Locus 1111

Sequence ID 3L_DroMel_CAF1
Location 3,250,335 – 3,250,542
Length 207
Max. P 0.981539
window1717 window1718 window1719 window1720 window1721 window1722

overview

Window 7

Location 3,250,335 – 3,250,442
Length 107
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 89.06
Mean single sequence MFE -27.55
Consensus MFE -24.95
Energy contribution -25.20
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.91
SVM decision value 1.24
SVM RNA-class probability 0.935206
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3250335 107 + 23771897
CUCGGUUAACGCUAACAGUCUGUCAUCGGUCAUUGUUUUGUUUUUCUUUUUUUC--CCUCCCCAUUUUGGCCCACUCGGAGUGUUUGGGCCAUGCGUGAGCCAAAUAAC
...((((.((((.(((((((((....)))..)))))).................--...........(((((((..(.....)..))))))).)))).))))....... ( -26.90)
>DroSec_CAF1 29195 98 + 1
CUCAGUUAACGCAAACCGUCUGUCAUCGGUCAUUGUUUUGUUU-------UUUC----CCCCCAUUUUGGCCCACUCAGAGUGUUUGGGCCAUGCGUGAGCCAAAUAAC
....(((.(((((.((((........)))).............-------....----.........(((((((..(.....)..)))))))))))).)))........ ( -25.40)
>DroSim_CAF1 32058 100 + 1
CUCGGUUAACGCAAACCGUCUGUCAUCGGUCAUUGUUUUGUUUUU-----UUUC----CCCCCAUUUUGGCCCACUCAGAGUGUUUGGGCCAUGCGUGAGCCAAAUAAC
...((((.(((((.((((........))))...............-----....----.........(((((((..(.....)..)))))))))))).))))....... ( -29.70)
>DroYak_CAF1 30565 104 + 1
CUCGGUUAACGCUAACCGUCUGUCAUCGGUCAUUGUUUUGUUUUU-----UUUUCGUAUUCGUAUUUUGGCCCACUCAAAGUGUUUGGGCCAUGCGUGAGCCAAAUAAC
...((((.((((..((((........))))...............-----.................(((((((..(.....)..))))))).)))).))))....... ( -28.20)
>consensus
CUCGGUUAACGCAAACCGUCUGUCAUCGGUCAUUGUUUUGUUUUU_____UUUC____CCCCCAUUUUGGCCCACUCAGAGUGUUUGGGCCAUGCGUGAGCCAAAUAAC
...((((.((((.....(.(((....))).)....................................(((((((..(.....)..))))))).)))).))))....... (-24.95 = -25.20 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 8

Location 3,250,335 – 3,250,442
Length 107
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 89.06
Mean single sequence MFE -26.40
Consensus MFE -24.91
Energy contribution -24.97
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.52
Structure conservation index 0.94
SVM decision value 0.65
SVM RNA-class probability 0.811093
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3250335 107 - 23771897
GUUAUUUGGCUCACGCAUGGCCCAAACACUCCGAGUGGGCCAAAAUGGGGAGG--GAAAAAAAGAAAAACAAAACAAUGACCGAUGACAGACUGUUAGCGUUAACCGAG
.....(((((((.(.(((((((((..(.....)..)))))))...)).)))).--......................((((...((((.....))))..)))).)))). ( -24.30)
>DroSec_CAF1 29195 98 - 1
GUUAUUUGGCUCACGCAUGGCCCAAACACUCUGAGUGGGCCAAAAUGGGGG----GAAA-------AAACAAAACAAUGACCGAUGACAGACGGUUUGCGUUAACUGAG
.....(..(...((((((((((((..(.....)..))))))).........----....-------............(((((........))))))))))...)..). ( -25.00)
>DroSim_CAF1 32058 100 - 1
GUUAUUUGGCUCACGCAUGGCCCAAACACUCUGAGUGGGCCAAAAUGGGGG----GAAA-----AAAAACAAAACAAUGACCGAUGACAGACGGUUUGCGUUAACCGAG
.....((((...((((((((((((..(.....)..))))))).........----....-----..............(((((........))))))))))...)))). ( -27.50)
>DroYak_CAF1 30565 104 - 1
GUUAUUUGGCUCACGCAUGGCCCAAACACUUUGAGUGGGCCAAAAUACGAAUACGAAAA-----AAAAACAAAACAAUGACCGAUGACAGACGGUUAGCGUUAACCGAG
.....((((...((((.(((((((..(.....)..))))))).................-----.............((((((........))))))))))...)))). ( -28.80)
>consensus
GUUAUUUGGCUCACGCAUGGCCCAAACACUCUGAGUGGGCCAAAAUGGGGA____GAAA_____AAAAACAAAACAAUGACCGAUGACAGACGGUUAGCGUUAACCGAG
.....((((...((((.(((((((..(.....)..)))))))....................................(((((........))))).))))...)))). (-24.91 = -24.97 +   0.06) 

alignment

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secondary structure

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dotplot

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Window 9

Location 3,250,368 – 3,250,477
Length 109
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 75.28
Mean single sequence MFE -32.70
Consensus MFE -16.70
Energy contribution -17.07
Covariance contribution 0.37
Combinations/Pair 1.33
Mean z-score -2.12
Structure conservation index 0.51
SVM decision value 1.15
SVM RNA-class probability 0.923389
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3250368 109 + 23771897
UGUUUUGUUUUUCUUUUUUUC--CCUCCCCAUUUUGGCCCACUCGGAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU-GGGCGAA--AGA
...............((((((--...(((((((.(((((((..(.....).-.)))))))..((((.(((((.............)))))))))...)))).-))).)))--))) ( -30.22)
>DroPse_CAF1 30068 93 + 1
UGGU-UGCUUUU-----UGG-------CCCGUUUCGU---------GGUGUGCUGGGCCAGGCGUGAGCCAAAUAACUUAUGGAAUUGGCCAUGGCCUGUAGAAGGCGAGAAGAA
....-..(((((-----(((-------((.(((((((---------(((.......))).(((....))).........))))))).))))...((((.....)))))))))).. ( -34.10)
>DroSec_CAF1 29228 100 + 1
UGUUUUGUUU-------UUUC----CCCCCAUUUUGGCCCACUCAGAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU-GGGCGAA--AGA
........((-------((((----(((.((((.(((((((..(.....).-.)))))))..((((.(((((.............)))))))))...)))).-))).)))--))) ( -33.12)
>DroSim_CAF1 32091 102 + 1
UGUUUUGUUUUU-----UUUC----CCCCCAUUUUGGCCCACUCAGAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU-GGGCGAA--AGA
..........((-----((((----(((.((((.(((((((..(.....).-.)))))))..((((.(((((.............)))))))))...)))).-))).)))--))) ( -33.12)
>DroYak_CAF1 30598 106 + 1
UGUUUUGUUUUU-----UUUUCGUAUUCGUAUUUUGGCCCACUCAAAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU-GGGCGAA--GCA
.(((((((((..-----..(((.......((((((((((((..(.....).-.))))))).((....)).)))))......)))((((((....))))))..-)))))))--)). ( -31.52)
>DroPer_CAF1 30874 93 + 1
UGGU-UGCUUUU-----UGG-------CCCGUUUCGU---------GGUGUGCUGGGCCAGGCGUGAGCCAAAUAACUUAUGGAAUUGGCCAUGGCCUGUAGAAGGCGAGAAGAA
....-..(((((-----(((-------((.(((((((---------(((.......))).(((....))).........))))))).))))...((((.....)))))))))).. ( -34.10)
>consensus
UGUUUUGUUUUU_____UUUC_____CCCCAUUUUGGCCCACUCAGAGUGU_UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU_GGGCGAA__AGA
...(((((((...................((((((((.....)))))))).....(((((((.....(((((.............))))))))))))......)))))))..... (-16.70 = -17.07 +   0.37) 

alignment

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secondary structure

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dotplot

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Window 0

Location 3,250,368 – 3,250,477
Length 109
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 75.28
Mean single sequence MFE -27.46
Consensus MFE -11.89
Energy contribution -13.50
Covariance contribution 1.61
Combinations/Pair 1.12
Mean z-score -2.68
Structure conservation index 0.43
SVM decision value 1.89
SVM RNA-class probability 0.981539
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3250368 109 - 23771897
UCU--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAAGUUAUUUGGCUCACGCAUGGCCCAA-ACACUCCGAGUGGGCCAAAAUGGGGAGG--GAAAAAAAGAAAAACAAAACA
(((--(((.(((-(...((.....((((((.............))))))....))(((((((.-.(.....)..)))))))...))))))))--))................... ( -31.32)
>DroPse_CAF1 30068 93 - 1
UUCUUCUCGCCUUCUACAGGCCAUGGCCAAUUCCAUAAGUUAUUUGGCUCACGCCUGGCCCAGCACACC---------ACGAAACGGG-------CCA-----AAAAGCA-ACCA
........((.......((((...((((((.............))))))...))))(((((........---------.......)))-------)).-----....)).-.... ( -24.08)
>DroSec_CAF1 29228 100 - 1
UCU--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAAGUUAUUUGGCUCACGCAUGGCCCAA-ACACUCUGAGUGGGCCAAAAUGGGGG----GAAA-------AAACAAAACA
..(--(((.(((-.((((......((((((.............))))))......(((((((.-.(.....)..))))))).))))))).----))))-------.......... ( -31.72)
>DroSim_CAF1 32091 102 - 1
UCU--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAAGUUAUUUGGCUCACGCAUGGCCCAA-ACACUCUGAGUGGGCCAAAAUGGGGG----GAAA-----AAAAACAAAACA
..(--(((.(((-.((((......((((((.............))))))......(((((((.-.(.....)..))))))).))))))).----))))-----............ ( -31.72)
>DroYak_CAF1 30598 106 - 1
UGC--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAAGUUAUUUGGCUCACGCAUGGCCCAA-ACACUUUGAGUGGGCCAAAAUACGAAUACGAAAA-----AAAAACAAAACA
...--((((...-....((.....((((((.............))))))....))(((((((.-.(.....)..)))))))...........))))..-----............ ( -21.82)
>DroPer_CAF1 30874 93 - 1
UUCUUCUCGCCUUCUACAGGCCAUGGCCAAUUCCAUAAGUUAUUUGGCUCACGCCUGGCCCAGCACACC---------ACGAAACGGG-------CCA-----AAAAGCA-ACCA
........((.......((((...((((((.............))))))...))))(((((........---------.......)))-------)).-----....)).-.... ( -24.08)
>consensus
UCC__UUCGCCC_ACAUUGACCAUGGCCAAUUUCUUAAGUUAUUUGGCUCACGCAUGGCCCAA_ACACUCUGAGUGGGCCAAAAUGGGG_____GAAA_____AAAAACAAAACA
.........(((............((((((.............))))))......(((((((............)))))))....)))........................... (-11.89 = -13.50 +   1.61) 

alignment

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secondary structure

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dotplot

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Window 1

Location 3,250,406 – 3,250,506
Length 100
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 74.30
Mean single sequence MFE -23.57
Consensus MFE -12.39
Energy contribution -12.55
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.53
SVM decision value 0.28
SVM RNA-class probability 0.664160
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3250406 100 + 23771897
ACUCGGAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU---GGGCGAAAGAGGAGG-------AAGACCAGCGAAAAAGGCAAACAA
........(((-(((((((..((....))..........((....)))))).(((((.....---...(....)......-------..)))))..........)))))). ( -25.29)
>DroSec_CAF1 29257 80 + 1
ACUCAGAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU---GGGCGAAAGAGGAGG-------AAGA--------------------
.(((....(.(-((.(.((((((....))...............((((((....))))))))---)).).))).).))).-------....-------------------- ( -21.00)
>DroSim_CAF1 32122 80 + 1
ACUCAGAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU---GGGCGAAAGAGGAGG-------AAGA--------------------
.(((....(.(-((.(.((((((....))...............((((((....))))))))---)).).))).).))).-------....-------------------- ( -21.00)
>DroEre_CAF1 29736 90 + 1
-------GUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCACUGU---GGGCGAAGCAGCAGG-------AAGACCGGCGAAAGAGGCAA---C
-------((.(-((..(((....(((.(((((.............))))))))((((.((((---..((...)).)))).-------..)))))))...))).))..---. ( -26.62)
>DroYak_CAF1 30633 97 + 1
ACUCAAAGUGU-UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU---GGGCGAAGCAGAAGG-------AAGAGCAGCGAAAAAGGCAG---C
..((....(((-((.(.((((((....))...............((((((....))))))))---)).).)))))....)-------)...((.((.......)).)---) ( -24.00)
>DroAna_CAF1 30465 97 + 1
------AGUGUGUUGGGGCAUGCGUGAGCCAAAUAACUUAUAAAAUUGGCCAUGGUCGAAACAAAAGGCUAAA--GGAGGGCUCCCCAAAA------CAAAAGGCAAACUA
------..(((.((((((...(((((.(((((.............))))))))((((.........))))...--.....)).)))))).)------))............ ( -23.52)
>consensus
ACUCAGAGUGU_UUGGGCCAUGCGUGAGCCAAAUAACUUAAGAAAUUGGCCAUGGUCAAUGU___GGGCGAAAGAGGAGG_______AAGA______AAAAAGGCAA____
...............(((((((.....(((((.............))))))))))))...................................................... (-12.39 = -12.55 +   0.17) 

alignment

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secondary structure

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dotplot

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Window 2

Location 3,250,442 – 3,250,542
Length 100
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 68.13
Mean single sequence MFE -20.63
Consensus MFE -7.08
Energy contribution -7.67
Covariance contribution 0.59
Combinations/Pair 1.38
Mean z-score -1.92
Structure conservation index 0.34
SVM decision value 0.44
SVM RNA-class probability 0.737941
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3250442 100 - 23771897
UGCACCUGCAAUUCCCCCAGUUGGCCGGCCAGGUGUUUGUUUGCCUUUUUCGCUGGUCUUCCUCCUCU--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAA
(((....)))........(((((((((((.(((((......))))).....)))((((..........--.......-.....))))..))))))))...... ( -22.85)
>DroPse_CAF1 30123 89 - 1
UGC-CUUCCAAUUCUUUCACUUGGCCAGCUGUGUG----UUGGCCACGUUC---------CCUCUUUCUUCUCGCCUUCUACAGGCCAUGGCCAAUUCCAUAA
.((-(.............((.((((((((.....)----))))))).))..---------.............((((.....))))...)))........... ( -23.20)
>DroSec_CAF1 29293 79 - 1
UGCACCUGCAAUUCCCCCAGUUGGCCUGCCAGGUG---------------------UCUUCCUCCUCU--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAA
(((....)))........((((((((((...((((---------------------(...........--.......-)))))...)).))))))))...... ( -14.87)
>DroSim_CAF1 32158 79 - 1
UGCACCUGCAAUUCCCCCAGUUGGCCUGCCAGGUG---------------------UCUUCCUCCUCU--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAA
(((....)))........((((((((((...((((---------------------(...........--.......-)))))...)).))))))))...... ( -14.87)
>DroEre_CAF1 29765 85 - 1
------------UUGGCCAGCCUGGUAGCCAGGUGUG---UUGCCUCUUUCGCCGGUCUUCCUGCUGC--UUCGCCC-ACAGUGACCAUGGCCAAUUUCUUAA
------------(((((((((((((...))))))...---..............((((...(((..((--...))..-.))).)))).)))))))........ ( -26.80)
>DroYak_CAF1 30669 97 - 1
UGCACCUGCAAUUCCCCCAGUUGGCCAGCCAGGUGUG---CUGCCUUUUUCGCUGCUCUUCCUUCUGC--UUCGCCC-ACAUUGACCAUGGCCAAUUUCUUAA
(((....)))........(((((((((..((((((.(---(.((.......)).((..........))--...)).)-)).)))....)))))))))...... ( -21.20)
>consensus
UGCACCUGCAAUUCCCCCAGUUGGCCAGCCAGGUG_____UUGCCU_UUUC_____UCUUCCUCCUCC__UUCGCCC_ACAUUGACCAUGGCCAAUUUCUUAA
..................(((((((((....((((............................................)))).....)))))))))...... ( -7.08 =  -7.67 +   0.59) 

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 09:59:19 2006