Locus 4656

Sequence ID 2R_DroMel_CAF1
Location 15,199,617 – 15,199,743
Length 126
Max. P 0.998971
window7487 window7488 window7489

overview

Window 7

Location 15,199,617 – 15,199,719
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 88.58
Mean single sequence MFE -30.79
Consensus MFE -27.38
Energy contribution -27.38
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -5.07
Structure conservation index 0.89
SVM decision value 3.31
SVM RNA-class probability 0.998971
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15199617 102 + 20766785
AUA--------------UAAAAAUGAUA-AAGCAAAAUGGCGAAAAGUGGCAGUAAA---AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAAAAAC
...--------------...........-........(((((....((((((((...---...........))))))))....((((((....))))))...........)))))..... ( -28.94)
>DroVir_CAF1 37851 113 + 1
A--A-ACAAA--ACAUAUAAAAAUGAUA-AAGCAAAAUGGCGAAAAGUGGCAGUAAAAAAAAAUAAUAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAA-AAG
.--.-.....--................-........(((((....((((((((.................))))))))....((((((....))))))...........))))).-... ( -28.73)
>DroPse_CAF1 35851 111 + 1
A--U-ACAAU--ACAUAUAAAAAUGAUA-AAGCAAAAUGGCGAAAAGUGGCAGUAAA---AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAGAAAG
.--.-.....--................-........(((((....((((((((...---...........))))))))....((((((....))))))...........)))))..... ( -28.94)
>DroSec_CAF1 29748 115 + 1
AUAU-ACACUA-ACGUAUAAAAAUGACAAAAGCAAAAUGGCGAAAAGUGGCAGUAAA---AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAAAAAC
.(((-((....-..)))))..................(((((....((((((((...---...........))))))))....((((((....))))))...........)))))..... ( -31.54)
>DroMoj_CAF1 37458 111 + 1
A--AGGCAGC--GCAUAUAAAAAUGAUA-AAGCAAAAUGGCGAAAAGUGGCAGUAAAA--AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGGCA--AAG
.--..((.((--((((............-.....((((((((....((((((((....--...........)))))))).....))))))))(((.......))))))))).)).--... ( -37.26)
>DroAna_CAF1 25480 113 + 1
A--U-AUACGAUACAUAUAAAAAUGAUA-AAGCCAAAUGGCGAAAAGUGGCAGUAAA---AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAAAAAC
.--.-.......................-..(((((((((((....((((((((...---...........)))))))).....)))))))))..((((......))))))......... ( -29.34)
>consensus
A__U_ACAAU__ACAUAUAAAAAUGAUA_AAGCAAAAUGGCGAAAAGUGGCAGUAAA___AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAAAAAC
...............................((.((((((((....((((((((.................)))))))).....))))))))...((((......))))))......... (-27.38 = -27.38 +   0.00)

alignment

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secondary structure

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Window 8

Location 15,199,617 – 15,199,719
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.58
Mean single sequence MFE -25.10
Consensus MFE -20.71
Energy contribution -20.71
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.83
SVM decision value 0.98
SVM RNA-class probability 0.894552
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15199617 102 - 20766785
GUUUUUGGCGCGCAUGUGUUUAUGCCACAAAUGGCACUUUUGCGGCAGCGCAUUUUAUUU---UUUACUGCCACUUUUCGCCAUUUUGCUU-UAUCAUUUUUA--------------UAU
((...(((((.(((...((....((((....))))))...)))(((((............---....)))))......)))))....))..-...........--------------... ( -22.69)
>DroVir_CAF1 37851 113 - 1
CUU-UUGGCGCGCAUGUGUUUAUGCCACAAAUGGCACUUUUGCGGCAGCGCAUAUUAUUUUUUUUUACUGCCACUUUUCGCCAUUUUGCUU-UAUCAUUUUUAUAUGU--UUUGU-U--U
...-.(((((.(((...((....((((....))))))...)))(((((...................)))))......)))))........-................--.....-.--. ( -21.81)
>DroPse_CAF1 35851 111 - 1
CUUUCUGGCGCGCAUGUGUUUAUGCCACAAAUGGCACUUUUGCGGCAGCGCAUUUUAUUU---UUUACUGCCACUUUUCGCCAUUUUGCUU-UAUCAUUUUUAUAUGU--AUUGU-A--U
.....(((((.(((...((....((((....))))))...)))(((((............---....)))))......)))))...(((..-((.(((......))))--)..))-)--. ( -23.89)
>DroSec_CAF1 29748 115 - 1
GUUUUUGGCGCGCAUGUGUUUAUGCCACAAAUGGCACUUUUGCGGCAGCGCAUUUUAUUU---UUUACUGCCACUUUUCGCCAUUUUGCUUUUGUCAUUUUUAUACGU-UAGUGU-AUAU
((...(((((.(((...((....((((....))))))...)))(((((............---....)))))......)))))....))............(((((..-..))))-)... ( -25.49)
>DroMoj_CAF1 37458 111 - 1
CUU--UGCCGCGCAUGUGUUUAUGCCACAAAUGGCACUUUUGCGGCAGCGCAUUUUAUUU--UUUUACUGCCACUUUUCGCCAUUUUGCUU-UAUCAUUUUUAUAUGC--GCUGCCU--U
...--.((.(((((((((...(((....(((((((......(.(((((............--.....))))).).....))))))).....-...)))...)))))))--)).))..--. ( -30.03)
>DroAna_CAF1 25480 113 - 1
GUUUUUGGCGCGCAUGUGUUUAUGCCACAAAUGGCACUUUUGCGGCAGCGCAUUUUAUUU---UUUACUGCCACUUUUCGCCAUUUGGCUU-UAUCAUUUUUAUAUGUAUCGUAU-A--U
......((((.(((((....)))))).((((((((......(.(((((............---....))))).).....))))))))))).-.........((((((...)))))-)--. ( -26.69)
>consensus
CUUUUUGGCGCGCAUGUGUUUAUGCCACAAAUGGCACUUUUGCGGCAGCGCAUUUUAUUU___UUUACUGCCACUUUUCGCCAUUUUGCUU_UAUCAUUUUUAUAUGU__AGUGU_A__U
.........(((((((....)))))...(((((((......(.(((((...................))))).).....))))))).))............................... (-20.71 = -20.71 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,199,642 – 15,199,743
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.55
Mean single sequence MFE -26.20
Consensus MFE -21.81
Energy contribution -21.81
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.80
Structure conservation index 0.83
SVM decision value 1.28
SVM RNA-class probability 0.939426
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15199642 101 + 20766785
CGAAAAGUGGCAGUAAA---AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAAAAACUUUGAUAA----------------GACAAAAGCCGAGCCG
......((((((((...---...........))))))))....((((((....)))))).........((.((......(((....))----------------)......))))..... ( -22.54)
>DroVir_CAF1 37885 102 + 1
CGAAAAGUGGCAGUAAAAAAAAAUAAUAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAA-AAGUUUGAUAA----------------GACAAAAGGCGAC-GG
......((((((((.................))))))))....((((((....)))))).........((((((..-..((((....)----------------)))....)))).)-). ( -30.43)
>DroGri_CAF1 29093 98 + 1
CGAAAAGUGGCAGUAAAA--AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAA-AAGUUUGAUAA----------------GACAAAAGGCGAC---
......((((((((....--...........))))))))....((((((....))))))...........((((..-..((((....)----------------)))....))))..--- ( -28.36)
>DroWil_CAF1 80362 116 + 1
CGAAAAGUGGCAGUAAA---AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAAAAAGUUUGAUAACACACAUACACACAAAGACAAAAGACGAU-GG
((....((((((((...---...........))))))))....(((.....((((((((......))))..........(((....))).))))....)))............))..-.. ( -23.44)
>DroMoj_CAF1 37493 93 + 1
CGAAAAGUGGCAGUAAAA--AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGGCA--AAGUUUGAUAA----------------GACAAAAGG-------
......((((((((....--...........)))))))).....((((...((((.......)))).....))))--..((((....)----------------)))......------- ( -23.26)
>DroPer_CAF1 34314 101 + 1
CGAAAAGUGGCAGUAAA---AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAGAAAGUUUGAUAA----------------GACAAAGGCAGUGGCA
......((((((((...---...........)))))))).....(((((((.(((.(((......))))))(((.....((((....)----------------)))...)))))))))) ( -29.14)
>consensus
CGAAAAGUGGCAGUAAA___AAAUAAAAUGCGCUGCCGCAAAAGUGCCAUUUGUGGCAUAAACACAUGCGCGCCAA_AAGUUUGAUAA________________GACAAAAGGCGAC__G
((((..((((((((.................))))))))....((((....((((.......)))).)))).........)))).................................... (-21.81 = -21.81 +  -0.00)

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 11:25:55 2006