Locus 64

Sequence ID	2R_DroMel_CAF1
Location	1,319,877 – 1,320,051
Length	174
Max. P	0.992079

overview

Window 0

Location	1,319,877 – 1,319,976
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	86.87
Mean single sequence MFE	-29.25
Consensus MFE	-22.04
Energy contribution	-23.85
Covariance contribution	1.81
Combinations/Pair	1.05
Mean z-score	-2.53
Structure conservation index	0.75
SVM decision value	1.40
SVM RNA-class probability	0.950305
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1319877 99 - 20766785
UGGCCGACUGCCCGGACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACAAGCUGUAAAUAAAGAGGACCCUGGGAUCCGAAUCGGGGACACACAGC
...((..(((((((......)).)))))...........(((((((.......))))))).......)).((((((........))))))......... ( -30.70)
>DroSec_CAF1 38415 98 - 1
UGGCCGACUGCCC-GACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACGAGCUGUAAAUAAAGAGGACCCUGGGAUCCGAAUCGGGGACACACAGC
...((..((((((-(.....)).)))))...........(((((((.......))))))).......)).((((((........))))))......... ( -29.20)
>DroSim_CAF1 17493 99 - 1
UGGCCGACUGCCCGGACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACGAGCUGUAAAUAAAGAGGACCCUGGGAUCCGAAUCGGGGACACACAGC
...((..(((((((......)).)))))...........(((((((.......))))))).......)).((((((........))))))......... ( -30.70)
>DroYak_CAF1 5949 83 - 1
UGGCCGACUGUCCGGACAAACGAGGCAGAUAAAAAACUAUUGCAGCGAUACGAGCUGUAAAUAAAGGGAAACCUGGUAUCAA----------------C
..(((..(((((((......)).)))))...........(((((((.......)))))))....(((....)))))).....----------------. ( -26.40)
>consensus
UGGCCGACUGCCCGGACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACGAGCUGUAAAUAAAGAGGACCCUGGGAUCCGAAUCGGGGACACACAGC
...((..(((((((......)).)))))...........(((((((.......))))))).......)).((((((........))))))......... (-22.04 = -23.85 +   1.81)

alignment

secondary structure

dotplot

Window 1

Location	1,319,896 – 1,320,016
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.98
Mean single sequence MFE	-37.78
Consensus MFE	-32.36
Energy contribution	-32.92
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-1.59
Structure conservation index	0.86
SVM decision value	1.06
SVM RNA-class probability	0.908029
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1319896 120 + 20766785
GAUCCCAGGGUCCUCUUUAUUUACAGCUUGUAUCGCUGCAAUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAAUAAUAUGGGCUGACUGCGGACAUUUGCUUGCGGCCUGCU
.....((((..............((((.......))))..............((((..((..(((((..((((((((((.........)))))))))))))))..))...)))))))).. ( -39.60)
>DroSec_CAF1 38434 116 + 1
GAUCCCAGGGUCCUCUUUAUUUACAGCUCGUAUCGCUGCAAUCGUUUUUUAUCUGCCUCGUUUGUC-GGGCAGUCGGCCAA---UAUGGGCUGACUGCGGACAUUUGCUUGCGGCUCGCU
((((....))))................((..((((.((((..((((.....(((.(......).)-))((((((((((..---....))))))))))))))..))))..))))..)).. ( -37.10)
>DroSim_CAF1 17512 117 + 1
GAUCCCAGGGUCCUCUUUAUUUACAGCUCGUAUCGCUGCAAUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAA---UAUGGGCUGACUGCGGACAUUUGCUUGCGGCUCGCU
.......(((((...........((((.......))))................((..((..(((((..((((((((((..---....)))))))))))))))..))...)))))))... ( -39.20)
>DroEre_CAF1 19923 117 + 1
GAUCCCAGGGUCCGCUUUAUUUACAGCUCGUAUCGCUGCAAUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAA---UAUGGGCUGACUGCGGACACUCGCUUGCGGCUUGGU
....(((((..((((........((((.......))))....................((..(((((..((((((((((..---....)))))))))))))))..))...))))))))). ( -43.60)
>DroYak_CAF1 5952 117 + 1
GAUACCAGGUUUCCCUUUAUUUACAGCUCGUAUCGCUGCAAUAGUUUUUUAUCUGCCUCGUUUGUCCGGACAGUCGGCCAA---UAUGAACUGACUGCGGACAUUCGCUUGCCGCUUGCU
(((((..((((.............)))).)))))((.(((((((........)))...((..((((((..(((((((....---......)))))))))))))..)).)))).))..... ( -29.42)
>consensus
GAUCCCAGGGUCCUCUUUAUUUACAGCUCGUAUCGCUGCAAUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAA___UAUGGGCUGACUGCGGACAUUUGCUUGCGGCUUGCU
.......(((((...........((((.......))))................((..((..(((((..((((((((((.........)))))))))))))))..))...)))))))... (-32.36 = -32.92 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	1,319,896 – 1,320,016
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.98
Mean single sequence MFE	-37.50
Consensus MFE	-31.18
Energy contribution	-31.10
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-2.32
Structure conservation index	0.83
SVM decision value	2.31
SVM RNA-class probability	0.992079
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1319896 120 - 20766785
AGCAGGCCGCAAGCAAAUGUCCGCAGUCAGCCCAUAUUAUUGGCCGACUGCCCGGACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACAAGCUGUAAAUAAAGAGGACCCUGGGAUC
..((((((((...(...(((((((((((.(((.........))).))))))..)))))...)..)).............(((((((.......))))))).......))..))))..... ( -38.40)
>DroSec_CAF1 38434 116 - 1
AGCGAGCCGCAAGCAAAUGUCCGCAGUCAGCCCAUA---UUGGCCGACUGCCC-GACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACGAGCUGUAAAUAAAGAGGACCCUGGGAUC
.(((..((....).....)..)))......((((..---..((((..((((((-(.....)).)))))...........(((((((.......))))))).......)).)).))))... ( -33.60)
>DroSim_CAF1 17512 117 - 1
AGCGAGCCGCAAGCAAAUGUCCGCAGUCAGCCCAUA---UUGGCCGACUGCCCGGACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACGAGCUGUAAAUAAAGAGGACCCUGGGAUC
.....((((....)...(((((((((((.(((....---..))).))))))..))))).....))).............(((((((.......))))))).................... ( -35.30)
>DroEre_CAF1 19923 117 - 1
ACCAAGCCGCAAGCGAGUGUCCGCAGUCAGCCCAUA---UUGGCCGACUGCCCGGACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACGAGCUGUAAAUAAAGCGGACCCUGGGAUC
.(((..((((...((..(((((((((((.(((....---..))).))))))..)))))..)).................(((((((.......))))))).....))))....))).... ( -43.80)
>DroYak_CAF1 5952 117 - 1
AGCAAGCGGCAAGCGAAUGUCCGCAGUCAGUUCAUA---UUGGCCGACUGUCCGGACAAACGAGGCAGAUAAAAAACUAUUGCAGCGAUACGAGCUGUAAAUAAAGGGAAACCUGGUAUC
........((...((..(((((((((((.(((....---..))).)))))..))))))..))..)).((((........(((((((.......)))))))....(((....)))..)))) ( -36.40)
>consensus
AGCAAGCCGCAAGCAAAUGUCCGCAGUCAGCCCAUA___UUGGCCGACUGCCCGGACAAACGAGGCAGAUAAAAAACGAUUGCAGCGAUACGAGCUGUAAAUAAAGAGGACCCUGGGAUC
.....((((....)...(((((((((((.(((.........))).))))))..))))).....))).............(((((((.......))))))).................... (-31.18 = -31.10 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	1,319,936 – 1,320,051
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.97
Mean single sequence MFE	-33.20
Consensus MFE	-27.73
Energy contribution	-28.69
Covariance contribution	0.96
Combinations/Pair	1.04
Mean z-score	-1.66
Structure conservation index	0.84
SVM decision value	0.95
SVM RNA-class probability	0.888186
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1319936 115 + 20766785
AUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAAUAAUAUGGGCUGACUGCGGACAUUUGCUUGCGGCCUGCUCAUG-----CCGUUAUCCUUUUAUGCUCCGCUUUAUCAAA
..............(((.((......)))))((((((((.........))))))))((((((((......(((((........)-----)))).........))).)))))......... ( -34.96)
>DroSec_CAF1 38474 111 + 1
AUCGUUUUUUAUCUGCCUCGUUUGUC-GGGCAGUCGGCCAA---UAUGGGCUGACUGCGGACAUUUGCUUGCGGCUCGCUCAUG-----CCGUUAUCCUUUUAUGCUGCGCUUUAUCAAA
..............(((.((.....)-))))((((((((..---....))))))))((((.(((......(((((........)-----)))).........)))))))........... ( -34.56)
>DroSim_CAF1 17552 112 + 1
AUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAA---UAUGGGCUGACUGCGGACAUUUGCUUGCGGCUCGCUCAUG-----CCGUUAUCCUUUUAUGCUGCGCUUUAUCAAA
..............((..((..(((((..((((((((((..---....)))))))))))))))..))...(((((........)-----))))..............))........... ( -36.00)
>DroEre_CAF1 19963 116 + 1
AUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAA---UAUGGGCUGACUGCGGACACUCGCUUGCGGCUUGGUCAUCCUUAUCCGUUAUCCUU-UGUGCUGCGCUUUAUCAAA
..............((..((..(((((..((((((((((..---....)))))))))))))))..))...(((((..((.................))..-...)))))))......... ( -36.23)
>DroYak_CAF1 5992 112 + 1
AUAGUUUUUUAUCUGCCUCGUUUGUCCGGACAGUCGGCCAA---UAUGAACUGACUGCGGACAUUCGCUUGCCGCUUGCUUAUG-----CCGUUAUCCUUUUAUGCUGCGCCUUAUCAAA
..............((..((..((((((..(((((((....---......)))))))))))))..))...))(((..((.....-----...............)).))).......... ( -24.25)
>consensus
AUCGUUUUUUAUCUGCCUCGUUUGUCCGGGCAGUCGGCCAA___UAUGGGCUGACUGCGGACAUUUGCUUGCGGCUUGCUCAUG_____CCGUUAUCCUUUUAUGCUGCGCUUUAUCAAA
..............((..((..(((((..((((((((((.........)))))))))))))))..))...(((((.............................)))))))......... (-27.73 = -28.69 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:25:18 2006