Locus 7397

Sequence ID	2L_DroMel_CAF1
Location	20,573,346 – 20,573,509
Length	163
Max. P	0.990086

overview

Window 2

Location	20,573,346 – 20,573,447
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.23
Mean single sequence MFE	-35.65
Consensus MFE	-20.58
Energy contribution	-20.08
Covariance contribution	-0.50
Combinations/Pair	1.25
Mean z-score	-2.74
Structure conservation index	0.58
SVM decision value	1.80
SVM RNA-class probability	0.977606
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20573346 101 + 22407834
CAAAUUU-GCUGAGACUGCAGAUUGUCUGCAGG--GUGCUCCAUCUAUGGC-AGCAUCUGUCAGCC--------GGGGACAGCUUGGCCAUAUGUCUCGGCCAUACAUCACGU-------
.......-(((((((((((((.....)))))((--((((((((....))).-)))))))((((((.--------(....).)).)))).....))))))))............------- ( -39.40)
>DroPse_CAF1 133102 91 + 1
CAAAUUUAGCUGAGACUGCAGAUUAUCUGCAGAAUGUGUUCAAUCUAUGGCCGGCAUCUGUCG----------------------GGCCAUAUGUCUCGGCCAUAUAUCACGU-------
........(((((((((((((.....)))))).............((((((((((....))).----------------------)))))))..)))))))............------- ( -33.80)
>DroEre_CAF1 80054 99 + 1
CAAAUGU-GCUGAGACUGCAGAUUGUCGGCAGA--GUGCUCCAUCCAUGGC-GGCAUCUGUCAGGC---------GGGACA-CUUGGCCAUAUGUGCCGGCCAUACAUCACGU-------
...((((-(.((.(((........)))((((((--.(((((((....))).-)))))))))).(((---------.((.((-(..........))))).)))...)).)))))------- ( -35.40)
>DroYak_CAF1 82495 109 + 1
CAAAUUU-GCUGAGACUGCAGAUUGUCUGCAGA--GUGCUCCAUCUAUGGC-AGCAUCUGUCAGCUUGGCAGCCGGGGACAGCCUGGCCAUAUGUCUUGGCCAUACAUCACGU-------
.......-(((((.(((((((.....)))))).--((((((((....))).-))))).).))))).((((.((((((.....))))))((.......))))))..........------- ( -40.00)
>DroAna_CAF1 80434 108 + 1
UAAAUUU-GCUGAGACUGCAGAUUAUCUGCAGA--AUGUUCAAUCUACGGC-AGCAUCUGUCAGCC--------GGAGACAACUUGGCCAUAUGUCUUGGCCAUACAUCAAGCCAGAAAC
.....((-(((((((((((((.....)))))).--........))).))))-))..((((.(....--------(....)....((((((.......))))))........).))))... ( -31.50)
>DroPer_CAF1 139011 91 + 1
CAAAUUUAGCUGAGACUGCAGAUUAUCUGCAGAAUGUGUUCAAUCUAUGGCCGGCAUCUGUCG----------------------GGCCAUAUGUCUCGGCCAUAUAUCACGU-------
........(((((((((((((.....)))))).............((((((((((....))).----------------------)))))))..)))))))............------- ( -33.80)
>consensus
CAAAUUU_GCUGAGACUGCAGAUUAUCUGCAGA__GUGCUCAAUCUAUGGC_AGCAUCUGUCAGCC_________GGGACA_CUUGGCCAUAUGUCUCGGCCAUACAUCACGU_______
........(((((((((((((.....)))))((..(((((............)))))...))...............................))))))))................... (-20.58 = -20.08 +  -0.50)

alignment

secondary structure

dotplot

Window 3

Location	20,573,346 – 20,573,447
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.23
Mean single sequence MFE	-32.47
Consensus MFE	-18.92
Energy contribution	-19.17
Covariance contribution	0.25
Combinations/Pair	1.17
Mean z-score	-1.89
Structure conservation index	0.58
SVM decision value	0.65
SVM RNA-class probability	0.810367
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20573346 101 - 22407834
-------ACGUGAUGUAUGGCCGAGACAUAUGGCCAAGCUGUCCCC--------GGCUGACAGAUGCU-GCCAUAGAUGGAGCAC--CCUGCAGACAAUCUGCAGUCUCAGC-AAAUUUG
-------.((.(((((.((((((.......)))))).)).)))..)--------)(((((....((((-.(((....))))))).--.((((((.....))))))..)))))-....... ( -34.60)
>DroPse_CAF1 133102 91 - 1
-------ACGUGAUAUAUGGCCGAGACAUAUGGCC----------------------CGACAGAUGCCGGCCAUAGAUUGAACACAUUCUGCAGAUAAUCUGCAGUCUCAGCUAAAUUUG
-------..........((((.(((((.(((((((----------------------.(.(....)).)))))))..............(((((.....)))))))))).))))...... ( -30.20)
>DroEre_CAF1 80054 99 - 1
-------ACGUGAUGUAUGGCCGGCACAUAUGGCCAAG-UGUCCC---------GCCUGACAGAUGCC-GCCAUGGAUGGAGCAC--UCUGCCGACAAUCUGCAGUCUCAGC-ACAUUUG
-------..(((((.((((((.((((....((..((.(-((...)---------)).)).))..))))-)))))).)).(((...--.((((.(.....).)))).)))..)-))..... ( -28.10)
>DroYak_CAF1 82495 109 - 1
-------ACGUGAUGUAUGGCCAAGACAUAUGGCCAGGCUGUCCCCGGCUGCCAAGCUGACAGAUGCU-GCCAUAGAUGGAGCAC--UCUGCAGACAAUCUGCAGUCUCAGC-AAAUUUG
-------..........((((((.......))))))(((.((.....)).)))..(((((.((.((((-.(((....))))))))--)((((((.....))))))..)))))-....... ( -39.10)
>DroAna_CAF1 80434 108 - 1
GUUUCUGGCUUGAUGUAUGGCCAAGACAUAUGGCCAAGUUGUCUCC--------GGCUGACAGAUGCU-GCCGUAGAUUGAACAU--UCUGCAGAUAAUCUGCAGUCUCAGC-AAAUUUA
((((((((...((((..((((((.......))))))...))))...--------(((((.(((((.((-((...(((........--)))))))...)))))))))))))).-))))... ( -32.60)
>DroPer_CAF1 139011 91 - 1
-------ACGUGAUAUAUGGCCGAGACAUAUGGCC----------------------CGACAGAUGCCGGCCAUAGAUUGAACACAUUCUGCAGAUAAUCUGCAGUCUCAGCUAAAUUUG
-------..........((((.(((((.(((((((----------------------.(.(....)).)))))))..............(((((.....)))))))))).))))...... ( -30.20)
>consensus
_______ACGUGAUGUAUGGCCGAGACAUAUGGCCAAG_UGUCCC_________GGCUGACAGAUGCC_GCCAUAGAUGGAACAC__UCUGCAGACAAUCUGCAGUCUCAGC_AAAUUUG
...................((.(((((.((((((...................................))))))..............(((((.....)))))))))).))........ (-18.92 = -19.17 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	20,573,383 – 20,573,474
Length	91
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	75.18
Mean single sequence MFE	-32.89
Consensus MFE	-14.57
Energy contribution	-15.91
Covariance contribution	1.34
Combinations/Pair	1.09
Mean z-score	-2.22
Structure conservation index	0.44
SVM decision value	0.93
SVM RNA-class probability	0.884945
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20573383 91 + 22407834
CCAUCUAUGGCAGCAUCUGUCAGCC--------GGGGACAGCUUGGCCAUAUGUCUCGGCCAUACAUCACGU-------ACACAUAGUAUCU----UUGUGUGUACUGGC---------
(((..((((((.((((..((((((.--------(....).)).))))...))))....))))))......((-------((((((((.....----))))))))))))).--------- ( -31.80)
>DroSec_CAF1 88140 89 + 1
CCAUCUAUGGCAGCAUCUGUCAGCC--------GGGGACAGCUUGGCCAUAUGUCUCGGCCAUACAUCACGU-------ACACAUAGUAUCU------GUGUGUGCUGGC---------
(((..((((((.((((..((((((.--------(....).)).))))...))))....))))))......((-------((((((((...))------))))))))))).--------- ( -32.10)
>DroSim_CAF1 88815 89 + 1
CCAUCUAUGGCAGCAUCUGUCAGCC--------GGGGACAGCUUGGCCAUAUGUCUCGGCCAUACAUCACGU-------ACACAUAGUAUCU------GUGUGUACUGGC---------
(((..((((((.((((..((((((.--------(....).)).))))...))))....))))))......((-------((((((((...))------))))))))))).--------- ( -32.10)
>DroEre_CAF1 80091 93 + 1
CCAUCCAUGGCGGCAUCUGUCAGGC---------GGGACA-CUUGGCCAUAUGUGCCGGCCAUACAUCACGU-------ACAUAUGGUAUGUAUGUACUGCUGUACUGGC---------
(((....)))((((((.(((..(((---------.((...-.)).)))))).))))))((((((((.((.((-------((((((.....)))))))))).)))).))))--------- ( -32.80)
>DroYak_CAF1 82532 98 + 1
CCAUCUAUGGCAGCAUCUGUCAGCUUGGCAGCCGGGGACAGCCUGGCCAUAUGUCUUGGCCAUACAUCACGU-------AUAUG-----UGUAUGUACGGGUGUGCUGGC---------
(((....((((((...))))))...)))..(((((.(.((.((((((((.......))))))(((((((((.-------...))-----)).))))).)).))).)))))--------- ( -37.10)
>DroAna_CAF1 80471 101 + 1
CAAUCUACGGCAGCAUCUGUCAGCC--------GGAGACAACUUGGCCAUAUGUCUUGGCCAUACAUCAAGCCAGAAACAUACAUAGCACU--------G--GCACUGGCUACGAGGCU
........(((((...)))))((((--------((.((.....((((((.......))))))....))..(((((..............))--------)--)).))))))........ ( -31.44)
>consensus
CCAUCUAUGGCAGCAUCUGUCAGCC________GGGGACAGCUUGGCCAUAUGUCUCGGCCAUACAUCACGU_______ACACAUAGUAUCU______GGGUGUACUGGC_________
.....((((((.....(((((..((........)).)))))....)))))).......(((((((((.................................))))).))))......... (-14.57 = -15.91 +   1.34)

alignment

secondary structure

dotplot

Window 5

Location	20,573,414 – 20,573,509
Length	95
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	76.15
Mean single sequence MFE	-29.90
Consensus MFE	-14.18
Energy contribution	-14.26
Covariance contribution	0.09
Combinations/Pair	1.37
Mean z-score	-2.87
Structure conservation index	0.47
SVM decision value	2.20
SVM RNA-class probability	0.990086
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20573414 95 + 22407834
AGCUUGGCCAUAUGUCUCGGCCAUACAUCACGUACACAUAGUAUCU----UUGUGUGUACUGGCCACACCCCUUGCGAAAGUAAACAGAAAGCGCUAUU
.(((((((((((((.......))))......((((((((((.....----))))))))))))))).......((((....)))).....))))...... ( -30.00)
>DroSec_CAF1 88171 93 + 1
AGCUUGGCCAUAUGUCUCGGCCAUACAUCACGUACACAUAGUAUCU------GUGUGUGCUGGCCACACCCCCUGCGAAAGUAAACAGAAAGCGCUAUU
.(((((((((((((.......))))......((((((((((...))------)))))))))))))........(((....)))......))))...... ( -29.40)
>DroSim_CAF1 88846 93 + 1
AGCUUGGCCAUAUGUCUCGGCCAUACAUCACGUACACAUAGUAUCU------GUGUGUACUGGCCACACCCCCUGCGAAAGUAAACAGAAAGCGCUAUU
.(((((((((((((.......))))......((((((((((...))------)))))))))))))........(((....)))......))))...... ( -29.40)
>DroEre_CAF1 80121 98 + 1
A-CUUGGCCAUAUGUGCCGGCCAUACAUCACGUACAUAUGGUAUGUAUGUACUGCUGUACUGGCCACACCCGUUGCGAAAGUAAGCGGAAAGCGCUAUU
.-..(((((....(((..(((((((((.((.((((((((.....)))))))))).)))).))))).)))(((((((....)).)))))...).)))).. ( -37.50)
>DroYak_CAF1 82571 93 + 1
AGCCUGGCCAUAUGUCUUGGCCAUACAUCACGUAUAUG-----UGUAUGUACGGGUGUGCUGGCCACACCC-UUGCGAAAGUAAACAGAAAGCGCUAUU
((((((((((.......))))).(((((((((....))-----)).))))).(((((((.....)))))))-((((....))))......)).)))... ( -33.60)
>DroPer_CAF1 139074 72 + 1
-----GGCCAUAUGUCUCGGCCAUAUAUCACGUUCCU-------------U-----GGCCUGUC----CUCGAGGCGAAGGCAAACAAAUAGCGCAAUU
-----((((.........)))).........((((((-------------(-----.((((...----....)))).))))..)))............. ( -19.50)
>consensus
AGCUUGGCCAUAUGUCUCGGCCAUACAUCACGUACACAUAGUAUCU______GUGUGUACUGGCCACACCCCUUGCGAAAGUAAACAGAAAGCGCUAUU
......((....(((...(((((........((((((.................)))))))))))........(((....))).)))....))...... (-14.18 = -14.26 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:44 2006