Locus 4825

Sequence ID	2R_DroMel_CAF1
Location	15,842,970 – 15,843,137
Length	167
Max. P	0.996748

overview

Window 7

Location	15,842,970 – 15,843,068
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	97.75
Mean single sequence MFE	-26.50
Consensus MFE	-24.38
Energy contribution	-24.06
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-2.16
Structure conservation index	0.92
SVM decision value	2.74
SVM RNA-class probability	0.996748
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15842970 98 + 20766785
GGCAGCCGACAGCUGCCCGCAUAACAGGUACCUGAACUGAAACUUCUACCAACUACCAGCAAGCAACUGCAUAGAAGUGGGAAAACCCAAUUACCUCG
((((((.....))))))........(((((...........(((((((..........(((......))).)))))))(((....)))...))))).. ( -24.50)
>DroSec_CAF1 56 98 + 1
GGCAGCCGACAGCUGCCCGCAUAACAGGUACCUGAACUGAAACUUCUACCAACUACCAGCAAGCAACUGCAUAGAAGUGGGAAAACCCAAAUGCCUCG
((((((.....)))))).((((..(((....))).......(((((((..........(((......))).)))))))(((....)))..)))).... ( -26.40)
>DroSim_CAF1 51 98 + 1
GGCAGCCGACAGCUGCCCGCAUAACAGGUACCUGAACUGAAACUUCUACCAACUACCAGCAAGCAACUGUAUAGAAGUGGGAAAACCCAAAUGCCUCG
((((((.....)))))).((((..(((....))).......(((((((.....(((.((.......))))))))))))(((....)))..)))).... ( -26.20)
>DroEre_CAF1 1345 96 + 1
GGCAGCCGACAGCUGCCCGCAUAACAGGUACCUGAACUGAAACUUCUACCAACUACCAGCA-GCAACUGCAUAGAAGUGGGAAAACCCA-AUGCCUCG
((((((.....)))))).((((..(((....))).......(((((((..........(((-(...)))).)))))))(((....))).-)))).... ( -27.70)
>DroYak_CAF1 51 97 + 1
GGCAGCCGACAGCUGCCCGCAUAACAGGUACCUGAACUGAAACUUCUACCAACUACCAGCA-GCAACUGCAUAGAAGUGGGAAAACCCAAAUGCCUCG
((((((.....)))))).((((..(((....))).......(((((((..........(((-(...)))).)))))))(((....)))..)))).... ( -27.70)
>consensus
GGCAGCCGACAGCUGCCCGCAUAACAGGUACCUGAACUGAAACUUCUACCAACUACCAGCAAGCAACUGCAUAGAAGUGGGAAAACCCAAAUGCCUCG
((((((.....))))))........(((((...........(((((((..........(((......))).)))))))(((....)))...))))).. (-24.38 = -24.06 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	15,842,970 – 15,843,068
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	97.75
Mean single sequence MFE	-33.28
Consensus MFE	-33.22
Energy contribution	-33.30
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.51
Structure conservation index	1.00
SVM decision value	1.66
SVM RNA-class probability	0.970338
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15842970 98 - 20766785
CGAGGUAAUUGGGUUUUCCCACUUCUAUGCAGUUGCUUGCUGGUAGUUGGUAGAAGUUUCAGUUCAGGUACCUGUUAUGCGGGCAGCUGUCGGCUGCC
..(((((.(((..((.....((((((((.((..((((....))))..))))))))))...))..))).)))))........((((((.....)))))) ( -33.10)
>DroSec_CAF1 56 98 - 1
CGAGGCAUUUGGGUUUUCCCACUUCUAUGCAGUUGCUUGCUGGUAGUUGGUAGAAGUUUCAGUUCAGGUACCUGUUAUGCGGGCAGCUGUCGGCUGCC
...((((..((((....)))).......((((((((((((.((((.((((..((....))...)))).))))......))))))))))))....)))) ( -34.80)
>DroSim_CAF1 51 98 - 1
CGAGGCAUUUGGGUUUUCCCACUUCUAUACAGUUGCUUGCUGGUAGUUGGUAGAAGUUUCAGUUCAGGUACCUGUUAUGCGGGCAGCUGUCGGCUGCC
...((((..((((....)))).......((((((((((((.((((.((((..((....))...)))).))))......))))))))))))....)))) ( -34.50)
>DroEre_CAF1 1345 96 - 1
CGAGGCAU-UGGGUUUUCCCACUUCUAUGCAGUUGC-UGCUGGUAGUUGGUAGAAGUUUCAGUUCAGGUACCUGUUAUGCGGGCAGCUGUCGGCUGCC
.(((((..-((((....)))).((((((.((..(((-.....)))..))))))))))))).((.(((....)))....)).((((((.....)))))) ( -32.00)
>DroYak_CAF1 51 97 - 1
CGAGGCAUUUGGGUUUUCCCACUUCUAUGCAGUUGC-UGCUGGUAGUUGGUAGAAGUUUCAGUUCAGGUACCUGUUAUGCGGGCAGCUGUCGGCUGCC
.(((((...((((....)))).((((((.((..(((-.....)))..))))))))))))).((.(((....)))....)).((((((.....)))))) ( -32.00)
>consensus
CGAGGCAUUUGGGUUUUCCCACUUCUAUGCAGUUGCUUGCUGGUAGUUGGUAGAAGUUUCAGUUCAGGUACCUGUUAUGCGGGCAGCUGUCGGCUGCC
...((((..((((....)))).......((((((((((((.((((.((((..((....))...)))).))))......))))))))))))....)))) (-33.22 = -33.30 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	15,843,038 – 15,843,137
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.62
Mean single sequence MFE	-31.38
Consensus MFE	-21.02
Energy contribution	-21.72
Covariance contribution	0.70
Combinations/Pair	1.20
Mean z-score	-1.51
Structure conservation index	0.67
SVM decision value	0.39
SVM RNA-class probability	0.716894
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15843038 99 + 20766785
GCAUAGAAGUGGGAA------AACCCAAUUACCUCG----CCGGGAUUAGCGAU------GUCU-AAGGGCCCAUAAACCCAUCAGCCCGUCUUAGGGGCUUCCCGGAACAAAGCA----
((.......((((..------..)))).........----((((((..(((...------....-..(((........))).....(((......))))))))))))......)).---- ( -30.80)
>DroSec_CAF1 124 99 + 1
GCAUAGAAGUGGGAA------AACCCAAAUGCCUCG----CCGGGAUUAGCGAU------GUCU-AAGGGCCCAUAAACCCAUCAGCCCGUCUUAGGGGCUUCCCGGAACAAAGCA----
((((.....((((..------..)))).))))....----((((((..(((...------....-..(((........))).....(((......)))))))))))).........---- ( -31.00)
>DroSim_CAF1 119 99 + 1
GUAUAGAAGUGGGAA------AACCCAAAUGCCUCG----CCGGGAUUAGCGAU------GUCU-AAGGGCCCAUAAACCCAUCAGCCCGUCUUAGGGGCUUCCCGGAACAAAGCA----
.........((((..------..))))..(((....----((((((..(((...------....-..(((........))).....(((......))))))))))))......)))---- ( -30.00)
>DroEre_CAF1 1412 98 + 1
GCAUAGAAGUGGGAA------AACCCA-AUGCCUCG----CCGGGAUUAGCGAU------GUCU-AAGGGCCCAUAAACCCAUCAGCCCGCCUUAGGGGCUUCCCGGAACCAAGCA----
((.......((((..------..))))-........----((((((..(((...------....-..(((........))).....(((......))))))))))))......)).---- ( -30.80)
>DroYak_CAF1 118 99 + 1
GCAUAGAAGUGGGAA------AACCCAAAUGCCUCG----CCGGGAUUAGCGAU------GUCU-AAGGGCCCAUAAACCCAUCAGCCGGUCUUAAGGGUUUCCCGGAACUAAGCA----
((.(((...((((..------..)))).........----((((((((((....------..))-)).(((((.(((..((.......))..))).)))))))))))..))).)).---- ( -29.70)
>DroAna_CAF1 111 118 + 1
GCCUAGAACUAGGAAUCCUCCAACCAAA--ACCUCGCUGGCUGGGAUUAGCCAAAAGCCGGCCGGACGGACCCCUAAUAAAAUAAUAAAAACUAAAGGGAUUCCCAGGAAGGCGGAUCAG
.((((....)))).((((.((..((...--.((..(((((((.((.....))...))))))).))..(((.((((....................))))..)))..))..)).))))... ( -35.95)
>consensus
GCAUAGAAGUGGGAA______AACCCAAAUGCCUCG____CCGGGAUUAGCGAU______GUCU_AAGGGCCCAUAAACCCAUCAGCCCGUCUUAGGGGCUUCCCGGAACAAAGCA____
((.......((((..........)))).............((((((.....................(((........)))...(((((.......)))))))))))......))..... (-21.02 = -21.72 +   0.70)

alignment

secondary structure

dotplot

Window 0

Location	15,843,038 – 15,843,137
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.62
Mean single sequence MFE	-37.53
Consensus MFE	-23.88
Energy contribution	-26.02
Covariance contribution	2.14
Combinations/Pair	1.15
Mean z-score	-2.11
Structure conservation index	0.64
SVM decision value	0.95
SVM RNA-class probability	0.889056
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15843038 99 - 20766785
----UGCUUUGUUCCGGGAAGCCCCUAAGACGGGCUGAUGGGUUUAUGGGCCCUU-AGAC------AUCGCUAAUCCCGG----CGAGGUAAUUGGGUU------UUCCCACUUCUAUGC
----(((((((..((((((((((((......)))((((.(((((....)))))))-))..------...)))..))))))----)))))))..((((..------..))))......... ( -36.00)
>DroSec_CAF1 124 99 - 1
----UGCUUUGUUCCGGGAAGCCCCUAAGACGGGCUGAUGGGUUUAUGGGCCCUU-AGAC------AUCGCUAAUCCCGG----CGAGGCAUUUGGGUU------UUCCCACUUCUAUGC
----(((((((..((((((((((((......)))((((.(((((....)))))))-))..------...)))..))))))----)))))))..((((..------..))))......... ( -37.80)
>DroSim_CAF1 119 99 - 1
----UGCUUUGUUCCGGGAAGCCCCUAAGACGGGCUGAUGGGUUUAUGGGCCCUU-AGAC------AUCGCUAAUCCCGG----CGAGGCAUUUGGGUU------UUCCCACUUCUAUAC
----(((((((..((((((((((((......)))((((.(((((....)))))))-))..------...)))..))))))----)))))))..((((..------..))))......... ( -37.80)
>DroEre_CAF1 1412 98 - 1
----UGCUUGGUUCCGGGAAGCCCCUAAGGCGGGCUGAUGGGUUUAUGGGCCCUU-AGAC------AUCGCUAAUCCCGG----CGAGGCAU-UGGGUU------UUCCCACUUCUAUGC
----(((((.(..((((((.(((.....)))(((((.(((....))).)))))..-....------........))))))----).))))).-((((..------..))))......... ( -36.50)
>DroYak_CAF1 118 99 - 1
----UGCUUAGUUCCGGGAAACCCUUAAGACCGGCUGAUGGGUUUAUGGGCCCUU-AGAC------AUCGCUAAUCCCGG----CGAGGCAUUUGGGUU------UUCCCACUUCUAUGC
----.((.(((....(((((((((..((..(((.((((.(((((....)))))))-)).)------.(((((......))----)))))..)).)))))------)))).....))).)) ( -33.80)
>DroAna_CAF1 111 118 - 1
CUGAUCCGCCUUCCUGGGAAUCCCUUUAGUUUUUAUUAUUUUAUUAGGGGUCCGUCCGGCCGGCUUUUGGCUAAUCCCAGCCAGCGAGGU--UUUGGUUGGAGGAUUCCUAGUUCUAGGC
.......((((..(((((((((((((((((............))))))).....((((((((((((((((((......)))))..)))))--..))))))))))))))))))....)))) ( -43.30)
>consensus
____UGCUUUGUUCCGGGAAGCCCCUAAGACGGGCUGAUGGGUUUAUGGGCCCUU_AGAC______AUCGCUAAUCCCGG____CGAGGCAUUUGGGUU______UUCCCACUUCUAUGC
....(((((((..(((((((((((.......)))))...(((((....))))).....................))))))....)))))))..((((..........))))......... (-23.88 = -26.02 +   2.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:08 2006