Locus 5601

Sequence ID 3L_DroMel_CAF1
Location 15,366,488 – 15,366,631
Length 143
Max. P 0.844337
window8853 window8854 window8855

overview

Window 3

Location 15,366,488 – 15,366,593
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.10
Mean single sequence MFE -29.66
Consensus MFE -19.04
Energy contribution -19.07
Covariance contribution 0.03
Combinations/Pair 1.16
Mean z-score -1.84
Structure conservation index 0.64
SVM decision value 0.76
SVM RNA-class probability 0.844337
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15366488 105 - 23771897
UUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCGACGACACUGAAACU---CGGU------------CGGAAAA
....((((............(((((((.((((((..........))))))...))))))).....((.......)))))).((((.(.......---.)))------------))..... ( -26.90)
>DroVir_CAF1 96342 91 - 1
UUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCCA-ACGAGCCAU---------AUAACU---CGGU------------G----AA
....(((.............(((((((.((((((..........))))))...))))))).........-.((((....---------....))---))))------------)----.. ( -22.50)
>DroPse_CAF1 99170 108 - 1
UUAAUGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCGACGACUCCG---CU---CGAG-----GG-GCCAUGAGCAG
....(((.......(((((.(((((((.((((((..........))))))...)))))))...........(((((.(.((....))))---))---))))-----))-)......))). ( -34.62)
>DroMoj_CAF1 95017 91 - 1
UUAACACGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCCA-ACGAGCCGU---------AUAACU---CGCC------------G----AA
......((............(((((((.((((((..........))))))...))))))).........-.((((....---------....))---)).)------------)----.. ( -19.80)
>DroAna_CAF1 233342 120 - 1
UUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCGACGACACUGAAAUUGGUCGGUUCGAGGGGGGCACGGAAAA
....((.(....(((((((.(((((((.((((((..........))))))...)))))))...........(((((((...(((........)))..))))))))))))))).))..... ( -39.50)
>DroPer_CAF1 98690 108 - 1
UUAAUGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCGACGACUCCG---CU---CGAG-----GG-GCCAUGAGCAG
....(((.......(((((.(((((((.((((((..........))))))...)))))))...........(((((.(.((....))))---))---))))-----))-)......))). ( -34.62)
>consensus
UUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCGACGAC_C_G_AACU___CGGU____________CG___AA
....((((............(((((((.((((((..........))))))...))))))).....((.......))))))........................................ (-19.04 = -19.07 +   0.03)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,366,513 – 15,366,631
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.93
Mean single sequence MFE -27.87
Consensus MFE -21.06
Energy contribution -21.25
Covariance contribution 0.19
Combinations/Pair 1.04
Mean z-score -1.26
Structure conservation index 0.76
SVM decision value 0.31
SVM RNA-class probability 0.682190
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15366513 118 + 23771897
CGCGGCUCGUUUCGCAUUUUACAGUCGCUGGCUCAUUUAUAAAUUUAUGAGCUCAACUGCCAGGGGAGUUAUCGCGUUAAAAUGCUUCGCUGU--UCCCACCGUAUUUUUCCUGGUUUUC
.((((((.((..........))))))))((((((((..........)))))).))...((((((..((.....((((....))))..((.((.--...)).))...))..)))))).... ( -30.40)
>DroVir_CAF1 96355 94 + 1
-AUGGCUCGU-UGGCAUUUUACAGUCGCUGGCUCAUUUAUAAAUUUAUGAGCUCAACUGCCAGGGGAGUUAUCGCGUUAAAAUGCUGCACGCU--CGC----------------------
-...((.(((-((((((((((....(((.(((((((..........))))))).((((.(....).))))...))).)))))))))).)))..--.))---------------------- ( -25.90)
>DroGri_CAF1 97168 92 + 1
-ACGGCUCGU-UGGCAUUUUACAGUCGCUGGCUCAUUUAUAAAUUUAUGAGCUCAACUGCCAGGGGAGUUAUCGCGUUAAAAUGCUGC--GCU--CUG----------------------
-.(((..(((-.(((((((((....(((.(((((((..........))))))).((((.(....).))))...))).)))))))))))--)..--)))---------------------- ( -27.10)
>DroMoj_CAF1 95030 94 + 1
-ACGGCUCGU-UGGCAUUUUACAGUCGCUGGCUCAUUUAUAAAUUUAUGAGCUCAACUGCCAGGGGAGUUAUCGUGUUAAAAUGCUGUGCUCU--CUG----------------------
-..(((..((-(((.......(((...)))((((((..........))))))))))).))).(((((((...(((......)))....)))))--)).---------------------- ( -25.40)
>DroAna_CAF1 233382 118 + 1
CGCGGCUCGUUUCGCAUUUUACAGUCGCUGGCUCAUUUAUAAAUUUAUGAGCUCAACUGCCAGGGGAGUUAUCGCGUUAAAAUGCUUCGCUGUUUUCCCGAUGUACUUUCCUCCGC--CC
.((((((.((..........))))))))((((((((..........)))))).))...((.(((..((((((((.(..(((..((...))..)))..)))))).)))..)))..))--.. ( -31.30)
>DroPer_CAF1 98718 93 + 1
CGCGGCUCGUUUCGCAUUUUACAGUCGCUGGCUCAUUUAUAAAUUUAUGAGCUCAACUGCCAGGGGAGUUAUCGCAUUAAAAAGCUCCGCUGU---------------------------
.((((((.((..........))))))))((((((((..........)))))).)).....(((.((((((............)))))).))).--------------------------- ( -27.10)
>consensus
_ACGGCUCGU_UCGCAUUUUACAGUCGCUGGCUCAUUUAUAAAUUUAUGAGCUCAACUGCCAGGGGAGUUAUCGCGUUAAAAUGCUGCGCUCU__CCC______________________
.............((((((((....(((.(((((((..........))))))).((((.(....).))))...))).))))))))................................... (-21.06 = -21.25 +   0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,366,513 – 15,366,631
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.93
Mean single sequence MFE -26.75
Consensus MFE -19.95
Energy contribution -20.12
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.75
SVM decision value 0.59
SVM RNA-class probability 0.791815
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15366513 118 - 23771897
GAAAACCAGGAAAAAUACGGUGGGA--ACAGCGAAGCAUUUUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCG
.....(((((.......((.((...--.)).))..((........)).........)))))((((((.((((((..........))))))...))))))......(((........))). ( -31.90)
>DroVir_CAF1 96355 94 - 1
----------------------GCG--AGCGUGCAGCAUUUUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCCA-ACGAGCCAU-
----------------------((.--..(((...((((((((.(((..(((((((...)).))))).((((((..........))))))..)))....))))))))..-))).))...- ( -26.30)
>DroGri_CAF1 97168 92 - 1
----------------------CAG--AGC--GCAGCAUUUUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCCA-ACGAGCCGU-
----------------------..(--..(--(..((((((((.(((..(((((((...)).))))).((((((..........))))))..)))....))))))))..-.))..)...- ( -22.30)
>DroMoj_CAF1 95030 94 - 1
----------------------CAG--AGAGCACAGCAUUUUAACACGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCCA-ACGAGCCGU-
----------------------...--.(.((.(.(((((((..((.(........).))(((((((.((((((..........))))))...))))))))))))))..-..).)))..- ( -20.60)
>DroAna_CAF1 233382 118 - 1
GG--GCGGAGGAAAGUACAUCGGGAAAACAGCGAAGCAUUUUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCG
..--((((.(....(((((..((((.....(((...........)))......)))).))(((((((.((((((..........))))))...)))))))....)))....)...)))). ( -32.90)
>DroPer_CAF1 98718 93 - 1
---------------------------ACAGCGGAGCUUUUUAAUGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCGAAACGAGCCGCG
---------------------------.(((.((((................)))).)))(((((((.((((((..........))))))...))))))).....(((........))). ( -26.49)
>consensus
______________________GAG__ACAGCGCAGCAUUUUAACGCGAUAACUCCCCUGGCAGUUGAGCUCAUAAAUUUAUAAAUGAGCCAGCGACUGUAAAAUGCCA_ACGAGCCGC_
...................................(((((((..........(......)(((((((.((((((..........))))))...))))))))))))))............. (-19.95 = -20.12 +   0.17)

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 11:54:24 2006