Locus 3531

Sequence ID	2R_DroMel_CAF1
Location	11,818,024 – 11,818,117
Length	93
Max. P	0.990426

overview

Window 7

Location	11,818,024 – 11,818,117
Length	93
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	68.94
Mean single sequence MFE	-27.24
Consensus MFE	-20.37
Energy contribution	-20.73
Covariance contribution	0.36
Combinations/Pair	1.06
Mean z-score	-2.03
Structure conservation index	0.75
SVM decision value	2.17
SVM RNA-class probability	0.989496
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11818024 93 + 20766785
-----------UUCUCCUCUAUGUUUGUUUUUUC-UUUUUUUCGGUCCCAUUCACUUG-GAGGCCUAAGGCUA-AAUCGGCG-----CAACUGGAGGCAAAGUGAAUGGUUU
-----------.......................-............((((((((((.-...((((.(((((.-....))).-----...))..)))).))))))))))... ( -21.80)
>DroPse_CAF1 7462 84 + 1
---------------CCACAGUG------------UGAGUGUGUGCCACAUUCACUUGUGGGGCCUAAGGCCUAAGAUCGCGACUGGAGACUGGAGGCAAAGUGAAUGGAA-
---------------((((((.(------------((((((((...)))))))))))))))((((...)))).......((..(((....).))..)).............- ( -28.60)
>DroSec_CAF1 8550 72 + 1
--------------------------------UU-UCUUUUUCGGCCCCAUUCACUUG-GAGGCCUAAAGCUA-AAUCGGCG-----CAACUGGAGGCAAAGUGAAUGGGUU
--------------------------------..-...........(((((((((((.-...((((...(((.-....))).-----.......)))).))))))))))).. ( -24.90)
>DroSim_CAF1 8468 73 + 1
-------------------------------UUU-UCUUUUUCGGCCCCAUUCACUUG-GAGGCCUAAGGCUA-AAUCGGCG-----CAACUGGAGGCAAAGUGAAUGGGUU
-------------------------------...-...........(((((((((((.-...((((.(((((.-....))).-----...))..)))).))))))))))).. ( -25.10)
>DroEre_CAF1 8392 85 + 1
-----------GGCUCCACUAU-------U-UUU-UUCUUUUGGGCCCCAUUCACUUG-GGGGCCUAAGGCUA-AAGCCGCG-----CAACUGGAGGCAAAGUGAAUGGGUU
-----------(((.(((....-------.-...-......))))))((((((((((.-...((((..(((..-..)))...-----.......)))).))))))))))... ( -30.04)
>DroYak_CAF1 8419 97 + 1
UUUUUUUUUUGUGCAACACUAU-------U-UUUACUCUGUUGGGCCCCAUUCACUUG-GGGGCCUAAGGCUA-AAGCCGCG-----CCACUGGAGGCAAAGUGAAUGGGUU
..........((.(((((....-------.-.......))))).))(((((((((((.-...((((..(((..-..)))...-----((...)))))).))))))))))).. ( -33.00)
>consensus
_______________CCACUAU_________UUU_UUUUUUUCGGCCCCAUUCACUUG_GAGGCCUAAGGCUA_AAUCCGCG_____CAACUGGAGGCAAAGUGAAUGGGUU
..............................................(((((((((((.....((((..((....................))..)))).))))))))))).. (-20.37 = -20.73 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	11,818,024 – 11,818,117
Length	93
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	68.94
Mean single sequence MFE	-24.32
Consensus MFE	-18.76
Energy contribution	-18.66
Covariance contribution	-0.11
Combinations/Pair	1.16
Mean z-score	-2.41
Structure conservation index	0.77
SVM decision value	2.21
SVM RNA-class probability	0.990426
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11818024 93 - 20766785
AAACCAUUCACUUUGCCUCCAGUUG-----CGCCGAUU-UAGCCUUAGGCCUC-CAAGUGAAUGGGACCGAAAAAAA-GAAAAAACAAACAUAGAGGAGAA-----------
...((((((((((.((((...((((-----........-))))...))))...-.))))))))))............-.......................----------- ( -19.70)
>DroPse_CAF1 7462 84 - 1
-UUCCAUUCACUUUGCCUCCAGUCUCCAGUCGCGAUCUUAGGCCUUAGGCCCCACAAGUGAAUGUGGCACACACUCA------------CACUGUGG---------------
-.............((((...((((..((.......)).))))...)))).(((((.((((.((((...)))).)))------------)..)))))--------------- ( -19.70)
>DroSec_CAF1 8550 72 - 1
AACCCAUUCACUUUGCCUCCAGUUG-----CGCCGAUU-UAGCUUUAGGCCUC-CAAGUGAAUGGGGCCGAAAAAGA-AA--------------------------------
..(((((((((((.((((..(((((-----........-)))))..))))...-.)))))))))))...........-..-------------------------------- ( -25.30)
>DroSim_CAF1 8468 73 - 1
AACCCAUUCACUUUGCCUCCAGUUG-----CGCCGAUU-UAGCCUUAGGCCUC-CAAGUGAAUGGGGCCGAAAAAGA-AAA-------------------------------
..(((((((((((.((((...((((-----........-))))...))))...-.)))))))))))...........-...------------------------------- ( -23.00)
>DroEre_CAF1 8392 85 - 1
AACCCAUUCACUUUGCCUCCAGUUG-----CGCGGCUU-UAGCCUUAGGCCCC-CAAGUGAAUGGGGCCCAAAAGAA-AAA-A-------AUAGUGGAGCC-----------
..(((((((((((.((((...(...-----..)(((..-..)))..))))...-.)))))))))))(((((..(...-...-.-------.)..))).)).----------- ( -28.10)
>DroYak_CAF1 8419 97 - 1
AACCCAUUCACUUUGCCUCCAGUGG-----CGCGGCUU-UAGCCUUAGGCCCC-CAAGUGAAUGGGGCCCAACAGAGUAAA-A-------AUAGUGUUGCACAAAAAAAAAA
..(((((((((((.(((......))-----)..(((((-.......)))))..-.)))))))))))...(((((..((...-.-------))..)))))............. ( -30.10)
>consensus
AACCCAUUCACUUUGCCUCCAGUUG_____CGCCGAUU_UAGCCUUAGGCCCC_CAAGUGAAUGGGGCCCAAAAAAA_AAA_________AUAGUGG_______________
..(((((((((((.((((...((((..............))))...)))).....))))))))))).............................................. (-18.76 = -18.66 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:45 2006