Locus 7694

Sequence ID 2L_DroMel_CAF1
Location 21,755,946 – 21,756,083
Length 137
Max. P 0.994453
window12357 window12358 window12359 window12360

overview

Window 7

Location 21,755,946 – 21,756,049
Length 103
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 81.98
Mean single sequence MFE -33.58
Consensus MFE -20.78
Energy contribution -21.74
Covariance contribution 0.96
Combinations/Pair 1.21
Mean z-score -1.97
Structure conservation index 0.62
SVM decision value 0.38
SVM RNA-class probability 0.711939
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21755946 103 + 22407834
----UGGGGUGAAGGCUUCCGGUGUCAGUCACCGAGAAGUGGGCACACACUAGUUGUGGCCACAUGGCAUUUUCGUCAAAAAACAAAUACCAAGGGUUUAGAAAAUG
----...((((...((((((((((.....))))).))))).(((.((((.....)))))))...((((......)))).........))))................ ( -29.40)
>DroSec_CAF1 9529 103 + 1
----UGGGGUGAAGGCUUCCGGUGUCAGUCACCGGGAAGUGGGCACACACUAGUUGUGCCCACAUGAAAUUUUCGGCGAAAAACGAAAACCAAGGGCUUAUAAAAUG
----........((((((((((((.....)))))))).(((((((((.......)))))))))......((((((........))))))......))))........ ( -36.70)
>DroSim_CAF1 9538 102 + 1
----UGGGGUGAAGGCUUCCGGUGUCAGUCACCGGGAAGUGGGCACACACUAGUUGUGCCCACAUGAAAUUUUCGGCGAA-AACGAAAACCAAGGGCUUAUAAAAUG
----........((((((((((((.....)))))))).(((((((((.......)))))))))......((((((.....-..))))))......))))........ ( -36.40)
>DroEre_CAF1 8584 107 + 1
GCCCCCCGCAGAAGGCUUCCGGUGUCAGUCGUCAGGAAGUGGGCACACACUAGUUGUGGCGACAUGGCAUUUUCUACGGAAGACGAAUACCGAAGGUUUAGAAAAUG
((.....))...((((((.(((((((((((((((.((((((......))))..)).))))))).)))).(((((....))))).....)))).))))))........ ( -34.50)
>DroYak_CAF1 11199 104 + 1
---CCAUGCAUAAGGCUUUCGGUGUCAGUCACCAGGAAGUGGGCACACACUAGUUGUGCCGAUAUGGCGUUUUCGCCGAAAAAGGAUUAUCAAAGAUUUAGAUAAUG
---((.........((((((((((.....)))).)))))).((((((.......))))))....(((((....))))).....))((((((.........)))))). ( -30.90)
>consensus
____UGGGGUGAAGGCUUCCGGUGUCAGUCACCGGGAAGUGGGCACACACUAGUUGUGCCCACAUGGCAUUUUCGGCGAAAAACGAAUACCAAGGGUUUAGAAAAUG
.......(.((((((.((((((((.....)))))))).(((((((((.......)))))))))......)))))).).............................. (-20.78 = -21.74 +   0.96)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,755,946 – 21,756,049
Length 103
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 81.98
Mean single sequence MFE -29.26
Consensus MFE -17.64
Energy contribution -19.08
Covariance contribution 1.44
Combinations/Pair 1.11
Mean z-score -1.91
Structure conservation index 0.60
SVM decision value 0.19
SVM RNA-class probability 0.625980
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21755946 103 - 22407834
CAUUUUCUAAACCCUUGGUAUUUGUUUUUUGACGAAAAUGCCAUGUGGCCACAACUAGUGUGUGCCCACUUCUCGGUGACUGACACCGGAAGCCUUCACCCCA----
...............(((((((((((....)))))..))))))((.(((((((.....)))).)))))((((.(((((.....)))))))))...........---- ( -28.40)
>DroSec_CAF1 9529 103 - 1
CAUUUUAUAAGCCCUUGGUUUUCGUUUUUCGCCGAAAAUUUCAUGUGGGCACAACUAGUGUGUGCCCACUUCCCGGUGACUGACACCGGAAGCCUUCACCCCA----
................((((((((((..(((((((.....))..(((((((((.(....)))))))))).....)))))..)))...))))))).........---- ( -32.80)
>DroSim_CAF1 9538 102 - 1
CAUUUUAUAAGCCCUUGGUUUUCGUU-UUCGCCGAAAAUUUCAUGUGGGCACAACUAGUGUGUGCCCACUUCCCGGUGACUGACACCGGAAGCCUUCACCCCA----
..........((....((((((((..-.....))))))))....(((((((((.(....))))))))))...((((((.....))))))..))..........---- ( -31.60)
>DroEre_CAF1 8584 107 - 1
CAUUUUCUAAACCUUCGGUAUUCGUCUUCCGUAGAAAAUGCCAUGUCGCCACAACUAGUGUGUGCCCACUUCCUGACGACUGACACCGGAAGCCUUCUGCGGGGGGC
..........(((...)))....(((((((((((((....((.((((((((((.....)))).)).((.....))......))))..)).....))))))))))))) ( -28.60)
>DroYak_CAF1 11199 104 - 1
CAUUAUCUAAAUCUUUGAUAAUCCUUUUUCGGCGAAAACGCCAUAUCGGCACAACUAGUGUGUGCCCACUUCCUGGUGACUGACACCGAAAGCCUUAUGCAUGG---
.((((((.........))))))....((((((((....)))).....((((((.(....)))))))........((((.....))))))))((.....))....--- ( -24.90)
>consensus
CAUUUUCUAAACCCUUGGUAUUCGUUUUUCGCCGAAAAUGCCAUGUGGGCACAACUAGUGUGUGCCCACUUCCCGGUGACUGACACCGGAAGCCUUCACCCCA____
................(((.........................(((((((((.(....))))))))))...((((((.....))))))..)))............. (-17.64 = -19.08 +   1.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,755,979 – 21,756,083
Length 104
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 79.80
Mean single sequence MFE -27.78
Consensus MFE -13.89
Energy contribution -16.17
Covariance contribution 2.28
Combinations/Pair 1.16
Mean z-score -2.79
Structure conservation index 0.50
SVM decision value 1.91
SVM RNA-class probability 0.982191
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21755979 104 + 22407834
AGUGGGCACACACUAGUUGUGGCCACAUGGCAUUUUCGUCAAAAAACAAAUACCAAGGGUUUAGAAAAUGCAACAUUUCUUAAACCAAAAG-----UUUUCAGUUUUUA-
.((((.((((.......)))).)))).((((......))))((((((....((....((((((..(((((...)))))..))))))....)-----).....)))))).- ( -26.50)
>DroSec_CAF1 9562 104 + 1
AGUGGGCACACACUAGUUGUGCCCACAUGAAAUUUUCGGCGAAAAACGAAAACCAAGGGCUUAUAAAAUGCAUAAUUUUUUAAACCAAAAG-----UUUUCAGAAUUUA-
.(((((((((.......))))))))).(((((((((((........)))))).....((.(((.(((((.....))))).))).)).....-----.))))).......- ( -28.30)
>DroSim_CAF1 9571 103 + 1
AGUGGGCACACACUAGUUGUGCCCACAUGAAAUUUUCGGCGAA-AACGAAAACCAAGGGCUUAUAAAAUGCAUAAUUUUUUAAACCAAAAG-----UUUUCAGAAUUUA-
.(((((((((.......))))))))).(((((((((((.....-..)))))).....((.(((.(((((.....))))).))).)).....-----.))))).......- ( -28.00)
>DroEre_CAF1 8621 109 + 1
AGUGGGCACACACUAGUUGUGGCGACAUGGCAUUUUCUACGGAAGACGAAUACCGAAGGUUUAGAAAAUGCUUAGUUUGUAAAACCGAAAGUUCCGUUUUCAGAAUUUC-
.((.(.((((.......)))).).))..((((((((((((....).((.....))......)))))))))))...((((.(((((.((....)).))))))))).....- ( -26.30)
>DroYak_CAF1 11233 110 + 1
AGUGGGCACACACUAGUUGUGCCGAUAUGGCGUUUUCGCCGAAAAAGGAUUAUCAAAGAUUUAGAUAAUGCAAUGGUUAUAAAACCGAAAGCUCCGUUUUCAGAAAUACC
.((.((((((.......)))))).))..((((....))))(((((.((((((((.........))))).((..(((((....)))))...))))).)))))......... ( -29.80)
>consensus
AGUGGGCACACACUAGUUGUGCCCACAUGGCAUUUUCGGCGAAAAACGAAUACCAAGGGUUUAGAAAAUGCAUAAUUUUUUAAACCAAAAG_____UUUUCAGAAUUUA_
.(((((((((.......)))))))))..............(((((............(((((((.((((.....)))).)))))))..........)))))......... (-13.89 = -16.17 +   2.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,755,979 – 21,756,083
Length 104
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 79.80
Mean single sequence MFE -29.06
Consensus MFE -13.30
Energy contribution -15.42
Covariance contribution 2.12
Combinations/Pair 1.14
Mean z-score -3.18
Structure conservation index 0.46
SVM decision value 2.48
SVM RNA-class probability 0.994453
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21755979 104 - 22407834
-UAAAAACUGAAAA-----CUUUUGGUUUAAGAAAUGUUGCAUUUUCUAAACCCUUGGUAUUUGUUUUUUGACGAAAAUGCCAUGUGGCCACAACUAGUGUGUGCCCACU
-.............-----.....((((((..(((((...)))))..))))))..(((((((((((....)))))..)))))).((((.((((.(....))))).)))). ( -26.40)
>DroSec_CAF1 9562 104 - 1
-UAAAUUCUGAAAA-----CUUUUGGUUUAAAAAAUUAUGCAUUUUAUAAGCCCUUGGUUUUCGUUUUUCGCCGAAAAUUUCAUGUGGGCACAACUAGUGUGUGCCCACU
-........(((((-----((...((((((.(((((.....))))).))))))...))))))).....................(((((((((.(....)))))))))). ( -31.00)
>DroSim_CAF1 9571 103 - 1
-UAAAUUCUGAAAA-----CUUUUGGUUUAAAAAAUUAUGCAUUUUAUAAGCCCUUGGUUUUCGUU-UUCGCCGAAAAUUUCAUGUGGGCACAACUAGUGUGUGCCCACU
-........(((((-----((...((((((.(((((.....))))).))))))...)))))))(((-(((...)))))).....(((((((((.(....)))))))))). ( -31.70)
>DroEre_CAF1 8621 109 - 1
-GAAAUUCUGAAAACGGAACUUUCGGUUUUACAAACUAAGCAUUUUCUAAACCUUCGGUAUUCGUCUUCCGUAGAAAAUGCCAUGUCGCCACAACUAGUGUGUGCCCACU
-(((((((((....))))).))))((.............((((((((((......((.....)).......))))))))))......((((((.....)))).))))... ( -24.12)
>DroYak_CAF1 11233 110 - 1
GGUAUUUCUGAAAACGGAGCUUUCGGUUUUAUAACCAUUGCAUUAUCUAAAUCUUUGAUAAUCCUUUUUCGGCGAAAACGCCAUAUCGGCACAACUAGUGUGUGCCCACU
(((((....(((((.(((((..(.((((....)))))..)).(((((.........)))))))).)))))((((....)))))))))((((((.(....))))))).... ( -32.10)
>consensus
_UAAAUUCUGAAAA_____CUUUUGGUUUAAAAAAUUAUGCAUUUUCUAAACCCUUGGUAUUCGUUUUUCGCCGAAAAUGCCAUGUGGGCACAACUAGUGUGUGCCCACU
........................((((((.(((((.....))))).))))))...............................(((((((((.(....)))))))))). (-13.30 = -15.42 +   2.12)

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 12:42:57 2006