Locus 6139

Sequence ID	2R_DroMel_CAF1
Location	19,332,242 – 19,332,405
Length	163
Max. P	0.930601

overview

Window 9

Location	19,332,242 – 19,332,348
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.46
Mean single sequence MFE	-33.70
Consensus MFE	-22.76
Energy contribution	-24.27
Covariance contribution	1.50
Combinations/Pair	1.25
Mean z-score	-1.28
Structure conservation index	0.68
SVM decision value	0.67
SVM RNA-class probability	0.816672
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19332242 106 + 20766785
GAAGGCA--CA------------UGAACUCACCCACGAAGCCCAGAAGGACCAGAACGAAGAGUCCCAGUAGGGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGUG
.......--..------------..........(((((..(((.(..((.((........(((((((((.((((((........))))))...)))))))))))))..).)))..))))) ( -36.30)
>DroSec_CAF1 10233 106 + 1
GAAGGCA--CA------------CGAACUCACCCACGAAGCCCAGGAGGACCAGAACGAAGAGUCCCAGUAGGGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCG
....((.--..------------.(....).(((.....(((..((....))........(((((((((.((((((........))))))...)))))))))))).....)))....)). ( -33.50)
>DroSim_CAF1 10285 106 + 1
GAAGGCA--CA------------UGAACUCACCCAAGAAGCCCAGGAGGAUUAGGACGAAGAGUCCCAGUAGGGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCG
....((.--..------------((....))(((.......((....))....((.....(((((((((.((((((........))))))...)))))))))..))....)))....)). ( -32.20)
>DroEre_CAF1 10330 106 + 1
GAAGGCG--CU------------UGAACUCACCCGCGAGGCCCAGGAGAGUCAGGACGAAGAGUCCCAGCAGAGUCAGCGAAAGGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCG
...((((--((------------(((.(((..((....))(....).)))))))).)...(((((((((.((((((..(....)))))))...))))))))).))).((........)). ( -41.70)
>DroYak_CAF1 10551 107 + 1
AAAUGCU--AUC-----------UUAACUCACCCGCGAAGCCCAGAAGAACCAGAACGAAGACUCCCAGCAGAGUCAGCGAAAAGAUUCGCAUCUGGGACUCAGCCAGCUGGGAAUCGCG
.......--...-----------..........(((((..(((((.((..(((((.....(((((......))))).(((((....))))).)))))..)).......)))))..))))) ( -36.90)
>DroAna_CAF1 11400 120 + 1
UAAAAUAUUUUCAUUUUCAUCAAAAAACUCACCCAAACAGCCGAGGAACAUAAGAAAACCAAUGCCCAGGAGAGUUAACAGCAGGAUUCGGAUUUGACCCUCGGCCGGUGGCAGGUCCUG
............................(((((......(((((((............((........)).(((((........))))).........))))))).)))))......... ( -21.60)
>consensus
GAAGGCA__CA____________UGAACUCACCCACGAAGCCCAGGAGGACCAGAACGAAGAGUCCCAGUAGAGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCG
.................................(((((..(((.................(((((((((.((((((........))))))...))))))))).(....).)))..))))) (-22.76 = -24.27 +   1.50)

alignment

secondary structure

dotplot

Window 0

Location	19,332,242 – 19,332,348
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.46
Mean single sequence MFE	-36.79
Consensus MFE	-23.19
Energy contribution	-23.78
Covariance contribution	0.59
Combinations/Pair	1.36
Mean z-score	-1.42
Structure conservation index	0.63
SVM decision value	0.59
SVM RNA-class probability	0.790997
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19332242 106 - 20766785
CACGAUUCCCUGCUGGCCGAGUCCCAGAUGAGAAUCUUUACGCUGACCCUACUGGGACUCUUCGUUCUGGUCCUUCUGGGCUUCGUGGGUGAGUUCA------------UG--UGCCUUC
(((((..(((.(..(((((((((((((...((..((........))..)).)))))))))........)).))..).)))..)))))((((......------------..--))))... ( -35.30)
>DroSec_CAF1 10233 106 - 1
CGCGAUUCCCUGCUGGCCGAGUCCCAGAUGAGAAUCUUUACGCUGACCCUACUGGGACUCUUCGUUCUGGUCCUCCUGGGCUUCGUGGGUGAGUUCG------------UG--UGCCUUC
((((((((((..(.(((((((((((((...((..((........))..)).)))))))))........((....))..))))..)..)).))).)))------------))--....... ( -39.30)
>DroSim_CAF1 10285 106 - 1
CGCGAUUCCCUGCUGGCCGAGUCCCAGAUGAGAAUCUUUACGCUGACCCUACUGGGACUCUUCGUCCUAAUCCUCCUGGGCUUCUUGGGUGAGUUCA------------UG--UGCCUUC
.(((.......(((.((((((((((((...((..((........))..)).)))))))))...((((..........))))......))).)))...------------..--))).... ( -33.20)
>DroEre_CAF1 10330 106 - 1
CGCGAUUCCCUGCUGGCCGAGUCCCAGAUGAGAAUCCUUUCGCUGACUCUGCUGGGACUCUUCGUCCUGACUCUCCUGGGCCUCGCGGGUGAGUUCA------------AG--CGCCUUC
(((((((((((((.(((((((((((((...(((.((........)).))).)))))))))...((....)).......))))..))))).)))))..------------.)--))..... ( -42.10)
>DroYak_CAF1 10551 107 - 1
CGCGAUUCCCAGCUGGCUGAGUCCCAGAUGCGAAUCUUUUCGCUGACUCUGCUGGGAGUCUUCGUUCUGGUUCUUCUGGGCUUCGCGGGUGAGUUAA-----------GAU--AGCAUUU
(((((..(((((......(((..(((((.(((((....))))).((((((....)))))).....)))))..))))))))..))))).....((((.-----------..)--))).... ( -39.70)
>DroAna_CAF1 11400 120 - 1
CAGGACCUGCCACCGGCCGAGGGUCAAAUCCGAAUCCUGCUGUUAACUCUCCUGGGCAUUGGUUUUCUUAUGUUCCUCGGCUGUUUGGGUGAGUUUUUUGAUGAAAAUGAAAAUAUUUUA
...(((..(((..(((((((((..((.....(((((.((((.............))))..))))).....))..)))))))))....)))..)))((((.((....)).))))....... ( -31.12)
>consensus
CGCGAUUCCCUGCUGGCCGAGUCCCAGAUGAGAAUCUUUACGCUGACCCUACUGGGACUCUUCGUUCUGAUCCUCCUGGGCUUCGUGGGUGAGUUCA____________AG__UGCCUUC
...((((((((((.(((((((((((((...((..((........))..)).)))))))))............(....)))))..))))).)))))......................... (-23.19 = -23.78 +   0.59)

alignment

secondary structure

dotplot

Window 1

Location	19,332,268 – 19,332,385
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	68.68
Mean single sequence MFE	-34.53
Consensus MFE	-18.88
Energy contribution	-19.88
Covariance contribution	1.00
Combinations/Pair	1.28
Mean z-score	-1.76
Structure conservation index	0.55
SVM decision value	1.21
SVM RNA-class probability	0.930601
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19332268 117 + 20766785
CCCAGAAGGACCAGAACGAAGAGUCCCAGUAGGGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGUGACU---UCCAUGGCCAUUCCCAUUCCCAUUCCGAUUCCCA
.......((.((........(((((((((.((((((........))))))...)))))))))))))....((((((((.((..---...((((......))))......)))))))))). ( -41.30)
>DroSec_CAF1 10259 111 + 1
CCCAGGAGGACCAGAACGAAGAGUCCCAGUAGGGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU---UCCAUGCCCACUCCCAUUUCCAUUCCU------A
...(((((((..........(((((((((.((((((........))))))...)))))))))((...(((.((((.......)---))).))))).........)))..))))------. ( -36.70)
>DroSim_CAF1 10311 111 + 1
CCCAGGAGGAUUAGGACGAAGAGUCCCAGUAGGGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU---UCCAUGCCCACUCCCAUUUCCAUUCCU------A
...(((((((...(((....(((((((((.((((((........))))))...)))))))))((...(((.((((.......)---))).)))))..)))....)))..))))------. ( -39.60)
>DroEre_CAF1 10356 93 + 1
CCCAGGAGAGUCAGGACGAAGAGUCCCAGCAGAGUCAGCGAAAGGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU---UCCAUUACCA------------------------
....(((.((((.((.....(((((((((.((((((..(....)))))))...)))))))))..)).((........))))))---))).......------------------------ ( -35.90)
>DroYak_CAF1 10578 93 + 1
CCCAGAAGAACCAGAACGAAGACUCCCAGCAGAGUCAGCGAAAAGAUUCGCAUCUGGGACUCAGCCAGCUGGGAAUCGCGACU---UUCAUUCCCA------------------------
((((((..............(((((......))))).(((((....))))).))))))............((((((.......---...)))))).------------------------ ( -28.90)
>DroAna_CAF1 11440 108 + 1
CCGAGGAACAUAAGAAAACCAAUGCCCAGGAGAGUUAACAGCAGGAUUCGGAUUUGACCCUCGGCCGGUGGCAGGUCCUGAAUAUUUGCAAUCCCG------------AUCAGACUAAGG
.((.(((...........((........))..........((((((((((((((((.((.((....)).))))))))).)))).)))))..)))))------------............ ( -24.80)
>consensus
CCCAGGAGGACCAGAACGAAGAGUCCCAGUAGAGUCAGCGUAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU___UCCAUGCCCA____________UUCC_______A
.......(((..((..(((.(((((((((.((((((........))))))...)))))))))..((....))...)))...))...)))............................... (-18.88 = -19.88 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	19,332,308 – 19,332,405
Length	97
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	65.16
Mean single sequence MFE	-24.67
Consensus MFE	-11.52
Energy contribution	-12.13
Covariance contribution	0.61
Combinations/Pair	1.33
Mean z-score	-1.58
Structure conservation index	0.47
SVM decision value	0.51
SVM RNA-class probability	0.762560
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19332308 97 + 20766785
UAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGUGACU---UCCAUGGCCAUUCCCAUUCCCAUUCCGAUUCCCACCCACCUGGCAAUGGAAUUG
....((.((((....)))).)).(((((..((((((((.((..---...((((......))))......))))))))))......))))).......... ( -28.10)
>DroSec_CAF1 10299 91 + 1
UAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU---UCCAUGCCCACUCCCAUUUCCAUUCCU------AUACACCUGGCAAUGGAAUUG
....(((((((..((((.......))))..)))))))......---..............((.(((((((((.------........)).))))))).)) ( -22.90)
>DroSim_CAF1 10351 91 + 1
UAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU---UCCAUGCCCACUCCCAUUUCCAUUCCU------AUCCACCUGGCAAUGGAAUUG
....(((((((..((((.......))))..)))))))......---..............((.(((((((((.------........)).))))))).)) ( -22.90)
>DroEre_CAF1 10396 73 + 1
AAAGGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU---UCCAUUACCA------------------------UUUGCUUGGCAUUGGAAUUG
....(((((((..((((.......))))..))))))).....(---((((...(((------------------------......)))...)))))... ( -21.30)
>DroYak_CAF1 10618 73 + 1
AAAAGAUUCGCAUCUGGGACUCAGCCAGCUGGGAAUCGCGACU---UUCAUUCCCA------------------------AAUCCUUGGCAAUGGAAUUG
....(((((.((.((((.......)))).)).))))).....(---((((((.(((------------------------(....)))).)))))))... ( -22.50)
>DroAna_CAF1 11480 88 + 1
GCAGGAUUCGGAUUUGACCCUCGGCCGGUGGCAGGUCCUGAAUAUUUGCAAUCCCG------------AUCAGACUAAGGCCACCAAGGCCGUCGCAUCG
((((((((((((((((.((.((....)).))))))))).)))).))))).....((------------((..(((...((((.....)))))))..)))) ( -30.30)
>consensus
UAAAGAUUCUCAUCUGGGACUCGGCCAGCAGGGAAUCGCGACU___UCCAUGCCCA____________UUCC_______AUCCACCUGGCAAUGGAAUUG
....(((((((..((((.......))))..))))))).........(((((..((................................))..))))).... (-11.52 = -12.13 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:45 2006