Locus 6338

Sequence ID X_DroMel_CAF1
Location 15,993,075 – 15,993,329
Length 254
Max. P 0.992512
window10338 window10339 window10340 window10341 window10342 window10343 window10344

overview

Window 8

Location 15,993,075 – 15,993,185
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.63
Mean single sequence MFE -33.88
Consensus MFE -30.03
Energy contribution -29.91
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.20
Structure conservation index 0.89
SVM decision value 1.65
SVM RNA-class probability 0.970006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15993075 110 + 22224390
U-------UCCAGAUGCGAGUAAUAACGUCGCAGUCAUGAAUUGAUAAUCGGAUGGCAAUGCAAGUG--GUGGGCUCAAGGGCAUUGCAAAA-AGGCGGGAAAGGUCACCGCCAAAUAAU
.-------(((...(((((((....)).)))))((((.....))))....)))..(((((((...((--(.....)))...)))))))....-.(((((((....)).)))))....... ( -35.00)
>DroSec_CAF1 61001 112 + 1
U-------UCCAGAUGCGAGUAAUAACGUCGCAGUCAUGAAUUGAUAAUCGGUUGGCAAUGCAAGUGGGGUGGGCUCAAGGGCAUUGCAAAA-AGGCGGGAAAGGUCACCGCCAAAUAAU
.-------.((...(((((((....)).)))))((((.....))))....))...(((((((...((((.....))))...)))))))....-.(((((((....)).)))))....... ( -36.20)
>DroEre_CAF1 59689 112 + 1
UUCCAUUUUCCAGAUGCGAGUAAUAACGUCGCAGUCAUGAAUUGAUAAUCGGAUGGCAGUGCAAGA-----GGGCUCAAGGGCAUUGCGAAAAGGGCGGGAAAGGUCACCGCCGAAU---
(((.....(((...(((((((....)).)))))((((.....))))....)))..(((((((..((-----....))....))))))))))...(((((((....)).)))))....--- ( -33.20)
>DroYak_CAF1 44043 105 + 1
U-------UCCAGAUGCGAGUAAUAACGUCGCAGUCAUGAAUUGAUAAUCGGAUGGCAAUGCAAGA-----GGGCUCAAGGGCAUUGCAAAAAAGGCGGGAAAGGUCACUGCCGAAU---
.-------(((...(((((((....)).)))))((((.....))))....)))..(((((((..((-----....))....)))))))......(((((((....)).)))))....--- ( -31.10)
>consensus
U_______UCCAGAUGCGAGUAAUAACGUCGCAGUCAUGAAUUGAUAAUCGGAUGGCAAUGCAAGA_____GGGCUCAAGGGCAUUGCAAAA_AGGCGGGAAAGGUCACCGCCAAAU___
........(((...(((((((....)).)))))((((.....))))....)))..(((((((...................)))))))......(((((((....)).)))))....... (-30.03 = -29.91 +  -0.12)

alignment

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secondary structure

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Window 9

Location 15,993,075 – 15,993,185
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.63
Mean single sequence MFE -27.15
Consensus MFE -24.20
Energy contribution -24.70
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.89
SVM decision value 1.02
SVM RNA-class probability 0.902264
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15993075 110 - 22224390
AUUAUUUGGCGGUGACCUUUCCCGCCU-UUUUGCAAUGCCCUUGAGCCCAC--CACUUGCAUUGCCAUCCGAUUAUCAAUUCAUGACUGCGACGUUAUUACUCGCAUCUGGA-------A
.......(((((.((....))))))).-....(((((((...((.......--))...)))))))..(((((........))..((.(((((.((....))))))))).)))-------. ( -29.10)
>DroSec_CAF1 61001 112 - 1
AUUAUUUGGCGGUGACCUUUCCCGCCU-UUUUGCAAUGCCCUUGAGCCCACCCCACUUGCAUUGCCAACCGAUUAUCAAUUCAUGACUGCGACGUUAUUACUCGCAUCUGGA-------A
.......(((((.((....))))))).-....(((((((...((.........))...)))))))..............((((.((.(((((.((....)))))))))))))-------. ( -27.90)
>DroEre_CAF1 59689 112 - 1
---AUUCGGCGGUGACCUUUCCCGCCCUUUUCGCAAUGCCCUUGAGCCC-----UCUUGCACUGCCAUCCGAUUAUCAAUUCAUGACUGCGACGUUAUUACUCGCAUCUGGAAAAUGGAA
---....(((((.((....)))))))......(((.(((....((....-----))..))).)))..((((.....)..((((.((.(((((.((....)))))))))))))....))). ( -27.50)
>DroYak_CAF1 44043 105 - 1
---AUUCGGCAGUGACCUUUCCCGCCUUUUUUGCAAUGCCCUUGAGCCC-----UCUUGCAUUGCCAUCCGAUUAUCAAUUCAUGACUGCGACGUUAUUACUCGCAUCUGGA-------A
---..((((..(((........))).......(((((((....((....-----))..)))))))...)))).......((((.((.(((((.((....)))))))))))))-------. ( -24.10)
>consensus
___AUUCGGCGGUGACCUUUCCCGCCU_UUUUGCAAUGCCCUUGAGCCC_____ACUUGCAUUGCCAUCCGAUUAUCAAUUCAUGACUGCGACGUUAUUACUCGCAUCUGGA_______A
.......(((((.((....)))))))......(((((((....(((.........))))))))))..............((((.((.(((((.((....)))))))))))))........ (-24.20 = -24.70 +   0.50)

alignment

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secondary structure

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Window 0

Location 15,993,108 – 15,993,220
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.86
Mean single sequence MFE -34.25
Consensus MFE -30.32
Energy contribution -29.76
Covariance contribution -0.56
Combinations/Pair 1.11
Mean z-score -2.69
Structure conservation index 0.89
SVM decision value 2.33
SVM RNA-class probability 0.992512
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15993108 112 + 22224390
AUUGAUAAUCGGAUGGCAAUGCAAGUG--GUGGGCUCAAGGGCAUUGCAAAA-AGGCGGGAAAGGUCACCGCCAAAUAAUGGUGG--ACCCAUCA---GAGGAGGGUAAUGUGUCAAAUG
.((((((((((....(((((((...((--(.....)))...)))))))....-.(((((((....)).)))))......))))..--((((.((.---...))))))....))))))... ( -34.40)
>DroSec_CAF1 61034 116 + 1
AUUGAUAAUCGGUUGGCAAUGCAAGUGGGGUGGGCUCAAGGGCAUUGCAAAA-AGGCGGGAAAGGUCACCGCCAAAUAAUGAUGGAGACCCAUCA---GAGGAGGGUAAUGUGUCAAAUG
.((((((.((.(((.(((((((...((((.....))))...)))))))....-.(((((((....)).))))).......))).)).((((.((.---...))))))....))))))... ( -39.30)
>DroEre_CAF1 59729 107 + 1
AUUGAUAAUCGGAUGGCAGUGCAAGA-----GGGCUCAAGGGCAUUGCGAAAAGGGCGGGAAAGGUCACCGCCGAAU---GGUGG--ACCCAUCG---UUGGAGGGUAAUGUGUCAAAUG
.((((((((((....(((((((..((-----....))....)))))))......(((((((....)).)))))...)---)))..--((((.((.---...))))))....))))))... ( -32.70)
>DroYak_CAF1 44076 110 + 1
AUUGAUAAUCGGAUGGCAAUGCAAGA-----GGGCUCAAGGGCAUUGCAAAAAAGGCGGGAAAGGUCACUGCCGAAU---GGUGG--ACCCAUCAGAGGAGGAGGGUAAUGUGUCAAAUG
.((((((((((....(((((((..((-----....))....)))))))......(((((((....)).)))))...)---)))..--((((..(......)..))))....))))))... ( -30.60)
>consensus
AUUGAUAAUCGGAUGGCAAUGCAAGA_____GGGCUCAAGGGCAUUGCAAAA_AGGCGGGAAAGGUCACCGCCAAAU___GGUGG__ACCCAUCA___GAGGAGGGUAAUGUGUCAAAUG
.(((((((((.....(((((((...................)))))))......(((((((....)).))))).......)))....((((..(......)..))))....))))))... (-30.32 = -29.76 +  -0.56)

alignment

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secondary structure

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Window 1

Location 15,993,108 – 15,993,220
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.86
Mean single sequence MFE -23.75
Consensus MFE -21.00
Energy contribution -21.50
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.88
SVM decision value 1.62
SVM RNA-class probability 0.968285
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15993108 112 - 22224390
CAUUUGACACAUUACCCUCCUC---UGAUGGGU--CCACCAUUAUUUGGCGGUGACCUUUCCCGCCU-UUUUGCAAUGCCCUUGAGCCCAC--CACUUGCAUUGCCAUCCGAUUAUCAAU
...((((...............---((((((..--...))))))...(((((.((....))))))).-....(((((((...((.......--))...)))))))..........)))). ( -25.70)
>DroSec_CAF1 61034 116 - 1
CAUUUGACACAUUACCCUCCUC---UGAUGGGUCUCCAUCAUUAUUUGGCGGUGACCUUUCCCGCCU-UUUUGCAAUGCCCUUGAGCCCACCCCACUUGCAUUGCCAACCGAUUAUCAAU
...((((...............---((((((....))))))......(((((.((....))))))).-....(((((((...((.........))...)))))))..........)))). ( -26.20)
>DroEre_CAF1 59729 107 - 1
CAUUUGACACAUUACCCUCCAA---CGAUGGGU--CCACC---AUUCGGCGGUGACCUUUCCCGCCCUUUUCGCAAUGCCCUUGAGCCC-----UCUUGCACUGCCAUCCGAUUAUCAAU
...((((......((((((...---.)).))))--.....---..(((((((.((....)))))))......(((.(((....((....-----))..))).))).....))...)))). ( -22.20)
>DroYak_CAF1 44076 110 - 1
CAUUUGACACAUUACCCUCCUCCUCUGAUGGGU--CCACC---AUUCGGCAGUGACCUUUCCCGCCUUUUUUGCAAUGCCCUUGAGCCC-----UCUUGCAUUGCCAUCCGAUUAUCAAU
...((((......((((..(......)..))))--.....---..((((..(((........))).......(((((((....((....-----))..)))))))...))))...)))). ( -20.90)
>consensus
CAUUUGACACAUUACCCUCCUC___UGAUGGGU__CCACC___AUUCGGCGGUGACCUUUCCCGCCU_UUUUGCAAUGCCCUUGAGCCC_____ACUUGCAUUGCCAUCCGAUUAUCAAU
...((((......((((..(......)..))))..............(((((.((....)))))))......(((((((....(((.........))))))))))..........)))). (-21.00 = -21.50 +   0.50)

alignment

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secondary structure

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Window 2

Location 15,993,146 – 15,993,259
Length 113
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 87.48
Mean single sequence MFE -38.65
Consensus MFE -35.53
Energy contribution -36.15
Covariance contribution 0.62
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.92
SVM decision value 1.01
SVM RNA-class probability 0.899931
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15993146 113 + 22224390
GGCAUUGCAAAA-AGGCGGGAAAGGUCACCGCCAAAUAAUGGUGG--ACCCAUCA---GAGGAGGGUAAUGUGUCAAAUGAGCACCCCGGGGUAGCGAUUUUCCCAGGGGACUUCAGGU
.(((((((....-.(((((((....)).)))))......(((((.--...)))))---.......)))))))......((((..((((((((.........)))).))))..))))... ( -38.30)
>DroSec_CAF1 61074 115 + 1
GGCAUUGCAAAA-AGGCGGGAAAGGUCACCGCCAAAUAAUGAUGGAGACCCAUCA---GAGGAGGGUAAUGUGUCAAAUGAGCAACCUGGGGUAGCGAUUUUCCAAGGGGACUUCAGGC
.(((((((....-.(((((((....)).)))))......((((((....))))))---.......))))))).............(((((((.........)))(((....))))))). ( -35.30)
>DroEre_CAF1 59764 111 + 1
GGCAUUGCGAAAAGGGCGGGAAAGGUCACCGCCGAAU---GGUGG--ACCCAUCG---UUGGAGGGUAAUGUGUCAAAUGAGCACCCUGGGGUACCGAUUUUCCCAGGGGAUUGCAGGU
.(((((((......(((((((....)).))))).(((---((((.--...)))))---)).....))))))).........(((((((((((.........))))))))...))).... ( -42.40)
>DroYak_CAF1 44111 114 + 1
GGCAUUGCAAAAAAGGCGGGAAAGGUCACUGCCGAAU---GGUGG--ACCCAUCAGAGGAGGAGGGUAAUGUGUCAAAUGAGCACCCUGGGGUACCGAUUUUCCCAGGGGAUUUCACUG
.(((((((......(((((((....)).)))))...(---((((.--...)))))..........)))))))......((((..((((((((.........))))))))...))))... ( -38.60)
>consensus
GGCAUUGCAAAA_AGGCGGGAAAGGUCACCGCCAAAU___GGUGG__ACCCAUCA___GAGGAGGGUAAUGUGUCAAAUGAGCACCCUGGGGUACCGAUUUUCCCAGGGGACUUCAGGU
.(((((((......(((((((....)).))))).......(((((....)))))...........)))))))......((((..((((((((.........))))))))...))))... (-35.53 = -36.15 +   0.62)

alignment

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secondary structure

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Window 3

Location 15,993,146 – 15,993,259
Length 113
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 87.48
Mean single sequence MFE -30.05
Consensus MFE -26.04
Energy contribution -26.60
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.37
Structure conservation index 0.87
SVM decision value 0.02
SVM RNA-class probability 0.545949
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15993146 113 - 22224390
ACCUGAAGUCCCCUGGGAAAAUCGCUACCCCGGGGUGCUCAUUUGACACAUUACCCUCCUC---UGAUGGGU--CCACCAUUAUUUGGCGGUGACCUUUCCCGCCU-UUUUGCAAUGCC
...(((.(..(((((((...........)))))))..)))).......((((.........---((((((..--...))))))...(((((.((....))))))).-......)))).. ( -33.30)
>DroSec_CAF1 61074 115 - 1
GCCUGAAGUCCCCUUGGAAAAUCGCUACCCCAGGUUGCUCAUUUGACACAUUACCCUCCUC---UGAUGGGUCUCCAUCAUUAUUUGGCGGUGACCUUUCCCGCCU-UUUUGCAAUGCC
((.(((.((..(((.((...........)).)))..))))).(((.((.............---((((((....))))))......(((((.((....))))))).-...))))).)). ( -25.30)
>DroEre_CAF1 59764 111 - 1
ACCUGCAAUCCCCUGGGAAAAUCGGUACCCCAGGGUGCUCAUUUGACACAUUACCCUCCAA---CGAUGGGU--CCACC---AUUCGGCGGUGACCUUUCCCGCCCUUUUCGCAAUGCC
....(((...(((((((...........)))))))(((..............((((((...---.)).))))--.....---....(((((.((....)))))))......))).))). ( -33.00)
>DroYak_CAF1 44111 114 - 1
CAGUGAAAUCCCCUGGGAAAAUCGGUACCCCAGGGUGCUCAUUUGACACAUUACCCUCCUCCUCUGAUGGGU--CCACC---AUUCGGCAGUGACCUUUCCCGCCUUUUUUGCAAUGCC
..(..(((.....(((((((((.((((((....)))))).))))..(((...((((..(......)..))))--...((---....))..))).....)))))....)))..)...... ( -28.60)
>consensus
ACCUGAAAUCCCCUGGGAAAAUCGCUACCCCAGGGUGCUCAUUUGACACAUUACCCUCCUC___UGAUGGGU__CCACC___AUUCGGCGGUGACCUUUCCCGCCU_UUUUGCAAUGCC
..........(((((((...........)))))))(((..............((((..(......)..))))..............(((((.((....)))))))......)))..... (-26.04 = -26.60 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,993,220 – 15,993,329
Length 109
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 72.10
Mean single sequence MFE -29.93
Consensus MFE -17.90
Energy contribution -18.90
Covariance contribution 1.00
Combinations/Pair 1.18
Mean z-score -1.75
Structure conservation index 0.60
SVM decision value 0.86
SVM RNA-class probability 0.867882
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15993220 109 + 22224390
AGCACCCCGGGGUAGCGAUUUUCCCAGGGGACUUCAGGUUACUGAUCUCAUACAGUCCG--AACUGGUUGAAUUUGCAACUGAAUAUUUUGUAUUAAGAUAAUACUCA--ACA
.........((((((((((((..((((.(((((((((....))))........))))).--..))))..))).)))).......(((((((...))))))).))))).--... ( -26.50)
>DroSec_CAF1 61150 110 + 1
AGCAACCUGGGGUAGCGAUUUUCCAAGGGGACUUCAGGCUACUGAUCUCAUACAGUCUA-AAACUGGGGGAAUUUGCUACUGAAUAUCUUGUAUUAAGAUGAUACUCA--ACA
.......(((((((((((.(((((...((((..((((....))))))))...((((...-..)))).))))).)))))))....(((((((...)))))))...))))--... ( -32.10)
>DroEre_CAF1 59836 95 + 1
AGCACCCUGGGGUACCGAUUUUCCCAGGGGAUUGCAGGUUACUGAUCUCCUGCUGCCAC--AGGCCGCGGAAUUUGCUACUGAAUG----------------CACUCAAAACA
.(((((((((((.........))))))))....(((((((.(((....((((......)--)))...)))))))))).......))----------------).......... ( -32.30)
>DroYak_CAF1 44186 97 + 1
AGCACCCUGGGGUACCGAUUUUCCCAGGGGAUUUCACUGUAGCGAUCUCAUACUGCCGCUCAACUGGUGGCAUUUGCUUCUGAUUA----------------CACUCAAAACA
((((((((((((.........))))))))((..((.(....).))..))....(((((((.....)))))))..))))........----------------........... ( -28.80)
>consensus
AGCACCCUGGGGUACCGAUUUUCCCAGGGGACUUCAGGUUACUGAUCUCAUACAGCCAC__AACUGGUGGAAUUUGCUACUGAAUA________________CACUCA__ACA
.(((((((((((.........))))))))((..((((....))))..))...(((((........)))))....))).................................... (-17.90 = -18.90 +   1.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:09 2006