Locus 6306

Sequence ID 2L_DroMel_CAF1
Location 17,570,318 – 17,570,481
Length 163
Max. P 0.997257
window10072 window10073 window10074

overview

Window 2

Location 17,570,318 – 17,570,409
Length 91
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 90.07
Mean single sequence MFE -22.17
Consensus MFE -20.19
Energy contribution -20.07
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.91
SVM decision value 2.83
SVM RNA-class probability 0.997257
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17570318 91 + 22407834
AAACCCUUGGGGUUCGCUGCUCCUCCAUUGUGCCACCCCGACCCACAUUUUU--------UUUUUGGCAUUCACAUCCCCCGCCACUCACCAGUGGUAG
......(((((((..((.((.........)))).)))))))...........--------.....................((((((....)))))).. ( -18.50)
>DroSec_CAF1 86654 99 + 1
AAACCCCUGGGGUUCGAUGCCCCUCCAUUGUGCCACCCCGACCCACAUUUUUUUUUUUUUUUUUUGGCAUUUACAUCCCCCGCCACUCCCCAGUGGUAG
..(((.((((((..(((((......)))))(((((.............................)))))..................)))))).))).. ( -21.35)
>DroSim_CAF1 85758 93 + 1
AAACCCCUGGGGUUCGCUGCCCCUCCAUUGUGCCACCCCGACCCACAUUUUUU------UUUUUUGGCAUUCACAUCCCCCGCCACUCCCCAGUGGUAG
..(((.((((((...((............((((((..................------.....))))))...........))....)))))).))).. ( -22.20)
>DroEre_CAF1 85339 90 + 1
AAACCCUUGGGGUUCGCUGCCCCUCCAUUGUGCCACCCCGACCCACAUUUUU---------UUUUGGCAUUCGCAUCCCCCGCCACUCCCCAGUGGCAG
........((((...((((((.......((((...........)))).....---------....))))...))...))))((((((....)))))).. ( -24.19)
>DroYak_CAF1 87008 87 + 1
AAACCCUUGGGGUUCGCUGCCCCUCCAUUGUGCC-CCCCGACCCACAUUU-----------UUUUGGCAUUCGCAUCUCCCGCCACUCCCCAGUGGUGG
......((((((..(((............)))..-)))))).........-----------.....((....)).....((((((((....)))))))) ( -24.60)
>consensus
AAACCCUUGGGGUUCGCUGCCCCUCCAUUGUGCCACCCCGACCCACAUUUUU________UUUUUGGCAUUCACAUCCCCCGCCACUCCCCAGUGGUAG
........(((((.....)))))......((((((.............................))))))...........((((((....)))))).. (-20.19 = -20.07 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,570,342 – 17,570,448
Length 106
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.56
Mean single sequence MFE -18.57
Consensus MFE -12.10
Energy contribution -13.38
Covariance contribution 1.28
Combinations/Pair 1.12
Mean z-score -1.39
Structure conservation index 0.65
SVM decision value 0.14
SVM RNA-class probability 0.602713
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17570342 106 + 22407834
CCAUUGUGCCACCCCGACCCACAUUUUU--------UUUUUGGCAUUCACAUCCCCCGCCACUCACCAGUGGUAGCAAAAAAAAAAAACCGGCAAAAAGCAACAACCGGUAAAA
....((((...........))))(((((--------(((((((......).......((((((....))))))..))))))))))).(((((.............))))).... ( -19.12)
>DroPse_CAF1 92351 92 + 1
CCCCUGUCCCCGCACCAGCCACUCCUCUC-------UCUCUGGCUUUU------C--------CCCUAGUGGUAGUAAA-AAAAAAACCCGGCAAAAAGCAACAACCGGUAAAA
.............(((.((((((((....-------.....)).....------.--------....))))))......-...........((.....)).......))).... ( -10.60)
>DroSec_CAF1 86678 108 + 1
CCAUUGUGCCACCCCGACCCACAUUUUUUUUUUUUUUUUUUGGCAUUUACAUCCCCCGCCACUCCCCAGUGGUAGCAAA------AAACCGGCAAAAAGCAACAACCGGUAAAA
...((((((((.............................)))).............((((((....)))))).)))).------..(((((.............))))).... ( -18.27)
>DroSim_CAF1 85782 102 + 1
CCAUUGUGCCACCCCGACCCACAUUUUUU------UUUUUUGGCAUUCACAUCCCCCGCCACUCCCCAGUGGUAGCAAA------AAACCGGCAAAAAGCAACAACCGGUAAAA
...((((((((..................------.....)))).............((((((....)))))).)))).------..(((((.............))))).... ( -18.52)
>DroEre_CAF1 85363 98 + 1
CCAUUGUGCCACCCCGACCCACAUUUUU---------UUUUGGCAUUCGCAUCCCCCGCCACUCCCCAGUGGCAGCAGA------AAACCGGCAA-AAGCAACAACCGGUAAAA
...((.(((.....(((.(((.(.....---------.).)))...)))........((((((....)))))).))).)------).(((((...-.........))))).... ( -21.00)
>DroYak_CAF1 87032 96 + 1
CCAUUGUGCC-CCCCGACCCACAUUU-----------UUUUGGCAUUCGCAUCUCCCGCCACUCCCCAGUGGUGGCAAG------AAGCCGGCAAAAAGCAACAACCGGUAAAA
((.((((((.-..(((..(((.....-----------...))).....((.(((.((((((((....))))))))..))------).)))))......)).))))..))..... ( -23.90)
>consensus
CCAUUGUGCCACCCCGACCCACAUUUUU________UUUUUGGCAUUCACAUCCCCCGCCACUCCCCAGUGGUAGCAAA______AAACCGGCAAAAAGCAACAACCGGUAAAA
.....(((((...............................)))))...........((((((....))))))..............(((((.............))))).... (-12.10 = -13.38 +   1.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,570,374 – 17,570,481
Length 107
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 80.13
Mean single sequence MFE -21.73
Consensus MFE -14.85
Energy contribution -15.60
Covariance contribution 0.75
Combinations/Pair 1.33
Mean z-score -1.40
Structure conservation index 0.68
SVM decision value 0.24
SVM RNA-class probability 0.647062
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17570374 107 + 22407834
UGGCAUUCACA---UCCCCCGCCACUCACCAGUGGUAGCAAAAAAAAAAAACCGGCAAAAAGCAACAACCGGUAAAAUCGAAUGUUCACUUUGCACACAGACACACAGAU
.(((((((...---......((((((....))))))..............(((((.............)))))......)))))))........................ ( -19.92)
>DroSec_CAF1 86718 101 + 1
UGGCAUUUACA---UCCCCCGCCACUCCCCAGUGGUAGCAAA------AAACCGGCAAAAAGCAACAACCGGUAAAAUCGAAUGUUCACUUUGCACACAGACUCACAGAU
.(((((((...---......((((((....))))))......------..(((((.............)))))......)))))))........................ ( -17.32)
>DroEre_CAF1 85394 100 + 1
UGGCAUUCGCA---UCCCCCGCCACUCCCCAGUGGCAGCAGA------AAACCGGCAA-AAGCAACAACCGGUAAAAUCGAAUGUUCACUUUGCACACAGACUCACAGAU
.((((((((..---......((((((....))))))......------..(((((...-.........))))).....))))))))........................ ( -23.30)
>DroYak_CAF1 87060 101 + 1
UGGCAUUCGCA---UCUCCCGCCACUCCCCAGUGGUGGCAAG------AAGCCGGCAAAAAGCAACAACCGGUAAAAUCGAAUGUUCACUUUGCACACAGACACACAGAU
.((((((((..---(((.((((((((....))))))))..))------).(((((.............))))).....))))))))........................ ( -27.42)
>DroMoj_CAF1 99966 94 + 1
UG-CCAUCGUU---UCCCCCACCUCUGAUGCUUGGUCGCAAA------AGACCGGCAAAAAGCAGCAACCGGUAAAAUCGAAUGUUCACUUGGCC------CACACACAC
.(-((((((((---(..((.....(((.((((.((((.....------.)))))))).....))).....))..))).))).........)))).------......... ( -19.70)
>DroAna_CAF1 92242 104 + 1
UGGCGCCCCCAGCCUCCCUGCCUACUACCCAGUGGUAGUAAA------AAACCGGCAAAAAGCAACAACCGGUAAAAUCGAAUGUUCACUUGGCUCACUCAUACACUCGU
.(((.......))).....((((((((((....)))))))..------..(((((.............)))))..................)))................ ( -22.72)
>consensus
UGGCAUUCGCA___UCCCCCGCCACUCCCCAGUGGUAGCAAA______AAACCGGCAAAAAGCAACAACCGGUAAAAUCGAAUGUUCACUUUGCACACAGACACACAGAU
.(((((((............((((((....))))))..............(((((.............)))))......)))))))........................ (-14.85 = -15.60 +   0.75)

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 12:07:48 2006