Locus 2846

Sequence ID	3L_DroMel_CAF1
Location	8,117,159 – 8,117,330
Length	171
Max. P	0.979832

overview

Window 5

Location	8,117,159 – 8,117,259
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.58
Mean single sequence MFE	-46.87
Consensus MFE	-26.27
Energy contribution	-27.68
Covariance contribution	1.42
Combinations/Pair	1.19
Mean z-score	-1.46
Structure conservation index	0.56
SVM decision value	-0.00
SVM RNA-class probability	0.533488
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8117159 100 + 23771897
GCUAUCAGGA---UUACCCCUCAACAGAGGAGCCCCAUGCUCGAGCAGACGCACUCCCGAAAUGGUGGAACCCAUGUCGAUGGGCGUGCUAUCGGUGGU------UGGC-----------
(((.......---.....((((....))))((((((.(((....)))...((((.(((((.((((......)))).))...))).))))....)).)))------))))----------- ( -31.20)
>DroVir_CAF1 14411 114 + 1
GCUGCUCGGCUGUUCGCCGCGCAGCAGCGGCGCUCCAUGCUCCAGCAGGCGCACGCCCGAUAUGGUUGAGCCCAUGUCGAUGGGCGUGCUGUCUGUGGU------GCGCGUAUUGCUGGU
(((((.((((.....)))).)))))(((.((((.....((.(((.((((((((((((((((((((......)))))))...)))))))).)))))))).------))))))...)))... ( -63.70)
>DroPse_CAF1 22662 106 + 1
GCUGUCGGGC---CGUCCUCGCAGCAGCGGUGCCCCGUGCUCCAGCAAACGCACCCCCGAGAUGGUCGAACCCAUGUCGAUGGGCGUGCUGUCUGUCGUCACUGGCGGC-----------
(((((((((.---((.(...(((((((((((((....(((....)))...)))))(((((.((((......)))).)))..)))).))))))..).)).).))))))))----------- ( -45.40)
>DroYak_CAF1 14086 100 + 1
GCUAUCGGGA---CUUCCUCGCAACAGAGGAGCCCCAUGCUCGAGCAGACGCACUCCCGAAAUGGUGGAACCCAUGUCAAUGGGCGUGCUAUCGGUGGU------UGGC-----------
(((((((((.---((.((((......)))))).))).(((....)))...((((.(((((.((((......)))).))...))).))))....))))))------....----------- ( -36.20)
>DroMoj_CAF1 13992 114 + 1
GCUGUCUGGCUGUUCGCCGCGCAGCAGUGGAGCUCCAUGCUCCAGCAGGCGCACGCCCGAUAUGGUCGAGCCCAUGUCAAUGGGCGUGCUGUCUGUGGU------GCGCGCCUCAUUGGC
.......(((.....)))(((((.(..((((((.....))))))(((((((((((((((((((((......)))))))...)))))))).))))))).)------))))(((.....))) ( -62.80)
>DroAna_CAF1 14053 100 + 1
GCUAUCCGGA---UCGCCUCUUAGCAAGGGGGCGCCAUGCUCCAGGAGACGCACUCCCGAAAUGGUGGAGCCCAUGUCAAUGGGCGUGCUAUCGGUGGU------GGGG-----------
....((((((---.((((((((....))))))))......))).)))..(.(((..((((..(((((..((((((....)))))).)))))))))..))------).).----------- ( -41.90)
>consensus
GCUAUCCGGA___UCGCCUCGCAGCAGAGGAGCCCCAUGCUCCAGCAGACGCACUCCCGAAAUGGUGGAACCCAUGUCAAUGGGCGUGCUAUCGGUGGU______GGGC___________
(((((.(((.......))).)))))...(((((.....))))).......((((.(((((.((((......)))).))...))).))))............................... (-26.27 = -27.68 +   1.42)

alignment

secondary structure

dotplot

Window 6

Location	8,117,196 – 8,117,290
Length	94
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	75.62
Mean single sequence MFE	-43.35
Consensus MFE	-22.39
Energy contribution	-23.50
Covariance contribution	1.11
Combinations/Pair	1.07
Mean z-score	-1.92
Structure conservation index	0.52
SVM decision value	0.67
SVM RNA-class probability	0.817978
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8117196 94 + 23771897
UCGAGCAGACGCACUCCCGAAAUGGUGGAACCCAUGUCGAUGGGCGUGCUAUCGGUGGU------UGGC---------------AAUGGUUUUAAGGCCACACCCACCGGCUGAA
((.(((....((((.(((((.((((......)))).))...))).))))...((((((.------((..---------------..(((((....))))))).))))))))))). ( -34.00)
>DroVir_CAF1 14451 109 + 1
UCCAGCAGGCGCACGCCCGAUAUGGUUGAGCCCAUGUCGAUGGGCGUGCUGUCUGUGGU------GCGCGUAUUGCUGGUCAGUUGCGGCCGCACUGCCACGCCCACCGGCUGAA
..(((((((((((((((((((((((......)))))))...)))))))).))))((((.------(((.(((.(((.((((......))))))).)))..)))))))..)))).. ( -55.90)
>DroPse_CAF1 22699 100 + 1
UCCAGCAAACGCACCCCCGAGAUGGUCGAACCCAUGUCGAUGGGCGUGCUGUCUGUCGUCACUGGCGGC---------------ACUGGCUUCAGGGCCACGCCCACCGGCUGAA
..((((...........(((.((((......)))).))).(((((((((((((.((....)).))))))---------------))(((((....))))).)))))...)))).. ( -43.60)
>DroGri_CAF1 14128 109 + 1
UCCAGCAGGCGCACACCCGAUAUGGUCGAGCCCAUGUCGAUGGGCGUGCUGUCUGUGGU------GCGUGCAUCGCUGCUCAGCUGCGGCCUCACUGCCACGCCCACCGGCUGCA
..((((((((((((.((((((((((......)))))))...))).)))).))))((((.------(((((((..(((((......))))).....)).)))))))))..)))).. ( -51.20)
>DroYak_CAF1 14123 94 + 1
UCGAGCAGACGCACUCCCGAAAUGGUGGAACCCAUGUCAAUGGGCGUGCUAUCGGUGGU------UGGC---------------AGUGGUUUUAGGGCCACGCCCACCGGUUGAA
((((.(....((((.(((((.((((......)))).))...))).))))....(((((.------..((---------------.((((((....)))))))))))))).)))). ( -36.50)
>DroAna_CAF1 14090 94 + 1
UCCAGGAGACGCACUCCCGAAAUGGUGGAGCCCAUGUCAAUGGGCGUGCUAUCGGUGGU------GGGG---------------AGUGAUUUUAAUGCCACGCCCACGGGCUGAA
....(....).(((((((.(..((((((.((((((....))))))...))))))....)------.)))---------------))))..........((.(((....))))).. ( -38.90)
>consensus
UCCAGCAGACGCACUCCCGAAAUGGUGGAACCCAUGUCGAUGGGCGUGCUAUCGGUGGU______GGGC_______________AGUGGCUUCAAGGCCACGCCCACCGGCUGAA
..((((....((((.(((((.((((......)))).))...))).))))...(.((((...........................(((((......)))))..)))).))))).. (-22.39 = -23.50 +   1.11)

alignment

secondary structure

dotplot

Window 7

Location	8,117,196 – 8,117,290
Length	94
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	75.62
Mean single sequence MFE	-41.55
Consensus MFE	-32.50
Energy contribution	-32.20
Covariance contribution	-0.30
Combinations/Pair	1.25
Mean z-score	-1.96
Structure conservation index	0.78
SVM decision value	1.85
SVM RNA-class probability	0.979832
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8117196 94 - 23771897
UUCAGCCGGUGGGUGUGGCCUUAAAACCAUU---------------GCCA------ACCACCGAUAGCACGCCCAUCGACAUGGGUUCCACCAUUUCGGGAGUGCGUCUGCUCGA
.(((((((((((...((((............---------------))))------.))))))...((((.(((...((.((((......)))).))))).))))....))).)) ( -35.80)
>DroVir_CAF1 14451 109 - 1
UUCAGCCGGUGGGCGUGGCAGUGCGGCCGCAACUGACCAGCAAUACGCGC------ACCACAGACAGCACGCCCAUCGACAUGGGCUCAACCAUAUCGGGCGUGCGCCUGCUGGA
.....((((..(((((((..(((((...((.........))....)))))------.)))).....((((((((...((.((((......)))).)))))))))))))..)))). ( -53.70)
>DroPse_CAF1 22699 100 - 1
UUCAGCCGGUGGGCGUGGCCCUGAAGCCAGU---------------GCCGCCAGUGACGACAGACAGCACGCCCAUCGACAUGGGUUCGACCAUCUCGGGGGUGCGUUUGCUGGA
.....((((..((((((((.(((....))).---------------)))))...............((((.(((..(((.((((......)))).)))))))))))))..)))). ( -43.20)
>DroGri_CAF1 14128 109 - 1
UGCAGCCGGUGGGCGUGGCAGUGAGGCCGCAGCUGAGCAGCGAUGCACGC------ACCACAGACAGCACGCCCAUCGACAUGGGCUCGACCAUAUCGGGUGUGCGCCUGCUGGA
.....((((..(((((((..((..(((....)))..)).(((.....)))------.)))).....((((((((...((.((((......)))).)))))))))))))..)))). ( -51.40)
>DroYak_CAF1 14123 94 - 1
UUCAACCGGUGGGCGUGGCCCUAAAACCACU---------------GCCA------ACCACCGAUAGCACGCCCAUUGACAUGGGUUCCACCAUUUCGGGAGUGCGUCUGCUCGA
......((((((((((((........)))).---------------))..------.))))))...((((.(((...((.((((......)))).))))).)))).......... ( -33.90)
>DroAna_CAF1 14090 94 - 1
UUCAGCCCGUGGGCGUGGCAUUAAAAUCACU---------------CCCC------ACCACCGAUAGCACGCCCAUUGACAUGGGCUCCACCAUUUCGGGAGUGCGUCUCCUGGA
(((((...(((((.((((........)))).---------------.)))------))....(((.((((.(((...((.((((......)))).))))).)))))))..))))) ( -31.30)
>consensus
UUCAGCCGGUGGGCGUGGCACUAAAACCACU_______________GCCC______ACCACAGACAGCACGCCCAUCGACAUGGGCUCCACCAUUUCGGGAGUGCGUCUGCUGGA
.....((((..(((((((........))))....................................((((.(((...((.((((......)))).))))).)))))))..)))). (-32.50 = -32.20 +  -0.30)

alignment

secondary structure

dotplot

Window 8

Location	8,117,236 – 8,117,330
Length	94
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	77.62
Mean single sequence MFE	-37.07
Consensus MFE	-26.86
Energy contribution	-26.19
Covariance contribution	-0.66
Combinations/Pair	1.30
Mean z-score	-1.34
Structure conservation index	0.72
SVM decision value	0.69
SVM RNA-class probability	0.824108
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8117236 94 - 23771897
CUACCAUCCAGGGGCGGCAGUCCAUAUCUGCCCCGUGGCCUUCAGCCGGUGGGUGUGGCCUUAAAACCAUU---------------GCCA------ACCACCGAUAGCACGCCCA
...........(((((((((.......)))))..(((((.....))((((((...((((............---------------))))------.))))))....))))))). ( -35.90)
>DroVir_CAF1 14491 109 - 1
CUGCCCUCGCGUGGUGGCAGCCCAUAUUUGCCGCGAGGCCUUCAGCCGGUGGGCGUGGCAGUGCGGCCGCAACUGACCAGCAAUACGCGC------ACCACAGACAGCACGCCCA
.(((..((..((((((((.((((((....(((....))).........)))))).(((((((((....)).)))).))).......)).)------))))).))..)))...... ( -44.32)
>DroPse_CAF1 22739 100 - 1
CUGCCCUCCCGGGGCGGAAGCCCCUAUCUGCCGCGUGGCCUUCAGCCGGUGGGCGUGGCCCUGAAGCCAGU---------------GCCGCCAGUGACGACAGACAGCACGCCCA
..((((.((.(((((....)))))............(((.....))))).))))(((((.(((....))).---------------)))))..(((.(........))))..... ( -43.70)
>DroSec_CAF1 14157 94 - 1
CUACCCUCCAGGGGCGGUAGUCCAUACCUGCCCCGUGGCCUUCAGCCGGUGGGUGUGGCCUUAAAACCAUU---------------ACCA------ACCACCGACAGCACGCCCA
..........(((((((((.....)))).)))))(.(((.......((((((..((((........)))).---------------....------.)))))).......)))). ( -33.84)
>DroYak_CAF1 14163 94 - 1
CUGCCCUCCAGGGGCGGCAGUCCAUAUCUGCCCCGAGGUCUUCAACCGGUGGGCGUGGCCCUAAAACCACU---------------GCCA------ACCACCGAUAGCACGCCCA
.(((((((..(((((((..........)))))))))))........((((((((((((........)))).---------------))..------.))))))...)))...... ( -35.30)
>DroAna_CAF1 14130 94 - 1
CUGCCCUCCAGAGGCGGAAGUCCCUAUCUGCCCCGUGGCCUUCAGCCCGUGGGCGUGGCAUUAAAAUCACU---------------CCCC------ACCACCGAUAGCACGCCCA
((((((....).)))))..((..(((((.((((((.(((.....))))).))))((((.............---------------....------.)))).))))).))..... ( -29.37)
>consensus
CUGCCCUCCAGGGGCGGCAGUCCAUAUCUGCCCCGUGGCCUUCAGCCGGUGGGCGUGGCCUUAAAACCACU_______________GCCA______ACCACCGACAGCACGCCCA
..(((.....(((((((..........)))))))..(((.....))))))(((((((..................................................))))))). (-26.86 = -26.19 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:14 2006