Locus 3108

Sequence ID	2R_DroMel_CAF1
Location	10,628,802 – 10,628,893
Length	91
Max. P	0.912918

overview

Window 8

Location	10,628,802 – 10,628,893
Length	91
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	80.07
Mean single sequence MFE	-22.78
Consensus MFE	-14.76
Energy contribution	-15.90
Covariance contribution	1.14
Combinations/Pair	1.18
Mean z-score	-2.15
Structure conservation index	0.65
SVM decision value	0.93
SVM RNA-class probability	0.883200
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10628802 91 + 20766785
GAAAAAGUGGACGAAAAAAUGACGAAAAUCUAAAAAUGAACGUCGUCAUGGCUA-AGUGGUAGCCAUUUUUUACCUGCAAUCGUUUUGCCAC--------------
......((((.(((((..(((((((...((.......))...)))))))(((((-.....)))))..................)))))))))-------------- ( -23.60)
>DroPse_CAF1 97033 100 + 1
GGGAAACGAGUAGAACUACUGACCAAA---UGGAAAGGAACGUCGUCAUGGCCA-AACGGAAAUCAUGUGUCA--GGCAAUCGAUUUCACAGGUAACCACCUUAGG
((......((((....)))).(((...---(((....((......))....)))-....((((((...((...--..))...))))))...)))..))........ ( -17.10)
>DroSec_CAF1 70950 91 + 1
GAAAAAGUGGACAAAAAAAUGACGAAAAUCUAAAAAUGAACGUCGUCACGGCUA-AGUGGUAGCCAUGUUUUACCUGCAAUCGUUUUGCCAC--------------
......((((.(((((...((((((...((.......))...)))))).(((((-.....)))))..................)))))))))-------------- ( -22.90)
>DroSim_CAF1 71875 91 + 1
GAAAAAGUGGAGAAAAAAAUGACGAAAAUCUAAAAAUGAACGUCGUCACGGCUA-AGUGGUAGCCAUGUUUUACCUGCAAUCGUUUUUCCAC--------------
......(((((((((....((((((...((.......))...)))))).(((((-.....)))))..................)))))))))-------------- ( -24.60)
>DroEre_CAF1 71357 91 + 1
GAAAAAGUGGACAAAAAAAUGACGAAAAUCUAAAAACGAACGUCGUCAUGGCUA-AGUGGUAGCCAUGUUUUACCUGAAAUCGUUUUGCCAC--------------
......((((.(((((..(((((((...((.......))...)))))(((((((-.....)))))))............))..)))))))))-------------- ( -23.30)
>DroYak_CAF1 78425 92 + 1
GCAAAAGUGGACAAAAAAAUGACGAAAAUCUAAAAACGAACGUCGUCAUGGGUAAAGUGGUAGCCAUGUUUUACCUGAAAUCGUUUUGCCAC--------------
......((((.(((((..(((((((...((.......))...)))))))(((((((((((...))))..))))))).......)))))))))-------------- ( -25.20)
>consensus
GAAAAAGUGGACAAAAAAAUGACGAAAAUCUAAAAAUGAACGUCGUCAUGGCUA_AGUGGUAGCCAUGUUUUACCUGCAAUCGUUUUGCCAC______________
......((((.(((((...((((((...((.......))...)))))).(((((......)))))..................))))))))).............. (-14.76 = -15.90 +   1.14)

alignment

secondary structure

dotplot

Window 9

Location	10,628,802 – 10,628,893
Length	91
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	80.07
Mean single sequence MFE	-22.67
Consensus MFE	-16.12
Energy contribution	-16.73
Covariance contribution	0.62
Combinations/Pair	1.33
Mean z-score	-2.13
Structure conservation index	0.71
SVM decision value	1.09
SVM RNA-class probability	0.912918
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10628802 91 - 20766785
--------------GUGGCAAAACGAUUGCAGGUAAAAAAUGGCUACCACU-UAGCCAUGACGACGUUCAUUUUUAGAUUUUCGUCAUUUUUUCGUCCACUUUUUC
--------------((((....((((.............(((((((.....-)))))))(((((...((.......))...)))))......))))))))...... ( -22.20)
>DroPse_CAF1 97033 100 - 1
CCUAAGGUGGUUACCUGUGAAAUCGAUUGCC--UGACACAUGAUUUCCGUU-UGGCCAUGACGACGUUCCUUUCCA---UUUGGUCAGUAGUUCUACUCGUUUCCC
......(((((((..((.(((((((..((..--...))..)))))))))..-)))))))(((((.........((.---...))...(((....)))))))).... ( -18.00)
>DroSec_CAF1 70950 91 - 1
--------------GUGGCAAAACGAUUGCAGGUAAAACAUGGCUACCACU-UAGCCGUGACGACGUUCAUUUUUAGAUUUUCGUCAUUUUUUUGUCCACUUUUUC
--------------(((((((((.(((...........((((((((.....-))))))))..((((.((.......))....))))))).))))).))))...... ( -24.80)
>DroSim_CAF1 71875 91 - 1
--------------GUGGAAAAACGAUUGCAGGUAAAACAUGGCUACCACU-UAGCCGUGACGACGUUCAUUUUUAGAUUUUCGUCAUUUUUUUCUCCACUUUUUC
--------------(((((((((.(((...........((((((((.....-))))))))..((((.((.......))....))))))).)))).)))))...... ( -22.60)
>DroEre_CAF1 71357 91 - 1
--------------GUGGCAAAACGAUUUCAGGUAAAACAUGGCUACCACU-UAGCCAUGACGACGUUCGUUUUUAGAUUUUCGUCAUUUUUUUGUCCACUUUUUC
--------------(((((((((.(((...........((((((((.....-))))))))..((((.((.......))....))))))).))))).))))...... ( -25.90)
>DroYak_CAF1 78425 92 - 1
--------------GUGGCAAAACGAUUUCAGGUAAAACAUGGCUACCACUUUACCCAUGACGACGUUCGUUUUUAGAUUUUCGUCAUUUUUUUGUCCACUUUUGC
--------------(((((((((........((((((...(((...))).)))))).(((((((...((.......))...)))))))..))))).))))...... ( -22.50)
>consensus
______________GUGGCAAAACGAUUGCAGGUAAAACAUGGCUACCACU_UAGCCAUGACGACGUUCAUUUUUAGAUUUUCGUCAUUUUUUUGUCCACUUUUUC
..............(((((((((...............((((((((......))))))))..((((...(((....)))...))))....))))).))))...... (-16.12 = -16.73 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:43 2006