Locus 7938

Sequence ID	3R_DroMel_CAF1
Location	21,303,225 – 21,303,400
Length	175
Max. P	0.933984

overview

Window 8

Location	21,303,225 – 21,303,324
Length	99
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	75.03
Mean single sequence MFE	-47.57
Consensus MFE	-22.26
Energy contribution	-23.27
Covariance contribution	1.00
Combinations/Pair	1.32
Mean z-score	-1.97
Structure conservation index	0.47
SVM decision value	0.52
SVM RNA-class probability	0.766760
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21303225 99 + 27905053
---GGCGGAAUGCCA---CCCAUGGGAGGUA---CACCGCCGCGACCGGGAAUGAUGCCCGGAAUGCCUCCGGGUGCAAUGCAACCCGGCGGACCCAUGCAGCCCAGU
---(((((..((((.---((....)).))))---..)))))(((.(((((.......)))))....((.((((((((...)).)))))).)).....)))........ ( -46.40)
>DroVir_CAF1 4935 102 + 1
CCUACGGGCAUGCAG---CCUAUGGGCGGCC---CCGGACCGAGACCCGGCUUAAUGAGCGGCAUGCCACCGGGCGGAAUGCCGUCCGUAGGUCAACUGCCUGCAGGA
(((.((((((....(---(((((((((((((---((((.(((.....)))..........((....)).)))))......)))))))))))))....)))))).))). ( -51.90)
>DroPse_CAF1 30899 103 + 1
-----CGGCAUGCAACAGCCCAUGGGUGGUGGGGUGCCACCACGUCCUGGCCUGAUGCCGGGCAUGCCACCAGGUGGCAUGUCGCCCGUGGGCCCUAUGCCACCGGGA
-----.(((((((............(((((((....)))))))...(((((.....)))))))))))).((.(((((((((..(((....)))..))))))))).)). ( -59.30)
>DroSec_CAF1 31846 99 + 1
---GGCGGAAUGCCA---CCCAUGGGCGGUA---CGCCGCCGCGACCAGGAAUGAUGCCCGGAAUGCCUCCGGGUGCAAUGCAACCCGGCGGACCCAUGCAGCCCAGU
---(((((..((((.---((....)).))))---..)))))(((....((........))((....((.((((((((...)).)))))).))..)).)))........ ( -42.50)
>DroEre_CAF1 50655 99 + 1
---GGCGGAAUGCCA---CCCAUGGGCGGUG---CUCCGCCGCGACCAGGAAUGAUGCCCGGAAUGCCACCGGGCGCAAUGCAACCCGGCGGACCCAUGCAACCCAGU
---((((((..(((.---((....)).))).---.)))))).((.((.((......((((((.......))))))((...))..)).))))................. ( -41.20)
>DroYak_CAF1 33283 99 + 1
---GGCGGAAUGCCA---CCCAUGGGCGGUA---CUCCGCCGCGACCAGGAAUGAUGCCCGGAAUGCCACCGGGUGCAAUGCAGCCCGGCGGACCCAUGCAACCCAGU
---((((((.((((.---((....)).))))---.))))))(((....((........))((....((.((((((((...))).))))).))..)).)))........ ( -44.10)
>consensus
___GGCGGAAUGCCA___CCCAUGGGCGGUA___CGCCGCCGCGACCAGGAAUGAUGCCCGGAAUGCCACCGGGUGCAAUGCAACCCGGCGGACCCAUGCAACCCAGU
....................((((((((((........)))))..((.((.......)).))....((.((((((........)))))).))..)))))......... (-22.26 = -23.27 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	21,303,225 – 21,303,324
Length	99
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	75.03
Mean single sequence MFE	-50.38
Consensus MFE	-23.75
Energy contribution	-25.67
Covariance contribution	1.92
Combinations/Pair	1.28
Mean z-score	-1.99
Structure conservation index	0.47
SVM decision value	0.59
SVM RNA-class probability	0.790481
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21303225 99 - 27905053
ACUGGGCUGCAUGGGUCCGCCGGGUUGCAUUGCACCCGGAGGCAUUCCGGGCAUCAUUCCCGGUCGCGGCGGUG---UACCUCCCAUGGG---UGGCAUUCCGCC---
((((((.(((.((((.((.((((((.((...)))))))).))...)))).))).....))))))...(((((.(---(.((.((....))---.)).)).)))))--- ( -45.10)
>DroVir_CAF1 4935 102 - 1
UCCUGCAGGCAGUUGACCUACGGACGGCAUUCCGCCCGGUGGCAUGCCGCUCAUUAAGCCGGGUCUCGGUCCGG---GGCCGCCCAUAGG---CUGCAUGCCCGUAGG
.(((((.((((((.(.((((.((.((((.....((((((((((.....)))......)))))))((((...)))---))))).)).))))---).)).)))).))))) ( -46.30)
>DroPse_CAF1 30899 103 - 1
UCCCGGUGGCAUAGGGCCCACGGGCGACAUGCCACCUGGUGGCAUGCCCGGCAUCAGGCCAGGACGUGGUGGCACCCCACCACCCAUGGGCUGUUGCAUGCCG-----
.((.((((((((.(.(((....)))..))))))))).)).(((((((.......(((.(((((..(((((((....))))))))).))).)))..))))))).----- ( -56.30)
>DroSec_CAF1 31846 99 - 1
ACUGGGCUGCAUGGGUCCGCCGGGUUGCAUUGCACCCGGAGGCAUUCCGGGCAUCAUUCCUGGUCGCGGCGGCG---UACCGCCCAUGGG---UGGCAUUCCGCC---
((..((.(((.((((.((.((((((.((...)))))))).))...)))).))).....))..))...(((((.(---(.(((((....))---))).)).)))))--- ( -46.10)
>DroEre_CAF1 50655 99 - 1
ACUGGGUUGCAUGGGUCCGCCGGGUUGCAUUGCGCCCGGUGGCAUUCCGGGCAUCAUUCCUGGUCGCGGCGGAG---CACCGCCCAUGGG---UGGCAUUCCGCC---
((..((.(((.((((.(((((((((.((...)))))))))))...)))).))).....))..))...(((((((---..(((((....))---)))..)))))))--- ( -53.10)
>DroYak_CAF1 33283 99 - 1
ACUGGGUUGCAUGGGUCCGCCGGGCUGCAUUGCACCCGGUGGCAUUCCGGGCAUCAUUCCUGGUCGCGGCGGAG---UACCGCCCAUGGG---UGGCAUUCCGCC---
((..((.(((.((((.((((((((.(((...)))))))))))...)))).))).....))..))...(((((((---(.(((((....))---))).))))))))--- ( -55.40)
>consensus
ACUGGGUUGCAUGGGUCCGCCGGGCUGCAUUGCACCCGGUGGCAUUCCGGGCAUCAUUCCUGGUCGCGGCGGAG___UACCGCCCAUGGG___UGGCAUUCCGCC___
...(((.(((....(.((.((((((........)))))).)))...(((((.......)))))....(((((.......)))))...........))).)))...... (-23.75 = -25.67 +   1.92)

alignment

secondary structure

dotplot

Window 0

Location	21,303,253 – 21,303,361
Length	108
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	79.40
Mean single sequence MFE	-55.60
Consensus MFE	-32.59
Energy contribution	-32.92
Covariance contribution	0.34
Combinations/Pair	1.38
Mean z-score	-2.49
Structure conservation index	0.59
SVM decision value	1.23
SVM RNA-class probability	0.933984
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21303253 108 - 27905053
GGAGCUGCUGCAUCUGCUGUGCCUGCAGCAUGU---GUGGACUGGGCUGCAUGGGUCCGCCGGGUUGCAUUGCACCCGGAGGCAUUCCGGGCAUCAUUCCCGGUCGCGGCG
...(((((.((((.((((((....)))))).))---)).(((((((.(((.((((.((.((((((.((...)))))))).))...)))).))).....)))))))))))). ( -54.60)
>DroVir_CAF1 4966 111 - 1
GCAGCUGCUGCAUUUGCUGCGCCUGCAGUAAAUGCUGUUGUCCUGCAGGCAGUUGACCUACGGACGGCAUUCCGCCCGGUGGCAUGCCGCUCAUUAAGCCGGGUCUCGGUC
.(((((((((((((((((((....)))))))))))(((......)))))))))))......(..((((((.((((...)))).))))))..).....((((.....)))). ( -48.60)
>DroPse_CAF1 30931 111 - 1
GGAGCUGCUGCAUUUGCUGGGCCUGCAGCAUAUGCUGUUGUCCCGGUGGCAUAGGGCCCACGGGCGACAUGCCACCUGGUGGCAUGCCCGGCAUCAGGCCAGGACGUGGUG
.......(((....((((((((..(((((....)))))((((((((((((((.(.(((....)))..))))))))).)).)))).)))))))).)))((((.....)))). ( -53.60)
>DroEre_CAF1 50683 111 - 1
GGAGCUGCUGCAUCUGCUGCGCCUGCAGCAUGUGCUGUGGACUGGGUUGCAUGGGUCCGCCGGGUUGCAUUGCGCCCGGUGGCAUUCCGGGCAUCAUUCCUGGUCGCGGCG
...(((((.((((.((((((....)))))).))))....(((..((.(((.((((.(((((((((.((...)))))))))))...)))).))).....))..)))))))). ( -59.80)
>DroYak_CAF1 33311 111 - 1
GGAGCUGCUGCAUUUGCUGCGCCUGCAGCAUGUGCUGUGGACUGGGUUGCAUGGGUCCGCCGGGCUGCAUUGCACCCGGUGGCAUUCCGGGCAUCAUUCCUGGUCGCGGCG
...(((((.((((.((((((....)))))).))))....(((..((.(((.((((.((((((((.(((...)))))))))))...)))).))).....))..)))))))). ( -60.20)
>DroPer_CAF1 39532 111 - 1
GGAGCUGCUGCAUUUGCUGGGCCUGCAGCAUAUGCUGUUGUCCCGGUGGCAUAGGGCCCACGGGCGACAUGCCACCUGGUGGCAUGCCCGGCAUUAGGCCAGGGCGUGGUG
((..(.((.((((.(((((......))))).)))).)).)..))((((((((.(.(((....)))..)))))))))......((((((((((.....))).)))))))... ( -56.80)
>consensus
GGAGCUGCUGCAUUUGCUGCGCCUGCAGCAUAUGCUGUGGACCGGGUGGCAUGGGUCCGACGGGCGGCAUUCCACCCGGUGGCAUGCCGGGCAUCAUGCCAGGUCGCGGCG
...(((((.((((.((((((....)))))).))))....(((((((........((((..((((..........))))..((....))))))......)))))))))))). (-32.59 = -32.92 +   0.34)

alignment

secondary structure

dotplot

Window 1

Location	21,303,290 – 21,303,400
Length	110
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.31
Mean single sequence MFE	-46.23
Consensus MFE	-26.15
Energy contribution	-25.43
Covariance contribution	-0.72
Combinations/Pair	1.35
Mean z-score	-1.88
Structure conservation index	0.57
SVM decision value	0.68
SVM RNA-class probability	0.821673
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21303290 110 - 27905053
UCC-UGUUUCAUUUGGGUGGCAUUUGUCUGCUUAUCAUGCGGAGCUGCUGCAUCUGCUGUGCCUGCAGCAUGU---GUGGACUGGGCUGCAUGGGUCCGCCGGGUUGCAUUGCA
.((-((.......))))..(((..(((..((((..(((((((..(..(..(((.((((((....)))))).))---)..)...)..)))))))((....)))))).))).))). ( -36.70)
>DroVir_CAF1 5003 105 - 1
------AAUCACUUGGGCGGCAG---UUUGCCCAUCAUGCGCAGCUGCUGCAUUUGCUGCGCCUGCAGUAAAUGCUGUUGUCCUGCAGGCAGUUGACCUACGGACGGCAUUCCG
------........(((.(((((---((.((.(.....).)))))))))(((((((((((....)))))))))))((((((((.(.((((....).))).))))))))).))). ( -41.90)
>DroPse_CAF1 30968 109 - 1
-CA-CUCCUCACUUGGGCGGCAG---CUUGCCCAUCAUGCGGAGCUGCUGCAUUUGCUGGGCCUGCAGCAUAUGCUGUUGUCCCGGUGGCAUAGGGCCCACGGGCGACAUGCCA
-..-..((......))(((((((---(((((.......)).))))))))))....((((((.(.(((((....))))).).))))))(((((.(.(((....)))..)))))). ( -51.10)
>DroSim_CAF1 31961 113 - 1
UCC-CGGUUCAUUUGGGUGGCAUUUGUCUGCCCAUCAUGCGGAGCUGCUGCAUCUGCUGUGCCUGCAGCAUGUGCUGUGGACUGGGCUGCAUGGGUCCGCCGGGUUGCAUUGCA
.((-((((.....((((((((....))).)))))(((((((((((..(.((((.((((((....)))))).)))).)..).))...))))))))....)))))).......... ( -48.90)
>DroYak_CAF1 33348 114 - 1
UCCCCAGUUCAUUUGGGUGGCAUUUGUCUGCCCAUCAUGCGGAGCUGCUGCAUUUGCUGCGCCUGCAGCAUGUGCUGUGGACUGGGUUGCAUGGGUCCGCCGGGCUGCAUUGCA
..(((((.....)))))..(((..(((..((((..((((((((((..(.((((.((((((....)))))).)))).)..).))...)))))))((....)))))).))).))). ( -49.00)
>DroPer_CAF1 39569 109 - 1
-CA-CUUCUCACUUGGGCGGCAG---CUUGCCCAUCAUGCGGAGCUGCUGCAUUUGCUGGGCCUGCAGCAUAUGCUGUUGUCCCGGUGGCAUAGGGCCCACGGGCGACAUGCCA
-..-............(((((((---(((((.......)).))))))))))....((((((.(.(((((....))))).).))))))(((((.(.(((....)))..)))))). ( -49.80)
>consensus
_CC_CGGUUCACUUGGGCGGCAG___UCUGCCCAUCAUGCGGAGCUGCUGCAUUUGCUGCGCCUGCAGCAUAUGCUGUGGACCGGGUGGCAUGGGUCCGACGGGCGGCAUUCCA
.............(((((((.......)))))))..((((...(((((.((((.((((((....)))))).)))).)).((((.(......).)))).....))).)))).... (-26.15 = -25.43 +  -0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:36 2006