Locus 5113

Sequence ID 3R_DroMel_CAF1
Location 13,470,992 – 13,471,122
Length 130
Max. P 0.887335
window8336 window8337 window8338 window8339

overview

Window 6

Location 13,470,992 – 13,471,088
Length 96
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 80.61
Mean single sequence MFE -21.47
Consensus MFE -18.17
Energy contribution -18.17
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.85
SVM decision value 0.61
SVM RNA-class probability 0.799212
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13470992 96 + 27905053
UUUA-AAAAGAAAC-------UAAAAUAAAA-CAGGAAGCUUUAUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCU
....-.........-------..........-..((.(((......((((.(((((((.......))))))).)))).....))).(((....)))...)).... ( -22.80)
>DroSec_CAF1 20900 96 + 1
UUUA-AAUCUAAAA-------UAAAACAAAA-AAGAAAGUUUUACUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCU
....-.........-------((((((....-......))))))..((((.(((((((.......))))))).))))...(((.(((((....))).)).))).. ( -19.50)
>DroSim_CAF1 20306 96 + 1
CUUA-AAUCUAAAC-------UAAAACAAAA-AAUAAAGUUUUACUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCU
....-.........-------((((((....-......))))))..((((.(((((((.......))))))).))))...(((.(((((....))).)).))).. ( -19.30)
>DroYak_CAF1 22977 103 + 1
UUAA-AGAAUGAUCAUCCAUCAAUCAUAAAA-AAAACAAUUGUCCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCU
....-.((.((((.....)))).))......-........(((...((((.(((((((.......))))))).)))).))).(((.....)))............ ( -21.30)
>DroAna_CAF1 23379 102 + 1
UUUGCAAUGGAAAU-UCCA--AAAAAUAAAAUAAAAAAGUCCCUAUGGAGAUGCGGGGUAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCU
(((((..(((....-.)))--......................(((((((((((((((.......)))))))..)))).))))....)))))............. ( -24.80)
>DroPer_CAF1 26223 88 + 1
UUUA-AAAAUAAA-----------AGCACAA-UA----UUAACUUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCU
....-........-----------(((((((-..----......)))(((((((((((.......)))))))..))))...)))).(((....)))......... ( -21.10)
>consensus
UUUA_AAAAUAAAC_______UAAAACAAAA_AAAAAAGUUUUACUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCU
..............................................((((.(((((((.......))))))).))))...(((.(((((....))).)).))).. (-18.17 = -18.17 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,470,992 – 13,471,088
Length 96
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 80.61
Mean single sequence MFE -26.28
Consensus MFE -21.73
Energy contribution -21.73
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.09
Structure conservation index 0.83
SVM decision value -0.01
SVM RNA-class probability 0.529160
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13470992 96 - 27905053
AGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAUAAAGCUUCCUG-UUUUAUUUUA-------GUUUCUUUU-UAAA
.....((.((((....)))).))...((.(((((.(((((.......))))).)))))))(((((((.....)-))))))....-------.........-.... ( -25.40)
>DroSec_CAF1 20900 96 - 1
AGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGUAAAACUUUCUU-UUUUGUUUUA-------UUUUAGAUU-UAAA
.....((.((((....)))).))...((.(((((.(((((.......))))).)))))))(((((((......-....))))))-------)........-.... ( -24.80)
>DroSim_CAF1 20306 96 - 1
AGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGUAAAACUUUAUU-UUUUGUUUUA-------GUUUAGAUU-UAAG
.....((.((((....)))).))...((.(((((.(((((.......))))).))))))).((((((......-....))))))-------.........-.... ( -24.00)
>DroYak_CAF1 22977 103 - 1
AGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGGACAAUUGUUUU-UUUUAUGAUUGAUGGAUGAUCAUUCU-UUAA
.((((((.((((....))))..(((.((.(((((.(((((.......))))).)))))))...((((..(...-....)..)))))))....))))))..-.... ( -26.90)
>DroAna_CAF1 23379 102 - 1
AGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUACCCCGCAUCUCCAUAGGGACUUUUUUAUUUUAUUUUU--UGGA-AUUUCCAUUGCAAA
........((((....)))).(((((((.(((((.(((((.......))))).)))))))))((((.((((..(........).--.)))-).))))..)))... ( -28.60)
>DroPer_CAF1 26223 88 - 1
AGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAGUUAA----UA-UUGUGCU-----------UUUAUUUU-UAAA
.((..(((((((((....(((((...((.(((((.(((((.......))))).)))))))..)))))----..-..)))).-----------)))))..)-)... ( -28.00)
>consensus
AGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGUAAAACUUUCUU_UUUUAUUUUA_______GUUUAUAUU_UAAA
.....((.((((....)))).))...((.(((((.(((((.......))))).)))))))............................................. (-21.73 = -21.73 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,471,021 – 13,471,122
Length 101
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 80.30
Mean single sequence MFE -30.17
Consensus MFE -23.70
Energy contribution -23.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.79
SVM decision value 0.95
SVM RNA-class probability 0.887335
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13471021 101 + 27905053
----GCUUU--AUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCCCUUAGUGAUUCAUUCGCGGG
----((((.--..(((((((((((((.......)))))))..)))).))....))))....((((........))))........(((...((((.....))))))) ( -31.80)
>DroPse_CAF1 29492 101 + 1
----UUAAC--UUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAUGUGUAUUUUCGCUCGUCCA
----.....--...((((.(((((((.......))))))).))))..........((((((((((........))))(((((......))))).....))))))... ( -33.40)
>DroWil_CAF1 21806 97 + 1
----CUUCCAAUUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUCUUG------CAUUCCGGCG
----...((.....((((.(((((((.......))))))).))))..........(((((.((((........))))..........))))------).....)).. ( -25.70)
>DroYak_CAF1 23013 101 + 1
----AUUGU--CCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCUCCUAAUCCAAACUCCCCGGA
----....(--((.((((.(((((((.......)))))))...((((.(((.(((((....))).)).))).))))......................))))..))) ( -26.50)
>DroMoj_CAF1 19398 99 + 1
CGAACUGUA--UUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCAAUUGGUAC------CGCAGA
((....(((--(.(((((.(((((((.......))))))).))).)).))))....)).((((((........)))).......((....))...------.))... ( -30.20)
>DroPer_CAF1 26244 101 + 1
----UUAAC--UUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGUGUGUAUUUCCGCUCGUCCA
----.....--...((((.(((((((.......))))))).))))..........((((((((((........))))(((((......))))).....))))))... ( -33.40)
>consensus
____CUUAC__UUUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCACUUGGUUCU_CAUUCGCGCA
..............((((.(((((((.......))))))).)))).....(((.....)))((((........)))).............................. (-23.70 = -23.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,471,021 – 13,471,122
Length 101
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 80.30
Mean single sequence MFE -34.48
Consensus MFE -32.92
Energy contribution -32.92
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.33
Structure conservation index 0.95
SVM decision value 0.47
SVM RNA-class probability 0.747856
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13471021 101 - 27905053
CCCGCGAAUGAAUCACUAAGGGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAU--AAAGC----
...((((.....)).......((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))...--...))---- ( -32.90)
>DroPse_CAF1 29492 101 - 1
UGGACGAGCGAAAAUACACAUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAA--GUUAA----
.((.((((((....(((.(((.(((......)))..))))))...))))))))((((...((.(((((.(((((.......))))).)))))))..--)))).---- ( -35.70)
>DroWil_CAF1 21806 97 - 1
CGCCGGAAUG------CAAGAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAAUUGGAAG----
.((......)------)....((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))..........---- ( -33.80)
>DroYak_CAF1 23013 101 - 1
UCCGGGGAGUUUGGAUUAGGAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGG--ACAAU----
(((((.....)))))......((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))...--.....---- ( -35.10)
>DroMoj_CAF1 19398 99 - 1
UCUGCG------GUACCAAUUGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAA--UACAGUUCG
.(((.(------....)..((((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))))).--..))).... ( -35.20)
>DroPer_CAF1 26244 101 - 1
UGGACGAGCGGAAAUACACACGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAA--GUUAA----
.((.(((((.....((((........))))((((........)))))))))))((((...((.(((((.(((((.......))))).)))))))..--)))).---- ( -34.20)
>consensus
UCCGCGAACG_AAAAACAAGAGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAAA__GAAAA____
.....................((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).............. (-32.92 = -32.92 +  -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 11:46:34 2006