACUUCGACUUCGGCUAUGGCUAUCUGCCU___
.........((((..((((((...........(((((((((((........))).))))))))..........))))))...))))..........(((.....))).... (-27.18 = -26.70 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:07 2006