Locus 968

Sequence ID 2L_DroMel_CAF1
Location 2,796,358 – 2,796,528
Length 170
Max. P 0.874954
window1552 window1553 window1554

overview

Window 2

Location 2,796,358 – 2,796,456
Length 98
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 77.72
Mean single sequence MFE -23.72
Consensus MFE -9.16
Energy contribution -9.88
Covariance contribution 0.72
Combinations/Pair 1.11
Mean z-score -2.14
Structure conservation index 0.39
SVM decision value 0.76
SVM RNA-class probability 0.843561
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2796358 98 - 22407834
GGGCAAAAAAAAAAAAAAAAAC--AGUGCCACGAAAU---------GCUGGCAGAAUGACAAAAGUGUGGCAACUGGCGCAUACAAUAUUUGUGACCUUCUUGUGCCUU
(((((................(--(((((((((...(---------..((.........))..).)))))).)))).((((.........)))).........))))). ( -21.90)
>DroSec_CAF1 19462 77 - 1
G---------------------UGAGUGCCACGAAAA---------GCUGGCAUAAUGACAAAAAUGU--CAGUUGCCACAUACAAUAUUUGUGACCUUCUUGUGCCUU
.---------------------.(((.((.((((.((---------(.(((((...(((((....)))--))..)))))..((((.....))))..))).))))))))) ( -19.80)
>DroSim_CAF1 20416 100 - 1
GAGCAAAAAAAAAAAAAAAAACUGAGUGCCACGAAAA---------GCUGGCAGAAUGACAAAAAUGUGGCAACUGGCGCAUACAAUAUUUGUGACCUUCUUGUGCCUU
..........................((((((.....---------).)))))...............((((...((((((.........)))).))......)))).. ( -17.20)
>DroEre_CAF1 19594 95 - 1
GGGCAAAAAACAAGUA--UAA--GAGUGGCACGAAAA---------GCUGGCAGAAUGACAAAAA-GUAGCAACUGCCGCAUACAAUAUUUGUGACCUUCUUAUGCCUU
.............(((--(((--(((.((((((((..---------((.(((((....((.....-)).....)))))))........)))))).)))))))))))... ( -24.30)
>DroYak_CAF1 18763 100 - 1
GGGCAAA-----AGCA--UAG--GAGUGGCACGAAAAGCUGGAAAAGCUGGCAGAAUGACAAAAAUGUGGCAAGUGCCGCAUACAAUAUUUGUGACCUUCUUAUGCCUU
.......-----.(((--(((--(((.((((((((..((..(.....)..))............(((((((....)))))))......)))))).)))))))))))... ( -35.40)
>consensus
GGGCAAAAAA_AAAAA__AAA__GAGUGCCACGAAAA_________GCUGGCAGAAUGACAAAAAUGUGGCAACUGCCGCAUACAAUAUUUGUGACCUUCUUGUGCCUU
(((((....................((((((...............(....)......((......))......)))))).((((.....)))).........))))). ( -9.16 =  -9.88 +   0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,796,421 – 2,796,528
Length 107
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 79.82
Mean single sequence MFE -36.48
Consensus MFE -20.42
Energy contribution -21.30
Covariance contribution 0.88
Combinations/Pair 1.12
Mean z-score -2.14
Structure conservation index 0.56
SVM decision value 0.37
SVM RNA-class probability 0.709791
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2796421 107 + 22407834
---AUUUCGUGGCACU--GUUUUUUUUUUUUUUUUUGCCCACGGGUCAACGGGGCGUAUGGGUGUGCUGGUUAUUUUGCGGUGCCCACUUGUCUGGGCAC-CAAGAAGUGGCA
---.......(((((.--.................(((((.((......))))))).......))))).((((((((..((((((((......)))))))-)..)))))))). ( -37.81)
>DroSec_CAF1 19523 89 + 1
---UUUUCGUGGCACUCA---------------------CACGGGUCAACGGGGCGUAUGGGUGUGCUGGUUAUUUUGCGGUGCCCACUUGUCUCGGCCAAAAAGAAGUGGCA
---..((((((.......---------------------))))))....(((((((..((((..(((..........)).)..))))..)))))))((((........)))). ( -31.20)
>DroEre_CAF1 19656 105 + 1
---UUUUCGUGCCACUC--UUA--UACUUGUUUUUUGCCCACGGGUCAACGGGGCGUAUGAGUGUUCUGGUUAUUUUGUGGUGCCCACUUGUCUGGGCCC-AAAGAAGUGGCA
---......((((((((--(((--((((..(....(((((.((......))))))).)..))))).............(((.(((((......)))))))-)))).))))))) ( -40.70)
>DroYak_CAF1 18832 103 + 1
AGCUUUUCGUGCCACUC--CUA--UGCU-----UUUGCCCACGGGUCAACGGGGCGUAUGAGUGUGCUGGUUAUUUUACGGUGCCCACUUGUCUGGCCCC-AAAGAAGUGGCA
.........(((((((.--((.--....-----.(((((....)).))).(((((..(..((((.(((.((......)).).)).))))..)...)))))-..)).))))))) ( -36.20)
>consensus
___UUUUCGUGCCACUC__UUA__U_CU_____UUUGCCCACGGGUCAACGGGGCGUAUGAGUGUGCUGGUUAUUUUGCGGUGCCCACUUGUCUGGGCCC_AAAGAAGUGGCA
.........(((((((....................((((.((......))))))(.(..((((.(((.((......)).).)).))))..)).............))))))) (-20.42 = -21.30 +   0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,796,421 – 2,796,528
Length 107
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 79.82
Mean single sequence MFE -29.23
Consensus MFE -17.80
Energy contribution -19.80
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.61
SVM decision value 0.89
SVM RNA-class probability 0.874954
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2796421 107 - 22407834
UGCCACUUCUUG-GUGCCCAGACAAGUGGGCACCGCAAAAUAACCAGCACACCCAUACGCCCCGUUGACCCGUGGGCAAAAAAAAAAAAAAAAAC--AGUGCCACGAAAU---
((.((((....(-(((((((......))))))))........................((((((......)).))))..................--)))).))......--- ( -29.10)
>DroSec_CAF1 19523 89 - 1
UGCCACUUCUUUUUGGCCGAGACAAGUGGGCACCGCAAAAUAACCAGCACACCCAUACGCCCCGUUGACCCGUG---------------------UGAGUGCCACGAAAA---
...(((((.((((.....)))).)))))(((((((((...((((..((..........))...)))).....))---------------------)).))))).......--- ( -19.70)
>DroEre_CAF1 19656 105 - 1
UGCCACUUCUUU-GGGCCCAGACAAGUGGGCACCACAAAAUAACCAGAACACUCAUACGCCCCGUUGACCCGUGGGCAAAAAACAAGUA--UAA--GAGUGGCACGAAAA---
(((((((.((((-(((((((......))))).))).......................((((((......)).))))............--.))--))))))))......--- ( -33.50)
>DroYak_CAF1 18832 103 - 1
UGCCACUUCUUU-GGGGCCAGACAAGUGGGCACCGUAAAAUAACCAGCACACUCAUACGCCCCGUUGACCCGUGGGCAAA-----AGCA--UAG--GAGUGGCACGAAAAGCU
((((((((((..-(((((......((((.((...((......))..)).)))).....))))).(((.((....))))).-----....--.))--))))))))......... ( -34.60)
>consensus
UGCCACUUCUUU_GGGCCCAGACAAGUGGGCACCGCAAAAUAACCAGCACACCCAUACGCCCCGUUGACCCGUGGGCAAA_____AG_A__UAA__GAGUGCCACGAAAA___
((((((((.......(((((......)))))...........................((((((......)).))))...................))))))))......... (-17.80 = -19.80 +   2.00)

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 09:49:54 2006