Locus 8714

Sequence ID	3L_DroMel_CAF1
Location	22,639,661 – 22,639,812
Length	151
Max. P	0.934341

overview

Window 6

Location	22,639,661 – 22,639,760
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.10
Mean single sequence MFE	-35.15
Consensus MFE	-23.31
Energy contribution	-23.40
Covariance contribution	0.09
Combinations/Pair	1.19
Mean z-score	-2.47
Structure conservation index	0.66
SVM decision value	1.24
SVM RNA-class probability	0.934341
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22639661 99 + 23771897
G------ACAAACACCGAGCUG--------------GUAUUUUAAAUUCAAUGAUGCGGCAGGCGGUAAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCGAAAG-GACGCCAACU
(------(((........((((--------------.((((...........))))))))(((((.....))))).....)))).......(((((((((((.....))-)).))))))) ( -31.30)
>DroSec_CAF1 8456 99 + 1
G------ACACACACCGAGCUG--------------GUAUUUUGAAUUCAAUGAUGCGGCAGGCGGUCAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCGAAAG-GACACCAGCC
.------...........((((--------------((.(((((((.(((((....((((((((((((((.....)))))))))))).))..)))))....))))))).-...)))))). ( -37.20)
>DroSim_CAF1 6849 99 + 1
G------ACACACACCGAGCUG--------------GUAUUUUGAAUUCAAUGAUGCGGCAGGCGGUCAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCGAAAG-GACACCAGCC
.------...........((((--------------((.(((((((.(((((....((((((((((((((.....)))))))))))).))..)))))....))))))).-...)))))). ( -37.20)
>DroEre_CAF1 5125 83 + 1
------------------------------------AUAUUUUGAAUUCAAUGAUGCGGCAGGCGGUCAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCAGAAG-GACACCAGCC
------------------------------------....................((((((((((((((.....)))))))))))).))..(((((.((((.....))-))..))))). ( -29.50)
>DroYak_CAF1 17279 99 + 1
G------ACACACACCAAGCUGC-------------AUAUUUUGAACUCAAUGAUGCGGCAGGCGGUCAACGCCUUCGACUGUCUGCACGAAGUUGGCUCCUUUAAAAG-GACACCAGC-
(------(((........(((((-------------((...(((....)))..)))))))(((((.....))))).....))))........(((((.((((.....))-))..)))))- ( -32.50)
>DroPer_CAF1 5628 119 + 1
GGGACACAUACACACAGAGCUGGACACUCUGCUGGGGUAUUUUGAAUUCAAUGAUGCAGCAAGCGGUCAACGCCUUUGACUGCUUGCAAGCAGCCGGCUCCUUCAAAAGGGACACCACC-
((..............(((((((.....(((((...((((((((....))).))))).((((((((((((.....)))))))))))).))))))))))))........((....)).))- ( -43.20)
>consensus
G______ACACACACCGAGCUG______________GUAUUUUGAAUUCAAUGAUGCGGCAGGCGGUCAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCAAAAG_GACACCAGCC
.......................................(((((((.(((((....((((((((((((((.....)))))))))))).))..)))))....)))))))............ (-23.31 = -23.40 +   0.09)

alignment

secondary structure

dotplot

Window 7

Location	22,639,681 – 22,639,791
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.16
Mean single sequence MFE	-40.83
Consensus MFE	-22.29
Energy contribution	-23.65
Covariance contribution	1.36
Combinations/Pair	1.13
Mean z-score	-2.52
Structure conservation index	0.55
SVM decision value	0.53
SVM RNA-class probability	0.773072
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22639681 110 + 23771897
UUUAAAUUCAAUGAUGCGGCAGGCGGUAAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCGAAAG-GACGCCAACUCGGCCAGCUGGUGAAAAAAACC---------GGCGAGACC
......(((......((.(((((((((...........))))))))).(((.((((((((((.....))-)).)))))))))))..((((((.......)))---------))))))... ( -42.70)
>DroPse_CAF1 5614 111 + 1
UUUGAAUUCAAUGAUGCAGCAAGCGGUCAACGCCUUUGACUGCUUGCAAGCAGCCGGCUCCUUCAAAAGGGACACCACC--GGGCA------CAAA-AAACCAGGCUCUCGGCCGAGGCA
...........((.(((.((((((((((((.....))))))))))))......((((.((((......)))).....))--)))))------))..-...((.(((.....)))..)).. ( -38.10)
>DroSim_CAF1 6869 109 + 1
UUUGAAUUCAAUGAUGCGGCAGGCGGUCAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCGAAAG-GACACCAGCCCGGCCAGCUGGUGAAA-AAACC---------GGCGAGACC
......(((.......((((((((((((((.....)))))))))))).))..(((((.((((.....))-))(((((((.......)))))))...-...))---------))))))... ( -41.90)
>DroEre_CAF1 5129 109 + 1
UUUGAAUUCAAUGAUGCGGCAGGCGGUCAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCAGAAG-GACACCAGCCCGGCCAGCUGGUGAAA-AAACA---------GCCGAGACC
................((((((((((((((.....)))))))))))).))...(((((((((.....))-))(((((((.......)))))))...-.....---------))))).... ( -41.70)
>DroYak_CAF1 17300 108 + 1
UUUGAACUCAAUGAUGCGGCAGGCGGUCAACGCCUUCGACUGUCUGCACGAAGUUGGCUCCUUUAAAAG-GACACCAGC-CGGCCAGCUGGUGAAA-AAACU---------GCCGAGACC
......(((.......((((((((((((.........)))))))))).)).....(((((((.....))-))(((((((-......)))))))...-.....---------))))))... ( -41.50)
>DroPer_CAF1 5668 111 + 1
UUUGAAUUCAAUGAUGCAGCAAGCGGUCAACGCCUUUGACUGCUUGCAAGCAGCCGGCUCCUUCAAAAGGGACACCACC--GGGGA------CAAA-AAACCAGGCUCUCGGCCGAGGCA
..............(((.((((((((((((.....))))))))))))..)))(((((.((((......))))..)).((--(((..------(...-.......)..)))))....))). ( -39.10)
>consensus
UUUGAAUUCAAUGAUGCGGCAGGCGGUCAACGCCUUUGACUGUCUGCACGAAGUUGGCUCCUUCAAAAG_GACACCAGC_CGGCCAGCUGGUGAAA_AAACC_________GCCGAGACC
......(((.........((((((((((((.....))))))))))))....((((((((......................)))))))).........................)))... (-22.29 = -23.65 +   1.36)

alignment

secondary structure

dotplot

Window 8

Location	22,639,721 – 22,639,812
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	93.14
Mean single sequence MFE	-33.18
Consensus MFE	-26.38
Energy contribution	-27.30
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-1.86
Structure conservation index	0.80
SVM decision value	0.85
SVM RNA-class probability	0.865716
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22639721 91 + 23771897
UGUCUGCACGAAGUUGGCUCCUUCGAAAGGACGCCAACUCGGCCAGCUGGUGAAAAAAACCGGCGAGACCGUGCGGAAGCAACUGUGCCGU
..(((((((((.((((((((((.....)))).))))))))(((..((((((.......))))))..).))))))))).(((....)))... ( -40.70)
>DroSec_CAF1 8516 90 + 1
UGUCUGCACGAAGUUGGCUCCUUCGAAAGGACACCAGCCCGGCCAGCUGGUGAAA-AAACCGGCGAGACCGUGCGGAAGCAACUGUGCCGU
..(((((((...(((((.((((.....))))..)))))..(((..((((((....-..))))))..).))))))))).(((....)))... ( -34.80)
>DroSim_CAF1 6909 90 + 1
UGUCUGCACGAAGUUGGCUCCUUCGAAAGGACACCAGCCCGGCCAGCUGGUGAAA-AAACCGGCGAGACCGUGCGGAAGCAACUGUGCCGU
..(((((((...(((((.((((.....))))..)))))..(((..((((((....-..))))))..).))))))))).(((....)))... ( -34.80)
>DroEre_CAF1 5169 90 + 1
UGUCUGCACGAAGUUGGCUCCUUCAGAAGGACACCAGCCCGGCCAGCUGGUGAAA-AAACAGCCGAGACCAUGCGGAAGCAACUAUGCCGU
..((((((.(...(((((((((.....))))(((((((.......)))))))...-.....)))))...).)))))).(((....)))... ( -30.00)
>DroYak_CAF1 17340 89 + 1
UGUCUGCACGAAGUUGGCUCCUUUAAAAGGACACCAGC-CGGCCAGCUGGUGAAA-AAACUGCCGAGACCAUGAGGAAGCAACUAUGCCGU
.((.(((......(((((((((.....))))(((((((-......)))))))...-.....)))))..((....))..)))))........ ( -25.60)
>consensus
UGUCUGCACGAAGUUGGCUCCUUCGAAAGGACACCAGCCCGGCCAGCUGGUGAAA_AAACCGGCGAGACCGUGCGGAAGCAACUGUGCCGU
..(((((((...(((((.((((.....))))..)))))..(((..((((((.......))))))..).))))))))).(((....)))... (-26.38 = -27.30 +   0.92)

alignment

secondary structure

dotplot

Window 9

Location	22,639,721 – 22,639,812
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	93.14
Mean single sequence MFE	-32.96
Consensus MFE	-26.66
Energy contribution	-26.90
Covariance contribution	0.24
Combinations/Pair	1.17
Mean z-score	-1.53
Structure conservation index	0.81
SVM decision value	0.36
SVM RNA-class probability	0.705464
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22639721 91 - 23771897
ACGGCACAGUUGCUUCCGCACGGUCUCGCCGGUUUUUUUCACCAGCUGGCCGAGUUGGCGUCCUUUCGAAGGAGCCAACUUCGUGCAGACA
..((((....))))((.((((((((..((.(((.......))).)).))))((((((((.((((.....)))))))))))).)))).)).. ( -35.70)
>DroSec_CAF1 8516 90 - 1
ACGGCACAGUUGCUUCCGCACGGUCUCGCCGGUUU-UUUCACCAGCUGGCCGGGCUGGUGUCCUUUCGAAGGAGCCAACUUCGUGCAGACA
...((((((((((...(((.((((((.(((((((.-.......))))))).)))))))))((((.....))))).)))))..))))..... ( -33.40)
>DroSim_CAF1 6909 90 - 1
ACGGCACAGUUGCUUCCGCACGGUCUCGCCGGUUU-UUUCACCAGCUGGCCGGGCUGGUGUCCUUUCGAAGGAGCCAACUUCGUGCAGACA
...((((((((((...(((.((((((.(((((((.-.......))))))).)))))))))((((.....))))).)))))..))))..... ( -33.40)
>DroEre_CAF1 5169 90 - 1
ACGGCAUAGUUGCUUCCGCAUGGUCUCGGCUGUUU-UUUCACCAGCUGGCCGGGCUGGUGUCCUUCUGAAGGAGCCAACUUCGUGCAGACA
..((((....))))((.((((((....((((.(((-(..((((((((.....)))))))).......)))).))))....)))))).)).. ( -32.50)
>DroYak_CAF1 17340 89 - 1
ACGGCAUAGUUGCUUCCUCAUGGUCUCGGCAGUUU-UUUCACCAGCUGGCCG-GCUGGUGUCCUUUUAAAGGAGCCAACUUCGUGCAGACA
..((((....))))..(((((((....(((.....-...((((((((....)-)))))))((((.....)))))))....))))).))... ( -29.80)
>consensus
ACGGCACAGUUGCUUCCGCACGGUCUCGCCGGUUU_UUUCACCAGCUGGCCGGGCUGGUGUCCUUUCGAAGGAGCCAACUUCGUGCAGACA
...(((((((((.((((...(((.....)))........((((((((.....))))))))..........)))).)))))..))))..... (-26.66 = -26.90 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:57 2006