Locus 7511

Sequence ID	2L_DroMel_CAF1
Location	20,825,248 – 20,825,488
Length	240
Max. P	0.948232

overview

Window 2

Location	20,825,248 – 20,825,368
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-36.67
Consensus MFE	-34.20
Energy contribution	-34.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.72
Structure conservation index	0.93
SVM decision value	0.19
SVM RNA-class probability	0.624822
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20825248 120 - 22407834
UACAUGGGCGCCAGGGGAAAGACAGCCCAAGAAAUGAGGGAUGUUUUGAAACUGCCCGACGACAAGAAGGAAGUGGCAGCCAAAUUCAAGGAUCUUCUGAGUAAACUCGAAGGGCGCGAG
.......(((((.((...((((((.(((.(....)..))).))))))....((((((..(........)...).)))))))............((((.(((....))))))))))))... ( -36.20)
>DroSec_CAF1 3788 120 - 1
UUCAUGGGCGCCAGGGCAAAGACAGCCCAAGAAAUGAGGGAUGUGUUGAAACUGCCCGACGACAAAAAGGAAGUGGCAGCCAAAUUCAAGGAUCUUCUGAGUAAGCUCGAAGGGCGCGAG
.......(((((.((((.......))))......((((...((.((((..(((..((...........)).)))..))))))..)))).....((((.(((....))))))))))))... ( -36.90)
>DroSim_CAF1 3804 120 - 1
UUCAUGGGCGCCAGGGCAAAGACAGCCCAAGAAAUGAGGGAUGUGUUGAAACUGCCCGACGACAAAAAGGAAGUGGCAGCCAAAUUCAAGGAUCUUCUGAGUAAGCUCGAAGGGCGCGAG
.......(((((.((((.......))))......((((...((.((((..(((..((...........)).)))..))))))..)))).....((((.(((....))))))))))))... ( -36.90)
>consensus
UUCAUGGGCGCCAGGGCAAAGACAGCCCAAGAAAUGAGGGAUGUGUUGAAACUGCCCGACGACAAAAAGGAAGUGGCAGCCAAAUUCAAGGAUCUUCUGAGUAAGCUCGAAGGGCGCGAG
.......(((((.((...((.(((.(((.(....)..))).))).))....((((((..(........)...).)))))))............((((.(((....))))))))))))... (-34.20 = -34.20 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	20,825,368 – 20,825,488
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.36
Mean single sequence MFE	-43.53
Consensus MFE	-34.55
Energy contribution	-34.55
Covariance contribution	0.01
Combinations/Pair	1.09
Mean z-score	-2.70
Structure conservation index	0.79
SVM decision value	0.78
SVM RNA-class probability	0.848137
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20825368 120 + 22407834
UGCCAGGCUCAGUGCGAUUUCCACCGAUAGGGGAGAGGUAAUGAGAUUCUUGUCGGCAUUUUCCUUGGCCAAAAGUUGGUAGAGAUCGUCGGUGAAGCGACAAGACACCGACGUGGCCAA
.((((.((.....))((((((.((((((..((..((((.((((.(((....)))..))))..))))..))....)))))).))))))(((((((...(.....).))))))).))))... ( -43.90)
>DroSec_CAF1 3908 117 + 1
UGCCAUGCUCAGUGCGAUUUCCACCGAUAGGGAU---CAAAUUAGAUUCCUUUCGGCGUUUUCCUUGGCCAAAAGUUGGUAGAAAUCGUCGGUAAAGCGAGAAGUCACCGACGUGGCCAA
.(((((((.....))((((((.(((((.((((((---(......))))))).))(((..........))).......))).))))))((((((...((.....)).)))))))))))... ( -43.20)
>DroSim_CAF1 3924 116 + 1
UGCCAUGCUCAGUGCGAUUUCCACCGAUAGGGAU---CAAAUUAGAUUCCUUUCGGCGUUUUCCUGGGCCAAACGUUGGUAGAAAUCGUCGGUAAAGCGAGAAGACACCGACGUGGCCA-
.(((((((.....))((((((.(((((.((((((---(......))))))).))(((.(......).))).......))).))))))((((((....(.....)..)))))))))))..- ( -43.50)
>consensus
UGCCAUGCUCAGUGCGAUUUCCACCGAUAGGGAU___CAAAUUAGAUUCCUUUCGGCGUUUUCCUUGGCCAAAAGUUGGUAGAAAUCGUCGGUAAAGCGAGAAGACACCGACGUGGCCAA
.(((((((.....))((((((.((((((((((((...........))))))...(((..........)))....)))))).))))))((((((.............)))))))))))... (-34.55 = -34.55 +   0.01)

alignment

secondary structure

dotplot

Window 4

Location	20,825,368 – 20,825,488
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.36
Mean single sequence MFE	-40.37
Consensus MFE	-35.12
Energy contribution	-35.56
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.79
Structure conservation index	0.87
SVM decision value	1.38
SVM RNA-class probability	0.948232
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20825368 120 - 22407834
UUGGCCACGUCGGUGUCUUGUCGCUUCACCGACGAUCUCUACCAACUUUUGGCCAAGGAAAAUGCCGACAAGAAUCUCAUUACCUCUCCCCUAUCGGUGGAAAUCGCACUGAGCCUGGCA
...((((.((((((((...((((......))))(((.((((((.....(((((..........)))))...(.....).................)))))).)))))))))).).)))). ( -34.30)
>DroSec_CAF1 3908 117 - 1
UUGGCCACGUCGGUGACUUCUCGCUUUACCGACGAUUUCUACCAACUUUUGGCCAAGGAAAACGCCGAAAGGAAUCUAAUUUG---AUCCCUAUCGGUGGAAAUCGCACUGAGCAUGGCA
...((((.((((((((.........))))))))((((((((((....((((((..........))))))(((.(((......)---)).)))...))))))))))((.....)).)))). ( -43.50)
>DroSim_CAF1 3924 116 - 1
-UGGCCACGUCGGUGUCUUCUCGCUUUACCGACGAUUUCUACCAACGUUUGGCCCAGGAAAACGCCGAAAGGAAUCUAAUUUG---AUCCCUAUCGGUGGAAAUCGCACUGAGCAUGGCA
-..((((.(((((((...........)))))))((((((((((..(((((..(....).)))))..((.(((.(((......)---)).))).))))))))))))((.....)).)))). ( -43.30)
>consensus
UUGGCCACGUCGGUGUCUUCUCGCUUUACCGACGAUUUCUACCAACUUUUGGCCAAGGAAAACGCCGAAAGGAAUCUAAUUUG___AUCCCUAUCGGUGGAAAUCGCACUGAGCAUGGCA
...((((.(((((((...........)))))))((((((((((.......(((..........)))((.(((.................))).))))))))))))((.....)).)))). (-35.12 = -35.56 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:38 2006