Locus 2576

Sequence ID	3L_DroMel_CAF1
Location	7,193,253 – 7,193,590
Length	337
Max. P	0.985436

overview

Window 0

Location	7,193,253 – 7,193,351
Length	98
Sequences	3
Columns	102
Reading direction	forward
Mean pairwise identity	77.00
Mean single sequence MFE	-29.83
Consensus MFE	-17.14
Energy contribution	-18.25
Covariance contribution	1.12
Combinations/Pair	1.13
Mean z-score	-2.05
Structure conservation index	0.57
SVM decision value	0.58
SVM RNA-class probability	0.787301
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193253 98 + 23771897
ACACACACAGAGCAAACACACAGGGCUGCAGCAAACGUAUAUGU----ACACACUUGUAUGCCCCGCAAGUCUGUGUGUGUGUGUGUGUGAUUGUUUGUCCG
.(((((((...(((.((((((((((((((((.....(((....)----))....))))).))))(....)..))))))).))))))))))............ ( -33.30)
>DroEre_CAF1 6667 86 + 1
ACACAUACAGUGCCAACACACAGGGCUGCAGCAAACGUAUAUGU--------------AUACCCAGUAAGUGUG--UAUGUGUGUGUGUGAUUGCUUGCCAG
.........(((......)))..(((.((((((.((((((((((--------------((((.(.....).)))--))))))))))).)).))))..))).. ( -23.80)
>DroYak_CAF1 3750 98 + 1
ACACAUACACAGCCAGCACACAGGGCUGCAGCAAAUGUAUAUGUAUGUAAACACUCGUAUACCCAGUAUGAGUG----UGUGUGUGUGUGAUUGUUUGCCCG
.((((((((((((((((.......))))..))..................((((((((((.....)))))))))----).))))))))))............ ( -32.40)
>consensus
ACACAUACAGAGCCAACACACAGGGCUGCAGCAAACGUAUAUGU____A_ACACU_GUAUACCCAGUAAGUGUG__U_UGUGUGUGUGUGAUUGUUUGCCCG
(((((((((.......(((((...((....))....(((((((............))))))).......)))))......)))))))))............. (-17.14 = -18.25 +   1.12)

alignment

secondary structure

dotplot

Window 1

Location	7,193,351 – 7,193,470
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.72
Mean single sequence MFE	-30.73
Consensus MFE	-27.06
Energy contribution	-26.88
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-2.44
Structure conservation index	0.88
SVM decision value	1.60
SVM RNA-class probability	0.966846
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193351 119 + 23771897
UAGAAUGCAAUAAGGGGUCAGGCUUUAAGAGCCAUAACAAAUGGGUUAAGUAAGACCG-AAGAUGGAAAAUGGGCAUCCAAGGGAAGGGCAAAAAGUCGCCCUGUUAUGCAUAACAAAGA
....(((((......((((.(((((...))))).((((......)))).....)))).-............((((.(((...)))..(((.....))))))).....)))))........ ( -29.70)
>DroSec_CAF1 6847 119 + 1
UAGAAUGCAAUAAGGGGUCAGGCUUUAAGAGCCAUAACAAAUGGGUUAAGUAAGACCG-AAGAUGGCAAAUGGACAUCCAAGGGAAGGGCAAAAAGUCGCCCCGUUAUGCAUAACAAAGA
....(((((....(((((..((((((....(((((......(.((((......)))).-)..)))))...(((....)))............)))))))))))....)))))........ ( -32.80)
>DroEre_CAF1 6753 120 + 1
UAGAAUGCAAUAAGGGGUCAGGCUUUAAGAGCCAUAACAAAUGGGUUAAGUAAGACCGGAAGAUGGGGAAUGUGCAUCCAGGGUACGGGCAAAAAGUCGCCCUGUUAUGCAUAACAAAGA
....(((((......((((.(((((...))))).((((......)))).....))))....(((((((..(((((.......)))))(((.....))).))))))).)))))........ ( -32.00)
>DroYak_CAF1 3848 119 + 1
UAGAAUGCAAUAAGGGGUCAGGCUUUAAGAGCCAUAACAAAUGGGUUAAGUAAGACCG-AAGAUGGGGAAUGUGCAUCCAGGGUAAGGGCAAAAAAUGGUCCUGCUAUGCAUAACAAAGA
....(((((......((((.(((((...))))).((((......)))).....)))).-..((((.(.....).))))...((((.((((........)))))))).)))))........ ( -28.40)
>consensus
UAGAAUGCAAUAAGGGGUCAGGCUUUAAGAGCCAUAACAAAUGGGUUAAGUAAGACCG_AAGAUGGGAAAUGGGCAUCCAAGGGAAGGGCAAAAAGUCGCCCUGUUAUGCAUAACAAAGA
....(((((......((((.(((((...))))).((((......)))).....))))....((((.........))))........((((........)))).....)))))........ (-27.06 = -26.88 +  -0.19)

alignment

secondary structure

dotplot

Window 2

Location	7,193,351 – 7,193,470
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.72
Mean single sequence MFE	-24.95
Consensus MFE	-23.21
Energy contribution	-23.15
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.24
Structure conservation index	0.93
SVM decision value	1.77
SVM RNA-class probability	0.976435
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193351 119 - 23771897
UCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCUUCCCUUGGAUGCCCAUUUUCCAUCUU-CGGUCUUACUUAACCCAUUUGUUAUGGCUCUUAAAGCCUGACCCCUUAUUGCAUUCUA
........(((((....(((((((....))))))).....((((.........))))....-.((((.....((((......)))).((((.....)))).))))......))))).... ( -26.20)
>DroSec_CAF1 6847 119 - 1
UCUUUGUUAUGCAUAACGGGGCGACUUUUUGCCCUUCCCUUGGAUGUCCAUUUGCCAUCUU-CGGUCUUACUUAACCCAUUUGUUAUGGCUCUUAAAGCCUGACCCCUUAUUGCAUUCUA
........((((((((((((((((....)))))))..((..(((((.(.....).))))).-.)).................)))))((((.....))))............)))).... ( -26.00)
>DroEre_CAF1 6753 120 - 1
UCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCGUACCCUGGAUGCACAUUCCCCAUCUUCCGGUCUUACUUAACCCAUUUGUUAUGGCUCUUAAAGCCUGACCCCUUAUUGCAUUCUA
....(((((....)))))((((((....)))))).......(((((((...............(((........))).....((((.((((.....)))))))).......))))))).. ( -27.40)
>DroYak_CAF1 3848 119 - 1
UCUUUGUUAUGCAUAGCAGGACCAUUUUUUGCCCUUACCCUGGAUGCACAUUCCCCAUCUU-CGGUCUUACUUAACCCAUUUGUUAUGGCUCUUAAAGCCUGACCCCUUAUUGCAUUCUA
........(((((....(((................(((..(((((.........))))).-.)))................((((.((((.....)))))))).)))...))))).... ( -20.20)
>consensus
UCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCUUACCCUGGAUGCACAUUCCCCAUCUU_CGGUCUUACUUAACCCAUUUGUUAUGGCUCUUAAAGCCUGACCCCUUAUUGCAUUCUA
....(((((....)))))((((((....)))))).......((((((................(((........))).....((((.((((.....))))))))........)))))).. (-23.21 = -23.15 +  -0.06)

alignment

secondary structure

dotplot

Window 3

Location	7,193,391 – 7,193,510
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.75
Mean single sequence MFE	-20.90
Consensus MFE	-18.64
Energy contribution	-18.57
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-1.57
Structure conservation index	0.89
SVM decision value	0.43
SVM RNA-class probability	0.734847
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193391 119 - 23771897
CCAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCUUCCCUUGGAUGCCCAUUUUCCAUCUU-CGGUCUUACUUAACCCAU
.(((((((......((((((...(...((((.......))))...).))))))....(((((((....)))))))....)))))))...............-.(((........)))... ( -23.30)
>DroSec_CAF1 6887 119 - 1
CUAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACGGGGCGACUUUUUGCCCUUCCCUUGGAUGUCCAUUUGCCAUCUU-CGGUCUUACUUAACCCAU
.(((((((......((((((...(...((((.......))))...).))))))....(((((((....)))))))....))))))).......(((.....-.))).............. ( -22.20)
>DroEre_CAF1 6793 120 - 1
CUAUCUAAUUCUUCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCGUACCCUGGAUGCACAUUCCCCAUCUUCCGGUCUUACUUAACCCAU
...............(((((((.....)))))))..........(((((....)))))((((((....))))))(.(((..(((((.........)))))...))))............. ( -21.80)
>DroYak_CAF1 3888 119 - 1
CUAUCUAAUUCUUCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAGCAGGACCAUUUUUUGCCCUUACCCUGGAUGCACAUUCCCCAUCUU-CGGUCUUACUUAACCCAU
..............((((((...(...((((.......))))...).))))))..((((((.....))))))....(((..(((((.........))))).-.))).............. ( -16.30)
>consensus
CUAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCUUACCCUGGAUGCACAUUCCCCAUCUU_CGGUCUUACUUAACCCAU
.((((((........(((((((.....)))))))..........(((((....)))))((((((....))))))......)))))).................(((........)))... (-18.64 = -18.57 +  -0.06)

alignment

secondary structure

dotplot

Window 4

Location	7,193,430 – 7,193,550
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.61
Mean single sequence MFE	-26.45
Consensus MFE	-23.89
Energy contribution	-23.95
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-1.69
Structure conservation index	0.90
SVM decision value	0.66
SVM RNA-class probability	0.813895
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193430 120 + 23771897
AGGGAAGGGCAAAAAGUCGCCCUGUUAUGCAUAACAAAGAUAAAUGGCAUAUCGCAGAAAUAUGCAGCAGAAUUAGAUGGUAAUAGAUGGCAGAAUGCAGCCCCAUCAAAUUCAAGUUAA
.....(((((........)))))....(((........((((.......))))(((......))).)))(((((.(((((........(((........)))))))).)))))....... ( -29.10)
>DroSec_CAF1 6926 120 + 1
AGGGAAGGGCAAAAAGUCGCCCCGUUAUGCAUAACAAAGAUAAAUGGCAUAUCGCAGAAAUAUGCAGCAGAAUUAGAUAGUAAUAGAUGGCAGAAUGCAGCCCCAUCAAAUUCAAGUUAG
.(((..((((........)))).....(((((..((........))((.(((((((......)))............((....))))))))...)))))..)))................ ( -23.30)
>DroEre_CAF1 6833 120 + 1
GGGUACGGGCAAAAAGUCGCCCUGUUAUGCAUAACAAAGAUAAAUGGCAUAUCGCAGAAAUAUGCAGAAGAAUUAGAUAGUAAUAGAUGGCAGAAUGCUGCCCUAUCAAACUCAAGUUAA
((((..((((........)))).....((((((.....((((.......)))).......)))))).........(((((........(((((....))))))))))..))))....... ( -27.60)
>DroYak_CAF1 3927 120 + 1
GGGUAAGGGCAAAAAAUGGUCCUGCUAUGCAUAACAAAGAUAAAUGGCAUAUCGCAGAAAUAUGCAGAAGAAUUAGAUAGUAAUAGAUGGCAGAAUGCAGCCCUAUCAAAUUCAAGUUAA
.((((.((((........)))))))).....((((...........((((((.......))))))....(((((.(((((........(((........)))))))).)))))..)))). ( -25.80)
>consensus
AGGGAAGGGCAAAAAGUCGCCCUGUUAUGCAUAACAAAGAUAAAUGGCAUAUCGCAGAAAUAUGCAGAAGAAUUAGAUAGUAAUAGAUGGCAGAAUGCAGCCCCAUCAAAUUCAAGUUAA
......((((........)))).........((((...........((((((.......))))))....(((((.(((((........(((........)))))))).)))))..)))). (-23.89 = -23.95 +   0.06)

alignment

secondary structure

dotplot

Window 5

Location	7,193,430 – 7,193,550
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.61
Mean single sequence MFE	-26.62
Consensus MFE	-25.35
Energy contribution	-24.85
Covariance contribution	-0.50
Combinations/Pair	1.16
Mean z-score	-2.29
Structure conservation index	0.95
SVM decision value	2.01
SVM RNA-class probability	0.985436
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193430 120 - 23771897
UUAACUUGAAUUUGAUGGGGCUGCAUUCUGCCAUCUAUUACCAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCUUCCCU
.((((..(((((.((((((((........)))........))))).)))))....(((((((.....)))))))...........))))........(((((((....)))))))..... ( -28.90)
>DroSec_CAF1 6926 120 - 1
CUAACUUGAAUUUGAUGGGGCUGCAUUCUGCCAUCUAUUACUAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACGGGGCGACUUUUUGCCCUUCCCU
.......(((((.((((((((........)))........))))).)))))...((((((...(...((((.......))))...).))))))....(((((((....)))))))..... ( -26.60)
>DroEre_CAF1 6833 120 - 1
UUAACUUGAGUUUGAUAGGGCAGCAUUCUGCCAUCUAUUACUAUCUAAUUCUUCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCGUACCC
.......(((((.((((((((((....)))))........))))).)))))....(((((((.....)))))))..........(((((....)))))((((((....))))))...... ( -29.90)
>DroYak_CAF1 3927 120 - 1
UUAACUUGAAUUUGAUAGGGCUGCAUUCUGCCAUCUAUUACUAUCUAAUUCUUCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAGCAGGACCAUUUUUUGCCCUUACCC
.((((..(((((.((((((((........)))........))))).)))))....(((((((.....)))))))...........))))......((((((.....))))))........ ( -21.10)
>consensus
UUAACUUGAAUUUGAUAGGGCUGCAUUCUGCCAUCUAUUACUAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUAUCUUUGUUAUGCAUAACAGGGCGACUUUUUGCCCUUACCC
.......(((((.((((((((........)))........))))).)))))....(((((((.....)))))))..........(((((....)))))((((((....))))))...... (-25.35 = -24.85 +  -0.50)

alignment

secondary structure

dotplot

Window 6

Location	7,193,470 – 7,193,590
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.86
Mean single sequence MFE	-28.66
Consensus MFE	-23.89
Energy contribution	-24.70
Covariance contribution	0.81
Combinations/Pair	1.12
Mean z-score	-2.01
Structure conservation index	0.83
SVM decision value	0.48
SVM RNA-class probability	0.752978
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7193470 120 - 23771897
UUUAACGGGUUAUUUUGCUUGAGUGCGAGCCAUCAAAUAUUUAACUUGAAUUUGAUGGGGCUGCAUUCUGCCAUCUAUUACCAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUA
.......(((......((..(((((((..(((((((((...........)))))))))..).)))))).))........))).............(((((((.....)))))))...... ( -27.64)
>DroSec_CAF1 6966 120 - 1
UUUAACUGGUUAUUUUGCUUGAGUGCGGGCCAUCAAAUAUCUAACUUGAAUUUGAUGGGGCUGCAUUCUGCCAUCUAUUACUAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUA
......((((....((((..((((((((.(((((((((.((......)))))))))))(((........))).....................))))))...)).))))...)))).... ( -32.10)
>DroEre_CAF1 6873 120 - 1
UUUAACGGGUGCUUUUGCUUGAGUGAGAGCCAUCAAAUAUUUAACUUGAGUUUGAUAGGGCAGCAUUCUGCCAUCUAUUACUAUCUAAUUCUUCUGCAUAUUUCUGCGAUAUGCCAUUUA
.......((((((((..(....)..)))).)))).............(((((.((((((((((....)))))........))))).)))))....(((((((.....)))))))...... ( -29.30)
>DroYak_CAF1 3967 120 - 1
UUUAACGGGUGAUUUUGCUUGAGUGAGAGCCAUCAAAUAUUUAACUUGAAUUUGAUAGGGCUGCAUUCUGCCAUCUAUUACUAUCUAAUUCUUCUGCAUAUUUCUGCGAUAUGCCAUUUA
.......((((((...((..(((((..(((((((((((...........)))))))..)))).))))).)).....)))))).............(((((((.....)))))))...... ( -25.60)
>consensus
UUUAACGGGUGAUUUUGCUUGAGUGAGAGCCAUCAAAUAUUUAACUUGAAUUUGAUAGGGCUGCAUUCUGCCAUCUAUUACUAUCUAAUUCUGCUGCAUAUUUCUGCGAUAUGCCAUUUA
.......((((((...((..((((((.(((((((((((.((......)))))))))..)))))))))).)).....)))))).............(((((((.....)))))))...... (-23.89 = -24.70 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:11 2006