Locus 3843

Sequence ID	2R_DroMel_CAF1
Location	12,689,093 – 12,689,226
Length	133
Max. P	0.951031

overview

Window 7

Location	12,689,093 – 12,689,192
Length	99
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.57
Mean single sequence MFE	-18.80
Consensus MFE	-10.16
Energy contribution	-10.22
Covariance contribution	0.06
Combinations/Pair	1.12
Mean z-score	-2.34
Structure conservation index	0.54
SVM decision value	0.48
SVM RNA-class probability	0.752308
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12689093 99 + 20766785
-AGCAG-AG------CCAACCGCAAUCGGUAGACAAAACAAAGAGACAUUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAG
-.....-..------...((((....))))............(((((.........((((...(((.......))).))))....((((.....))))..))))).. ( -19.60)
>DroVir_CAF1 62177 97 + 1
GAGAAA-AAAGCAAACCGAACCCAAUCAGUGGAUAAAAAAAA---------AACCACAGCAAUGCAUAUCAAUUGCUGCUGACAAUUUCAAAUAGAAAAUGUCUCAG
..((..-..(((................((((..........---------..))))((((((........)))))))))((((.((((.....)))).)))))).. ( -19.30)
>DroPse_CAF1 52510 100 + 1
-AGCAGCAA------CCAACCGCAAUCGGCAGACAAAACAAAGAGACAUUCAGCUGCAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAG
-.((.((..------......)).....))............(((((..(((((....(((((........))))).)))))...((((.....))))..))))).. ( -21.00)
>DroGri_CAF1 47733 92 + 1
AAGAGA-AG-ACAACUCGAACGCAAUCAGUAGACCAAAAAAA---------AA----AGAAAUGCAUAUCAAUUGCAGCUGACAAUUUCAAAUAGAAAAUGUCUCAG
..(((.-..-....)))((..((..((....)).........---------..----.....((((.......)))))).((((.((((.....)))).)))))).. ( -12.30)
>DroAna_CAF1 40993 99 + 1
-AUCAA-AG------CCAACCGCAAUCGGUAGACAAAACAAAGAGACACUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAG
-.....-..------...((((....))))............(((((.........((((...(((.......))).))))....((((.....))))..))))).. ( -19.60)
>DroPer_CAF1 43117 100 + 1
-AGCAGCAA------CCAACCGCAAUCGGCAGACAAAACAAAGAGACAUUCAGCUGCAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAG
-.((.((..------......)).....))............(((((..(((((....(((((........))))).)))))...((((.....))))..))))).. ( -21.00)
>consensus
_AGCAA_AA______CCAACCGCAAUCGGUAGACAAAACAAAGAGACAUUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAG
............................(.((((......................((((...(((.......))).))))....((((.....))))..))))).. (-10.16 = -10.22 +   0.06)

alignment

secondary structure

dotplot

Window 8

Location	12,689,093 – 12,689,192
Length	99
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.57
Mean single sequence MFE	-26.76
Consensus MFE	-16.00
Energy contribution	-16.08
Covariance contribution	0.09
Combinations/Pair	1.27
Mean z-score	-2.51
Structure conservation index	0.60
SVM decision value	0.95
SVM RNA-class probability	0.888769
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12689093 99 - 20766785
CUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAAUGUCUCUUUGUUUUGUCUACCGAUUGCGGUUGG------CU-CUGCU-
..(((((((((.((...(((.....)))((((((((........))))))))))..)))))))))...((...(((.((((....)))).))------).-..)).- ( -28.30)
>DroVir_CAF1 62177 97 - 1
CUGAGACAUUUUCUAUUUGAAAUUGUCAGCAGCAAUUGAUAUGCAUUGCUGUGGUU---------UUUUUUUUAUCCACUGAUUGGGUUCGGUUUGCUUU-UUUCUC
((((((((.((((.....)))).)))).((((((((........))))))))....---------........(((((.....)))))))))........-...... ( -21.90)
>DroPse_CAF1 52510 100 - 1
CUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGCAGCUGAAUGUCUCUUUGUUUUGUCUGCCGAUUGCGGUUGG------UUGCUGCU-
....((((.((((.....)))).))))(((((((((..((.((((...(.(((((.(((((......))))).).)))).)..))))))..)------))))))))- ( -34.80)
>DroGri_CAF1 47733 92 - 1
CUGAGACAUUUUCUAUUUGAAAUUGUCAGCUGCAAUUGAUAUGCAUUUCU----UU---------UUUUUUUGGUCUACUGAUUGCGUUCGAGUUGU-CU-UCUCUU
....((((.((((.....)))).))))....((((((((.(((((..((.----..---------...............)).))))))).))))))-..-...... ( -15.97)
>DroAna_CAF1 40993 99 - 1
CUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAGUGUCUCUUUGUUUUGUCUACCGAUUGCGGUUGG------CU-UUGAU-
..((((((.((((.....))))...(((((((((((........))))))))...))).))))))........(((.((((....)))).))------).-.....- ( -24.80)
>DroPer_CAF1 43117 100 - 1
CUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGCAGCUGAAUGUCUCUUUGUUUUGUCUGCCGAUUGCGGUUGG------UUGCUGCU-
....((((.((((.....)))).))))(((((((((..((.((((...(.(((((.(((((......))))).).)))).)..))))))..)------))))))))- ( -34.80)
>consensus
CUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAAUGUCUCUUUGUUUUGUCUACCGAUUGCGGUUGG______CU_CUGCU_
....((((.((((.....)))).)))).((((((((........))))))))......................((.((((....)))).))............... (-16.00 = -16.08 +   0.09)

alignment

secondary structure

dotplot

Window 9

Location	12,689,124 – 12,689,226
Length	102
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	86.76
Mean single sequence MFE	-17.75
Consensus MFE	-16.32
Energy contribution	-16.35
Covariance contribution	0.03
Combinations/Pair	1.05
Mean z-score	-1.93
Structure conservation index	0.92
SVM decision value	1.41
SVM RNA-class probability	0.951031
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12689124 102 + 20766785
AAAGAGACAUUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAGCAUGCCAAUACAAAU--GAAUGAACAGCA--A-GGAAAA
.......((((((......(((((........))))).(((((.(.((((.....))))...).))))).............)--))))).......--.-...... ( -17.90)
>DroPse_CAF1 52542 104 + 1
AAAGAGACAUUCAGCUGCAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAGCAUGCCAGUACAACUCCGAAUGAAUAACA--A-CAACAG
...(((((..(((((....(((((........))))).)))))...((((.....))))..)))))...............................--.-...... ( -19.30)
>DroSim_CAF1 45147 96 + 1
AAAGAGACAUUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAGCAUGCCAA------U--GAAUGAACAGCA--A-GGAAAA
.......((((((......(((((........))))).(((((.(.((((.....))))...).))))).......------)--))))).......--.-...... ( -17.90)
>DroYak_CAF1 44816 105 + 1
AAAGAGAUAUUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAGCAUGCCAAUACAAAU--GAAUGAACAACAACAUGGAAAA
.......((((((......(((((........))))).(((((.(.((((.....))))...).))))).............)--)))))................. ( -15.80)
>DroAna_CAF1 41024 89 + 1
AAAGAGACACUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAGCAUGCCAAUACAAAU--GAAUGG----------------
...(((((.........((((...(((.......))).))))....((((.....))))..))))).................--......---------------- ( -16.30)
>DroPer_CAF1 43149 104 + 1
AAAGAGACAUUCAGCUGCAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAGCAUGCCAGUACAACUCCGAAUGAAUAACA--A-CAACAG
...(((((..(((((....(((((........))))).)))))...((((.....))))..)))))...............................--.-...... ( -19.30)
>consensus
AAAGAGACAUUCAACUACAGCAAUGCAUAUCAAUUGCCGCUGACAAUUUCAAAUAGAAAACGUCUCAGCAUGCCAAUACAAAU__GAAUGAACAACA__A_GGAAAA
.......(((((.......(((((........))))).(((((.(.((((.....))))...).)))))................)))))................. (-16.32 = -16.35 +   0.03)

alignment

secondary structure

dotplot

Window 0

Location	12,689,124 – 12,689,226
Length	102
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	86.76
Mean single sequence MFE	-23.18
Consensus MFE	-20.86
Energy contribution	-20.45
Covariance contribution	-0.41
Combinations/Pair	1.12
Mean z-score	-1.40
Structure conservation index	0.90
SVM decision value	0.20
SVM RNA-class probability	0.629293
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12689124 102 - 20766785
UUUUCC-U--UGCUGUUCAUUC--AUUUGUAUUGGCAUGCUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAAUGUCUCUUU
......-.--(((((..((...--...))...)))))....(((((((((.((...(((.....)))((((((((........))))))))))..)))))))))... ( -23.20)
>DroPse_CAF1 52542 104 - 1
CUGUUG-U--UGUUAUUCAUUCGGAGUUGUACUGGCAUGCUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGCAGCUGAAUGUCUCUUU
......-.--.......(((((((((((((....))).)))..((((.((((.....)))).)))).((((((((........))))))))..)))))))....... ( -26.20)
>DroSim_CAF1 45147 96 - 1
UUUUCC-U--UGCUGUUCAUUC--A------UUGGCAUGCUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAAUGUCUCUUU
......-.--.(((((.((...--.------.))))).)).(((((((((.((...(((.....)))((((((((........))))))))))..)))))))))... ( -22.20)
>DroYak_CAF1 44816 105 - 1
UUUUCCAUGUUGUUGUUCAUUC--AUUUGUAUUGGCAUGCUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAAUAUCUCUUU
.............((((((.((--(..(((....)))...)))((((.((((.....)))).)))).((((((((........))))))))...))))))....... ( -20.30)
>DroAna_CAF1 41024 89 - 1
----------------CCAUUC--AUUUGUAUUGGCAUGCUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAGUGUCUCUUU
----------------.(((((--(......(..(....)..)((((.((((.....)))).)))).((((((((........))))))))...))))))....... ( -21.00)
>DroPer_CAF1 43149 104 - 1
CUGUUG-U--UGUUAUUCAUUCGGAGUUGUACUGGCAUGCUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGCAGCUGAAUGUCUCUUU
......-.--.......(((((((((((((....))).)))..((((.((((.....)))).)))).((((((((........))))))))..)))))))....... ( -26.20)
>consensus
UUUUCC_U__UGUUGUUCAUUC__AUUUGUAUUGGCAUGCUGAGACGUUUUCUAUUUGAAAUUGUCAGCGGCAAUUGAUAUGCAUUGCUGUAGUUGAAUGUCUCUUU
.................................((((((((..((((.((((.....)))).)))).((((((((........)))))))))))...)))))..... (-20.86 = -20.45 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:24 2006