Locus 1826

Sequence ID	2L_DroMel_CAF1
Location	5,043,178 – 5,043,299
Length	121
Max. P	0.847183

overview

Window 0

Location	5,043,178 – 5,043,285
Length	107
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	80.97
Mean single sequence MFE	-27.30
Consensus MFE	-20.29
Energy contribution	-18.97
Covariance contribution	-1.32
Combinations/Pair	1.35
Mean z-score	-1.67
Structure conservation index	0.74
SVM decision value	0.40
SVM RNA-class probability	0.722353
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5043178 107 + 22407834
GUUAGCCCAUCGAUUUUUGGGUUUAGCA-UCUGUGCAGCCCUGG-UGUUUCCACGCCCUACCAACACUGCCCACCUUGCUGUUAACUUUACAGCAGUGUUUGCUACGCG
(((((((((........)))).))))).-...(((.(((...((-(((....))))).....((((((((.........(((.......))))))))))).))).))). ( -29.30)
>DroSec_CAF1 6701 99 + 1
GUUAGCCCAUCGAUUUUUGGGCUUAGCAAUCUAUGCAGCCCUGG-GUUU---------UACCAACACUGCCCUACUUGCUGUUAACUUUACAGCAGUGUUUGGAACGCG
...((((((........))))))..((.......((((...(((-....---------..)))...))))((.(((((((((.......))))))).))..))...)). ( -30.90)
>DroSim_CAF1 6746 99 + 1
GUUAGCCCAUUGAUUUUUGGGCUUAGCAAUCUAUGCAGCCCUGG-GGUU---------UACCAACACUGCCCCACUUGCUGUUAACUUUACAGCGAUGUUUGGAACGCG
(((((((((........))))).))))..((((.(((....(((-(((.---------..........)))))).(((((((.......)))))))))).))))..... ( -33.40)
>DroEre_CAF1 6590 107 + 1
GUUUACCUAUUGAUUUUUAGGUAUGGCA-CAUACGCAGCCCUGU-UUUUUUCACACCCUACCAACACUGCCCACCUUGCUGUUAACUUUACAGUAGUGUUUGCUACGCG
...((((((........))))))(((((-.((((((((...(((-(................))))))))......((((((.......)))))))))).))))).... ( -23.69)
>DroYak_CAF1 6793 108 + 1
GUUUAUCCAUUGAUUUUUUGGUAUGGCA-UCUAUGCAGCCCUGGCUUUUUCCACAACCUAUCAACACUGACCACCCUGCUGUUAACUUUACAGUAGUGUUUGCUACGCG
.........(((((...(((((((((..-.))))))(((....))).......)))...)))))........((.(((((((.......))))))).)).......... ( -19.20)
>consensus
GUUAGCCCAUUGAUUUUUGGGUUUAGCA_UCUAUGCAGCCCUGG_UUUUU_CAC__CCUACCAACACUGCCCACCUUGCUGUUAACUUUACAGCAGUGUUUGCUACGCG
(((((((((........)))))).))).......((((...(((................)))...))))......((((((.......))))))((((.....)))). (-20.29 = -18.97 +  -1.32)

alignment

secondary structure

dotplot

Window 1

Location	5,043,178 – 5,043,285
Length	107
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	80.97
Mean single sequence MFE	-30.09
Consensus MFE	-20.45
Energy contribution	-21.25
Covariance contribution	0.80
Combinations/Pair	1.16
Mean z-score	-1.98
Structure conservation index	0.68
SVM decision value	0.77
SVM RNA-class probability	0.847183
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5043178 107 - 22407834
CGCGUAGCAAACACUGCUGUAAAGUUAACAGCAAGGUGGGCAGUGUUGGUAGGGCGUGGAAACA-CCAGGGCUGCACAGA-UGCUAAACCCAAAAAUCGAUGGGCUAAC
....(((((..(((((((((.......)))))..)))).(((((.(((((.....((....)))-)))).))))).....-)))))..((((........))))..... ( -34.40)
>DroSec_CAF1 6701 99 - 1
CGCGUUCCAAACACUGCUGUAAAGUUAACAGCAAGUAGGGCAGUGUUGGUA---------AAAC-CCAGGGCUGCAUAGAUUGCUAAGCCCAAAAAUCGAUGGGCUAAC
.(((.((.....((((((((.......))))).)))...(((((.((((..---------....-)))).)))))...)).)))..((((((........))))))... ( -34.10)
>DroSim_CAF1 6746 99 - 1
CGCGUUCCAAACAUCGCUGUAAAGUUAACAGCAAGUGGGGCAGUGUUGGUA---------AACC-CCAGGGCUGCAUAGAUUGCUAAGCCCAAAAAUCAAUGGGCUAAC
.(((.((((......(((((.......)))))...))))(((((.((((..---------....-)))).)))))......)))..((((((........))))))... ( -33.50)
>DroEre_CAF1 6590 107 - 1
CGCGUAGCAAACACUACUGUAAAGUUAACAGCAAGGUGGGCAGUGUUGGUAGGGUGUGAAAAAA-ACAGGGCUGCGUAUG-UGCCAUACCUAAAAAUCAAUAGGUAAAC
.(((((((..((((((((....)))...(((((..(....)..)))))....))))).......-.....)))))))...-.....((((((........))))))... ( -25.94)
>DroYak_CAF1 6793 108 - 1
CGCGUAGCAAACACUACUGUAAAGUUAACAGCAGGGUGGUCAGUGUUGAUAGGUUGUGGAAAAAGCCAGGGCUGCAUAGA-UGCCAUACCAAAAAAUCAAUGGAUAAAC
...(((((.((((((((..(...((.....))...)..)).))))))....((((........))))...))))).....-..((((............))))...... ( -22.50)
>consensus
CGCGUAGCAAACACUGCUGUAAAGUUAACAGCAAGGUGGGCAGUGUUGGUAGG__GUG_AAAAA_CCAGGGCUGCAUAGA_UGCUAAACCCAAAAAUCAAUGGGCUAAC
.((........(((((((((.......)))))..)))).(((((.(((..................))).))))).......))..((((((........))))))... (-20.45 = -21.25 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	5,043,206 – 5,043,299
Length	93
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	83.68
Mean single sequence MFE	-22.66
Consensus MFE	-15.40
Energy contribution	-15.40
Covariance contribution	0.00
Combinations/Pair	1.12
Mean z-score	-1.90
Structure conservation index	0.68
SVM decision value	0.36
SVM RNA-class probability	0.704059
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5043206 93 + 22407834
UCUGUGCAGCCCUGG-UGUUUCCACGCCCUACCAACACUGCCCACCUUGCUGUUAACUUUACAGCAGUGUUUGCUACGCGCCAGCCCUGACUUA
...((.(((..((((-(((......(......)......((..((.(((((((.......))))))).))..))...)))))))..)))))... ( -22.70)
>DroSec_CAF1 6730 84 + 1
UCUAUGCAGCCCUGG-GUUU---------UACCAACACUGCCCUACUUGCUGUUAACUUUACAGCAGUGUUUGGAACGCGCCAGCCCUGGCUUA
.....((((...(((-....---------..)))...))))((.(((((((((.......))))))).))..)).....((((....))))... ( -24.60)
>DroSim_CAF1 6775 84 + 1
UCUAUGCAGCCCUGG-GGUU---------UACCAACACUGCCCCACUUGCUGUUAACUUUACAGCGAUGUUUGGAACGCGCCAGCCCUGGCUUA
((((.(((....(((-(((.---------..........)))))).(((((((.......)))))))))).))))....((((....))))... ( -27.00)
>DroEre_CAF1 6618 93 + 1
CAUACGCAGCCCUGU-UUUUUUCACACCCUACCAACACUGCCCACCUUGCUGUUAACUUUACAGUAGUGUUUGCUACGCGCCAGCCCUGGCUUA
.....((((...(((-(................))))))))......((((((.......))))))((((.....))))((((....))))... ( -17.69)
>DroYak_CAF1 6821 94 + 1
UCUAUGCAGCCCUGGCUUUUUCCACAACCUAUCAACACUGACCACCCUGCUGUUAACUUUACAGUAGUGUUUGCUACGCGCCAGCCCUGGCUUA
.......(((((((((...............................((((((.......))))))((((.....)))))))))....)))).. ( -21.30)
>consensus
UCUAUGCAGCCCUGG_UUUUU_CAC__CCUACCAACACUGCCCACCUUGCUGUUAACUUUACAGCAGUGUUUGCUACGCGCCAGCCCUGGCUUA
......(((..((((................................((((((.......))))))((((.....)))).))))..)))..... (-15.40 = -15.40 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	5,043,206 – 5,043,299
Length	93
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	83.68
Mean single sequence MFE	-29.17
Consensus MFE	-19.13
Energy contribution	-20.21
Covariance contribution	1.08
Combinations/Pair	1.10
Mean z-score	-2.22
Structure conservation index	0.66
SVM decision value	0.71
SVM RNA-class probability	0.829355
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5043206 93 - 22407834
UAAGUCAGGGCUGGCGCGUAGCAAACACUGCUGUAAAGUUAACAGCAAGGUGGGCAGUGUUGGUAGGGCGUGGAAACA-CCAGGGCUGCACAGA
...(((...((..((((...((..((..((((((.......))))))..))..)).))))..))..)))(((....))-).............. ( -32.30)
>DroSec_CAF1 6730 84 - 1
UAAGCCAGGGCUGGCGCGUUCCAAACACUGCUGUAAAGUUAACAGCAAGUAGGGCAGUGUUGGUA---------AAAC-CCAGGGCUGCAUAGA
...((((....))))(((..((.(((((((((.((..((.....))...)).)))))))))((..---------....-)).))..)))..... ( -29.10)
>DroSim_CAF1 6775 84 - 1
UAAGCCAGGGCUGGCGCGUUCCAAACAUCGCUGUAAAGUUAACAGCAAGUGGGGCAGUGUUGGUA---------AACC-CCAGGGCUGCAUAGA
..((((.((((..((((((((((......(((((.......)))))...)))))).))))..)..---------..))-)...))))....... ( -30.00)
>DroEre_CAF1 6618 93 - 1
UAAGCCAGGGCUGGCGCGUAGCAAACACUACUGUAAAGUUAACAGCAAGGUGGGCAGUGUUGGUAGGGUGUGAAAAAA-ACAGGGCUGCGUAUG
...((((....))))(((((((..((((((((....)))...(((((..(....)..)))))....))))).......-.....)))))))... ( -26.74)
>DroYak_CAF1 6821 94 - 1
UAAGCCAGGGCUGGCGCGUAGCAAACACUACUGUAAAGUUAACAGCAGGGUGGUCAGUGUUGAUAGGUUGUGGAAAAAGCCAGGGCUGCAUAGA
...(((((.((((((((...))...((((.((((.......))))...)))))))))).)))...((((.(((......))).))))))..... ( -27.70)
>consensus
UAAGCCAGGGCUGGCGCGUAGCAAACACUGCUGUAAAGUUAACAGCAAGGUGGGCAGUGUUGGUAGG__GUG_AAAAA_CCAGGGCUGCAUAGA
...((((....))))..........(((((((((.......)))))..)))).(((((.(((..................))).)))))..... (-19.13 = -20.21 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:10 2006