Locus 5070

Sequence ID 2R_DroMel_CAF1
Location 16,465,187 – 16,465,324
Length 137
Max. P 0.970744
window8105 window8106 window8107

overview

Window 5

Location 16,465,187 – 16,465,284
Length 97
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 76.00
Mean single sequence MFE -20.60
Consensus MFE -11.97
Energy contribution -12.22
Covariance contribution 0.25
Combinations/Pair 1.25
Mean z-score -2.09
Structure conservation index 0.58
SVM decision value 1.40
SVM RNA-class probability 0.949965
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16465187 97 + 20766785
U--UUUUCAC-UUUUUGUGCCA-GGCCAUACUUUUCCCUGCUUUUUUAUUCCCUGUCAACAAACAGCAUCGAAAUUGAGCGAAUCGCUCAAUCAGAUGUGA
.--.......-..(((((..((-((..(((................)))..))))...)))))..(((((...((((((((...))))))))..))))).. ( -20.99)
>DroSec_CAF1 140470 96 + 1
UCAUUU----UUUUUUUUGCCA-GGCGAUACUUUUCCCUGCUUUUUUAUUCCCUGUCAACAAACAGCAUUGAAAUUGAGCGAAUCGCUCAAUCAAAUGUGA
......----..(((.(((.((-((.((((................)))).)))).))).)))..(((((...((((((((...))))))))..))))).. ( -19.39)
>DroSim_CAF1 137215 100 + 1
UCAUUUUCAUUUUUUUGUGCCA-GGCAAUACUUUUCCCUGCUUUUUUAUUCCCUGUCAACAAACAACAUCGAAAUUGAGCGAAUCGCUCAAUCAGAUGUGA
.............(((((..((-((.((((................)))).))))...)))))..(((((...((((((((...))))))))..))))).. ( -22.39)
>DroEre_CAF1 141740 86 + 1
--------AU-UUUCUGUACCA-GGCGAUACUUUUCCCUCUUUUUU-----GCUGUCAGCAAACAGCAUCGAAAUUGAGCGAAGCGCUCAAUCAGAUGUGA
--------..-...((((...(-((.((......))))).....((-----((.....))))))))((((...((((((((...))))))))..))))... ( -21.90)
>DroYak_CAF1 142263 95 + 1
UU----GGAU-UUUCUGUAGCA-GGCGAUACUUUUCCCUCUUUUUUUUGUCCCUGUCAACAAACAACAUCGAAAUUGAGCGAAUCGCUCAAUCAGAUGUGA
..----((((-.......((.(-((.((......))))))).......)))).............(((((...((((((((...))))))))..))))).. ( -23.84)
>DroPer_CAF1 174794 76 + 1
------------UUUUGUGCGAUUGCGAUACUUUU------------UUCCCCCGUCAACA-ACAGCGGCAAAAUCGGGCAAAUCGCUCAAUCAAAACUGA
------------..(((.((((((((((.......------------.))..((((.....-...)))).........)).)))))).))).......... ( -15.10)
>consensus
U_______AU_UUUUUGUGCCA_GGCGAUACUUUUCCCUGCUUUUUUAUUCCCUGUCAACAAACAGCAUCGAAAUUGAGCGAAUCGCUCAAUCAGAUGUGA
.................................................................(((((...(((((((.....)))))))..))))).. (-11.97 = -12.22 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,465,187 – 16,465,284
Length 97
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 76.00
Mean single sequence MFE -23.56
Consensus MFE -15.28
Energy contribution -15.07
Covariance contribution -0.22
Combinations/Pair 1.35
Mean z-score -2.07
Structure conservation index 0.65
SVM decision value 1.66
SVM RNA-class probability 0.970744
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16465187 97 - 20766785
UCACAUCUGAUUGAGCGAUUCGCUCAAUUUCGAUGCUGUUUGUUGACAGGGAAUAAAAAAGCAGGGAAAAGUAUGGCC-UGGCACAAAAA-GUGAAAA--A
(((((((.(((((((((...)))))))))..))).(((((....)))))...........((.(((..(....)..))-).)).......-))))...--. ( -24.40)
>DroSec_CAF1 140470 96 - 1
UCACAUUUGAUUGAGCGAUUCGCUCAAUUUCAAUGCUGUUUGUUGACAGGGAAUAAAAAAGCAGGGAAAAGUAUCGCC-UGGCAAAAAAAA----AAAUGA
...((((((((((((((...)))))))))....(.(((((....))))).)..........((((((......)).))-))..........----))))). ( -22.20)
>DroSim_CAF1 137215 100 - 1
UCACAUCUGAUUGAGCGAUUCGCUCAAUUUCGAUGUUGUUUGUUGACAGGGAAUAAAAAAGCAGGGAAAAGUAUUGCC-UGGCACAAAAAAAUGAAAAUGA
..(((((.(((((((((...)))))))))..)))))..(((((...((((.((((................)))).))-))..)))))............. ( -24.99)
>DroEre_CAF1 141740 86 - 1
UCACAUCUGAUUGAGCGCUUCGCUCAAUUUCGAUGCUGUUUGCUGACAGC-----AAAAAAGAGGGAAAAGUAUCGCC-UGGUACAGAAA-AU--------
((...((((((((((((...)))))))))....(((((((....))))))-----)....)))..))...(((((...-.))))).....-..-------- ( -24.90)
>DroYak_CAF1 142263 95 - 1
UCACAUCUGAUUGAGCGAUUCGCUCAAUUUCGAUGUUGUUUGUUGACAGGGACAAAAAAAAGAGGGAAAAGUAUCGCC-UGCUACAGAAA-AUCC----AA
..(((((.(((((((((...)))))))))..)))))..(((((.(.((((((.....................)).))-))).)))))..-....----.. ( -22.60)
>DroPer_CAF1 174794 76 - 1
UCAGUUUUGAUUGAGCGAUUUGCCCGAUUUUGCCGCUGU-UGUUGACGGGGGAA------------AAAAGUAUCGCAAUCGCACAAAA------------
(((((....)))))((((((.((...(((((.((.((((-(...))))).))..------------.)))))...))))))))......------------ ( -22.30)
>consensus
UCACAUCUGAUUGAGCGAUUCGCUCAAUUUCGAUGCUGUUUGUUGACAGGGAAUAAAAAAGCAGGGAAAAGUAUCGCC_UGGCACAAAAA_AU_______A
...((((.(((((((((...)))))))))..))))(((((....)))))..........................((....)).................. (-15.28 = -15.07 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,465,216 – 16,465,324
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 80.80
Mean single sequence MFE -22.28
Consensus MFE -14.07
Energy contribution -14.60
Covariance contribution 0.53
Combinations/Pair 1.21
Mean z-score -1.50
Structure conservation index 0.63
SVM decision value 0.01
SVM RNA-class probability 0.537081
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16465216 108 + 20766785
UUCCCUGCUUUUUUAUUCCCUGUCAACAAACAGCAUCGAAAUUGAGCGAAUCGCUCAAUCAGAUGUGAAGUGUUUGAAAGCGUUUCACAACUGAAAUCAAAUCGUAUG
...................((((......))))((((((..(((((((...)))))))((((.(((((((((((....))))))))))).)))).......))).))) ( -27.00)
>DroPse_CAF1 173877 94 + 1
UU------------UUCCCCCGUCAACA-ACAGCGGCAAAAUCGGGCAAAUCGCUCAAUCAAAACUGAAGUGUUUGAAAGCAU-UCUCAACCGAAAUCAAAUUGUACG
..------------......((((((..-....(((.......((((.....)))).........(((((((((....)))))-).))).)))........))).))) ( -13.84)
>DroSec_CAF1 140498 108 + 1
UUCCCUGCUUUUUUAUUCCCUGUCAACAAACAGCAUUGAAAUUGAGCGAAUCGCUCAAUCAAAUGUGAAGUGUUUGAAAGCGUUUCACAACUCAAAUCAAAUCGUAUG
.....(((...........((((......))))..((((.((((((((...))))))))....(((((((((((....))))))))))).......))))...))).. ( -21.90)
>DroEre_CAF1 141763 103 + 1
UUCCCUCUUUUUU-----GCUGUCAGCAAACAGCAUCGAAAUUGAGCGAAGCGCUCAAUCAGAUGUGAAGUGUUUGAAAGCGUUUCACAACUGAAAUCAAAUCGUAUG
............(-----(((((......)))))).(((..(((((((...)))))))((((.(((((((((((....))))))))))).)))).......))).... ( -30.80)
>DroYak_CAF1 142290 108 + 1
UUCCCUCUUUUUUUUGUCCCUGUCAACAAACAACAUCGAAAUUGAGCGAAUCGCUCAAUCAGAUGUGAAGUGUUUGAAAGCGUUUCACAACUGAAAUCAAAUCGUAUG
............(((((........)))))...((((((..(((((((...)))))))((((.(((((((((((....))))))))))).)))).......))).))) ( -26.30)
>DroPer_CAF1 174815 94 + 1
UU------------UUCCCCCGUCAACA-ACAGCGGCAAAAUCGGGCAAAUCGCUCAAUCAAAACUGAAGUGUUUGAAAGCAU-UCUCAACCGAAAUCAAAUUGUACG
..------------......((((((..-....(((.......((((.....)))).........(((((((((....)))))-).))).)))........))).))) ( -13.84)
>consensus
UUCCCU__UUUUU_UUUCCCUGUCAACAAACAGCAUCGAAAUUGAGCGAAUCGCUCAAUCAAAUGUGAAGUGUUUGAAAGCGUUUCACAACUGAAAUCAAAUCGUAUG
.................................((((((.(((((((.....)))))))....(((((((((((....)))))))))))............))).))) (-14.07 = -14.60 +   0.53)

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 11:35:46 2006