Locus 95

Sequence ID sy_sa.0
Location 2,477,926 – 2,478,046
Length 120
Max. P 0.995602
window485 window486 window487 window488 window489 window490 window491 window492

overview

Window 5

Location 2,477,926 – 2,478,042
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.96
Mean single sequence MFE -16.70
Consensus MFE -15.37
Energy contribution -13.60
Covariance contribution -1.77
Combinations/Pair 1.33
Mean z-score 0.13
Structure conservation index 0.92
SVM decision value 0.57
SVM RNA-class probability 0.786689
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 116 + 2516575/80-200
----AAUUCGAAAUAAUAGAAACACAGUAACAAGGAAAGUAGAACUUACACUGCUGACACAGAGAGUCUUCGUAACGCUGAAAGAAGAUACAGAAAGAAAGUUUGAAAAUGGCCUUUGAG
----...........................((((..(...((((((.(.(((......))).(.((((((............)))))).).....).)))))).....)..)))).... ( -14.60)
>sy_ha.0 2637323 114 + 2685015/80-200
----AAAAAAACACAAAUUACACACUGUAAUAAGGAAAGUAGAACUUACACUGCUAAUACAGAGAGUCUCC--AAAGCUGAGAAGAGACAUUGAAAGAAAGUUUGAAAAUGGCCUUUGAG
----............(((((.....)))))((((..(...((((((.(.(((......)))...(((((.--...........))))).......).)))))).....)..)))).... ( -16.50)
>sy_au.0 2370606 119 - 2809422/80-200
UAACAGUUUAAUGAAACGUAAACACAAUAAAGAGGAAAGUAAAACACACCCUGCUUAUACAGAGAGUCUUUA-GUAGCUGAGAGAAGAUUUUGAAAGCGUGUUUGAAAAUGGCCUUGGAG
.....(((((........)))))........((((..(...((((((...(((......)))(((((((((.-..........)))))))))......)))))).....)..)))).... ( -19.00)
>consensus
____AAUUAAAAAAAAAAUAAACACAGUAAAAAGGAAAGUAGAACUUACACUGCUAAUACAGAGAGUCUUC__AAAGCUGAGAGAAGAUAUUGAAAGAAAGUUUGAAAAUGGCCUUUGAG
...............................((((..(...((((((.(.(((......)))...((((((............)))))).......).)))))).....)..)))).... (-15.37 = -13.60 +  -1.77)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,477,926 – 2,478,046
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.29
Mean single sequence MFE -29.67
Consensus MFE -28.60
Energy contribution -27.17
Covariance contribution -1.43
Combinations/Pair 1.21
Mean z-score -0.54
Structure conservation index 0.96
SVM decision value 0.68
SVM RNA-class probability 0.821286
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 120 + 2516575/120-240
AGAACUUACACUGCUGACACAGAGAGUCUUCGUAACGCUGAAAGAAGAUACAGAAAGAAAGUUUGAAAAUGGCCUUUGAGUGUUGAUGCCAAUAUGAGGUAUCAACGGGCGCGCCCGUUA
.((((((.(.(((......))).(.((((((............)))))).).....).)))))).....((((........(((((((((.......)))))))))(((....))))))) ( -29.60)
>sy_ha.0 2637323 118 + 2685015/120-240
AGAACUUACACUGCUAAUACAGAGAGUCUCC--AAAGCUGAGAAGAGACAUUGAAAGAAAGUUUGAAAAUGGCCUUUGAGUGUUGAUGCCAAUACGAGGUGUCAACGGGUUCGCCCGUUA
.((((((.(.(((......)))...(((((.--...........))))).......).)))))).......(((((...((((((....)))))))))))...((((((....)))))). ( -29.70)
>sy_au.0 2370606 119 - 2809422/120-240
AAAACACACCCUGCUUAUACAGAGAGUCUUUA-GUAGCUGAGAGAAGAUUUUGAAAGCGUGUUUGAAAAUGGCCUUGGAGUGUUGAUGCCAAUAUGAGGUGUCUACGGGUUCGCCCGUUA
..(((((.((..(((....((((.((..((((-(...((......))...)))))..).).)))).....)))...)).)))))((((((.......)))))).(((((....))))).. ( -29.70)
>consensus
AGAACUUACACUGCUAAUACAGAGAGUCUUC__AAAGCUGAGAGAAGAUAUUGAAAGAAAGUUUGAAAAUGGCCUUUGAGUGUUGAUGCCAAUAUGAGGUGUCAACGGGUUCGCCCGUUA
.((((((.(.(((......)))...((((((............)))))).......).)))))).......(((((...((((((....)))))))))))...((((((....)))))). (-28.60 = -27.17 +  -1.43)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,477,926 – 2,478,042
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.07
Mean single sequence MFE -33.87
Consensus MFE -27.53
Energy contribution -27.77
Covariance contribution 0.23
Combinations/Pair 1.15
Mean z-score -2.65
Structure conservation index 0.81
SVM decision value 1.92
SVM RNA-class probability 0.982775
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 116 + 2516575/200-320
UGUUGAUGCCAAUAUGAGGUAUCAACGGGCGCGCCCGUUAUAGCGCUACAGUAUUAACAUUU--UGUUAAAUGGCGUACUGGAUUAUUCCACACGUUAUC--UUCUCGUUAAUACUCAUU
.(((((((((.......))))))))).(((((..........)))))..(((((((((....--.(....(((((((..((((....)))).))))))).--..)..))))))))).... ( -35.90)
>sy_ha.0 2637323 118 + 2685015/200-320
UGUUGAUGCCAAUACGAGGUGUCAACGGGUUCGCCCGUUAUAGCGAUACAGUAUUAACAUUUAUUGUUUAAUGGCGUACUGGA--AUUCUAGACGUCGCUAAUCAUCGUUAAUACUCAUU
.(((((((((.......)))))))))(((....)))((..(((((((((((((........))))))(((.((((((.((((.--...)))))))))).)))..)))))))..))..... ( -38.00)
>sy_au.0 2370606 115 - 2809422/200-320
UGUUGAUGCCAAUAUGAGGUGUCUACGGGUUCGCCCGUUAUAGCGAUACAGUAUUAACAUUGA-UGUUAAAUGGCGUACUGGA---UUCUUUACG-CACGAUUUUUUGUUAAUAAGUAUG
.((((((((...(((..(.(((..(((((....))))).))).).)))..))))))))(((((-((..((((((((((..(..---..)..))))-).).))))..)))))))....... ( -27.70)
>consensus
UGUUGAUGCCAAUAUGAGGUGUCAACGGGUUCGCCCGUUAUAGCGAUACAGUAUUAACAUUUA_UGUUAAAUGGCGUACUGGA__AUUCUACACGUCACCA_UUAUCGUUAAUACUCAUU
.(((((((((.......)))))))))(((....)))....((((((.......((((((.....)))))).((((((...(((....)))..)))))).......))))))......... (-27.53 = -27.77 +   0.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,477,926 – 2,478,042
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.07
Mean single sequence MFE -26.18
Consensus MFE -19.19
Energy contribution -20.42
Covariance contribution 1.23
Combinations/Pair 1.16
Mean z-score -1.76
Structure conservation index 0.73
SVM decision value 0.31
SVM RNA-class probability 0.681034
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 116 + 2516575/200-320
AAUGAGUAUUAACGAGAA--GAUAACGUGUGGAAUAAUCCAGUACGCCAUUUAACA--AAAUGUUAAUACUGUAGCGCUAUAACGGGCGCGCCCGUUGAUACCUCAUAUUGGCAUCAACA
....((((((((((...(--(((..((((((((....)))).))))..))))....--...))))))))))...(((((......)))))....((((((.((.......)).)))))). ( -32.30)
>sy_ha.0 2637323 118 + 2685015/200-320
AAUGAGUAUUAACGAUGAUUAGCGACGUCUAGAAU--UCCAGUACGCCAUUAAACAAUAAAUGUUAAUACUGUAUCGCUAUAACGGGCGAACCCGUUGACACCUCGUAUUGGCAUCAACA
..(((((....((((.(..(((((((.....)...--..(((((...((((........))))....)))))..))))))(((((((....)))))))...).))))....)).)))... ( -25.40)
>sy_au.0 2370606 115 - 2809422/200-320
CAUACUUAUUAACAAAAAAUCGUG-CGUAAAGAA---UCCAGUACGCCAUUUAACA-UCAAUGUUAAUACUGUAUCGCUAUAACGGGCGAACCCGUAGACACCUCAUAUUGGCAUCAACA
.((((.((((((((.........(-((((..(..---..)..))))).........-....))))))))..)))).((((..(((((....))))).((....))....))))....... ( -20.85)
>consensus
AAUGAGUAUUAACGAAAA_UAGUGACGUAUAGAAU__UCCAGUACGCCAUUUAACA_UAAAUGUUAAUACUGUAUCGCUAUAACGGGCGAACCCGUUGACACCUCAUAUUGGCAUCAACA
....((((((((((......((((.((((..((....))...)))).))))..........))))))))))...(((((......)))))....(((((..((.......))..))))). (-19.19 = -20.42 +   1.23) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,477,926 – 2,478,025
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 63.93
Mean single sequence MFE -24.58
Consensus MFE -10.95
Energy contribution -11.07
Covariance contribution 0.12
Combinations/Pair 1.19
Mean z-score -2.51
Structure conservation index 0.45
SVM decision value 2.04
SVM RNA-class probability 0.986383
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 99 + 2516575/240-360
UAGCGCUACAGUAUUAACAUUU--UGUUAAAUGGCGUACUGGAUUAUUCCACACGUUAUC--UUCUCGUUAAUACUCAUUUUAUUUAUAG--------AAUGGGUUUUUUA---------
(((((........(((((....--.)))))(((((((..((((....)))).))))))).--....)))))..((((((((((....)))--------)))))))......--------- ( -21.90)
>sy_ha.0 2637323 117 + 2685015/240-360
UAGCGAUACAGUAUUAACAUUUAUUGUUUAAUGGCGUACUGGA--AUUCUAGACGUCGCUAAUCAUCGUUAAUACUCAUUU-ACUUAUAAUCAAGUUAAAUGAGUUUUUUAAUGUGAACC
((((...((((((........)))))).....(((((.((((.--...))))))))))))).(((.((((((.((((((((-((((......))).)))))))))...)))))))))... ( -34.00)
>sy_au.0 2370606 99 - 2809422/240-360
UAGCGAUACAGUAUUAACAUUGA-UGUUAAAUGGCGUACUGGA---UUCUUUACG-CACGAUUUUUUGUUAAUAAGUAUGGGAUAGCACAU-------UACUAUAUCCUUA---------
.....((((..((((((((..((-.........(((((..(..---..)..))))-).....))..)))))))).))))((((((......-------.....))))))..--------- ( -17.84)
>consensus
UAGCGAUACAGUAUUAACAUUUA_UGUUAAAUGGCGUACUGGA__AUUCUACACGUCACCA_UUAUCGUUAAUACUCAUUU_AUUUAUAAU_______AAUGAGUUUUUUA_________
((((((.......((((((.....)))))).((((((...(((....)))..)))))).......))))))................................................. (-10.95 = -11.07 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,477,926 – 2,478,024
Length 98
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 57.10
Mean single sequence MFE -21.58
Consensus MFE -9.39
Energy contribution -10.51
Covariance contribution 1.12
Combinations/Pair 1.35
Mean z-score -1.90
Structure conservation index 0.43
SVM decision value 1.07
SVM RNA-class probability 0.910451
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 98 + 2516575/360-480
-----UUUACGAAAAAUG--AUAACACGAUUCAGUCAACGU------------UACAUAUACA---ACAAUUUAGCGUACUGGAUAAGGUUACUUUAGUGAUAAUGUAACAAACAAAGGU
-----.............--........(((((((..((((------------((.((.....---...)).)))))))))))))...(((((.(((....))).))))).......... ( -16.80)
>sy_ha.0 2637323 120 + 2685015/360-480
UUUCAUUCGCCUAAAGUGUCACAUAACGAUUAAAUUAGCGUCCACUAUCUCAGUACACUUUUAUUCACAAAAUGGCGUACUGUUUGAGGUUACUUUAGCAAUAAAGUAAUAAAUAAAGGU
.......(((.......(((.......))).......))).((.((....((((((.((.((........)).)).))))))....))(((((((((....))))))))).......)). ( -22.14)
>sy_au.0 2370606 97 - 2809422/360-480
-CUUACUGACUUUAAUUGUGAUA--AUUGUUCAGUAAGCAU-----------AUUUACUUUUA---------AUGCGUACUGAAUAAGGUUAUUUCAGCGAUGGAAUAACAAAUAAAGGU
-........(((((.........--.((((((((((.((((-----------...........---------)))).)))))))))).(((((((((....)))))))))...))))).. ( -25.80)
>consensus
__U_AUUCACCUAAAAUGU_AUA__ACGAUUCAGUAAGCGU____________UACACUUUUA___ACAA__UAGCGUACUGAAUAAGGUUACUUUAGCGAUAAAGUAACAAAUAAAGGU
............................(((((((..((((.................................)))))))))))...(((((((((....))))))))).......... ( -9.39 = -10.51 +   1.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,477,926 – 2,478,042
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.68
Mean single sequence MFE -45.86
Consensus MFE -43.97
Energy contribution -43.77
Covariance contribution -0.21
Combinations/Pair 1.21
Mean z-score -5.86
Structure conservation index 0.96
SVM decision value 1.18
SVM RNA-class probability 0.927036
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 116 + 2516575/435-555
CGUACUGGAUAAGGUUACUUUAGUGAUAAUGUAACAAACAAAGGUGGUACCGCGAGC--UAAGCUUUCGUCCUUUACAUCCGAAU--UUUCGGGUUUAAAGGACGGGAGCUUUUUUUAUU
....((.......(((((.(((....))).)))))......))(((....)))(((.--.(((((..(((((((((.((((((..--..)))))).)))))))))..)))))..)))... ( -42.02)
>sy_ha.0 2637323 118 + 2685015/435-555
CGUACUGUUUGAGGUUACUUUAGCAAUAAAGUAAUAAAUAAAGGUGGUACCGCGAAA--CAGGCUUUCGUCCUUUACAUCCGAUGCAUAUCGGGUUUAAAGGACGGGAGCUUUUUUUAUU
.((((..(((...(((((((((....)))))))))......)))..))))...((((--.(((((..(((((((((.(((((((....))))))).)))))))))..))))).))))... ( -50.00)
>sy_au.0 2370606 119 - 2809422/435-555
CGUACUGAAUAAGGUUAUUUCAGCGAUGGAAUAACAAAUAAAGGUGGUACCGCGAAACAUAAGCUUUCGUCCUUUUUAUCCGAUUCAU-UCGGGUACGAAGGACGGAAGCUUUUUUUAUU
.((((((......(((((((((....))))))))).........))))))...((((...(((((((((((((((.(((((((.....-))))))).))))))))))))))).))))... ( -45.56)
>consensus
CGUACUGAAUAAGGUUACUUUAGCGAUAAAGUAACAAAUAAAGGUGGUACCGCGAAA__UAAGCUUUCGUCCUUUACAUCCGAUUCAU_UCGGGUUUAAAGGACGGGAGCUUUUUUUAUU
.((((((..(...(((((((((....)))))))))......)..))))))..........((((((((((((((((.(((((((....))))))).))))))))))))))))........ (-43.97 = -43.77 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,477,926 – 2,478,042
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.68
Mean single sequence MFE -31.30
Consensus MFE -27.35
Energy contribution -28.58
Covariance contribution 1.23
Combinations/Pair 1.09
Mean z-score -3.55
Structure conservation index 0.87
SVM decision value 2.59
SVM RNA-class probability 0.995602
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 2477926 116 + 2516575/435-555
AAUAAAAAAAGCUCCCGUCCUUUAAACCCGAAA--AUUCGGAUGUAAAGGACGAAAGCUUA--GCUCGCGGUACCACCUUUGUUUGUUACAUUAUCACUAAAGUAACCUUAUCCAGUACG
........(((((..(((((((((...((((..--..))))...)))))))))..))))).--.......((((...........(((((.(((....))).)))))........)))). ( -29.41)
>sy_ha.0 2637323 118 + 2685015/435-555
AAUAAAAAAAGCUCCCGUCCUUUAAACCCGAUAUGCAUCGGAUGUAAAGGACGAAAGCCUG--UUUCGCGGUACCACCUUUAUUUAUUACUUUAUUGCUAAAGUAACCUCAAACAGUACG
..........(((..(((((((((...(((((....)))))...)))))))))..)))(((--(((...((.....))........((((((((....))))))))....)))))).... ( -33.00)
>sy_au.0 2370606 119 - 2809422/435-555
AAUAAAAAAAGCUUCCGUCCUUCGUACCCGA-AUGAAUCGGAUAAAAAGGACGAAAGCUUAUGUUUCGCGGUACCACCUUUAUUUGUUAUUCCAUCGCUGAAAUAACCUUAUUCAGUACG
........((((((.(((((((..((.((((-.....)))).))..))))))).)))))).(((((((((((.....................))))).))))))............... ( -31.50)
>consensus
AAUAAAAAAAGCUCCCGUCCUUUAAACCCGA_AUGAAUCGGAUGUAAAGGACGAAAGCUUA__UUUCGCGGUACCACCUUUAUUUGUUACUUUAUCGCUAAAGUAACCUUAUACAGUACG
........(((((..(((((((((...(((((....)))))...)))))))))..)))))..........((((...........(((((((((....)))))))))........)))). (-27.35 = -28.58 +   1.23) 
# Strand winner: forward (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 $RNAz::rnazVersion) on Thu Apr 6 18:57:23 2006