Locus 2340

Sequence ID	X_DroMel_CAF1
Location	6,267,939 – 6,268,158
Length	219
Max. P	0.967348

overview

Window 2

Location	6,267,939 – 6,268,048
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.96
Mean single sequence MFE	-29.26
Consensus MFE	-21.86
Energy contribution	-21.93
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.89
Structure conservation index	0.75
SVM decision value	0.39
SVM RNA-class probability	0.718393
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6267939 109 + 22224390
UCACAGCCGCCCAUUUUCG-----------UGCCUUUUUUGCGCUUUUUUCUUUUUGUGUAAUCGUAAGUUUUAUGUGAAAUAGGCGUAAAGUGAAGCGAAGUUAUGCCUUCUACGUGGC
.....(((((.........-----------.((...((((((((((......(((..(((((.(....)..)))))..))).))))))))))....))((((......))))...))))) ( -26.10)
>DroSec_CAF1 10116 109 + 1
UCACAGCCGCCCCAUUUCG-----------UUUCCUCUUUGCGCUUUUUUCUUUUUGUGUAAUCGUAAGUUUUAUGUGAAAUAGGCGUAAAGUGAAGCGAAGUUAUGCCUUCUACGUGGC
.....(((((.....((((-----------((((..((((((((((......(((..(((((.(....)..)))))..))).)))))))))).))))))))((..........))))))) ( -32.50)
>DroSim_CAF1 11463 109 + 1
UCACAGCCGCCCCAUUUCG-----------UUUCCUUUUUGCGCUUUUUUCUUUUUGUGUAAUCGUAAGUUUUAUGUGAAAUAGGCGUAAAGUGAAGCGAAGUUAUGCCUUCUACGUGGC
.....(((((.....((((-----------((((..((((((((((......(((..(((((.(....)..)))))..))).)))))))))).))))))))((..........))))))) ( -30.10)
>DroYak_CAF1 7275 120 + 1
UCACAGCCGCCCCUUUUUGGUGUUUUUUUUUGUUUUUUUGGCGCUUUCUUCCUUUUGUGUAAUCGUAAGUUUUAUGUGAAAUAGGCGUAAAGUGAAGCGAAGUUAUGCCUUCUACGUGGC
.....(((((........(((((....(((((((((....((((((......(((..(((((.(....)..)))))..))).)))))).....)))))))))..)))))......))))) ( -28.34)
>consensus
UCACAGCCGCCCCAUUUCG___________UGUCCUUUUUGCGCUUUUUUCUUUUUGUGUAAUCGUAAGUUUUAUGUGAAAUAGGCGUAAAGUGAAGCGAAGUUAUGCCUUCUACGUGGC
.....(((((..........................((((((((((......(((..(((((.........)))))..))).))))))))))......((((......))))...))))) (-21.86 = -21.93 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	6,268,048 – 6,268,158
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.91
Mean single sequence MFE	-33.92
Consensus MFE	-30.04
Energy contribution	-30.41
Covariance contribution	0.37
Combinations/Pair	1.07
Mean z-score	-2.19
Structure conservation index	0.89
SVM decision value	1.61
SVM RNA-class probability	0.967348
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6268048 110 + 22224390
CGCUGGCAACAUGGUUUCCAUUUUUUUUUUUUUUGCCUUCCUCGUA--------AAGGGCUGGCAACUUGCAGUCUGGGAA--UUUUCCACUGGGAACCGGUUGAAAGGCCAUAUAUUUC
.(((..((((.(((((((((............(((((..(((....--------..)))..)))))...........(((.--...)))..)))))))))))))...))).......... ( -32.80)
>DroSec_CAF1 10225 100 + 1
CGCUGGCAACAUGGUUUCCAUUU--------UUUGCCUUCCUCCUA--------AAGGGCUGGCAACUUGCAGUCUGGGAA--UUCCCCACUGGGAACCGGUUGAAAGGCCAU--AUUUC
.(((..((((.(((((((((...--------.(((((..(((....--------..)))..))))).........((((..--...)))).)))))))))))))...)))...--..... ( -35.40)
>DroSim_CAF1 11572 100 + 1
CGCUGGCAACAUGGUUUCCAUUU--------UUUGCCUUCCUCCUA--------AAGGGCUGGCAACUUGCAGUCUGGGAA--UUCCCCACUGGGAACCGGUUGAAAGGCCAU--AUUUC
.(((..((((.(((((((((...--------.(((((..(((....--------..)))..))))).........((((..--...)))).)))))))))))))...)))...--..... ( -35.40)
>DroYak_CAF1 7395 110 + 1
CGCUGGCAACAUGGCUACCAUUU--------UUUGCCCUCUUCCAAAAAGGCAAAAGGGCUGGCAACUUGCAGUCUGGGUAUAUUCCCCAUUGGGCACCGGUUGAAAGGCCAU--AUUUC
....(....)((((((.(((...--------...(((((.((((.....)).)).))))))))((((((((....((((.......))))....)))..)))))...))))))--..... ( -32.10)
>consensus
CGCUGGCAACAUGGUUUCCAUUU________UUUGCCUUCCUCCUA________AAGGGCUGGCAACUUGCAGUCUGGGAA__UUCCCCACUGGGAACCGGUUGAAAGGCCAU__AUUUC
.(((..((((.(((((((((............(((((..(((..............)))..))))).........((((.......)))).)))))))))))))...))).......... (-30.04 = -30.41 +   0.37)

alignment

secondary structure

dotplot

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