AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78532

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78532.t1 MTR_7g090590 73.134 67 18 0 30 96 54 120 1.00e-32 110
MS.gene78532.t1 MTR_5g095990 62.162 74 28 0 23 96 76 149 8.84e-32 108
MS.gene78532.t1 MTR_3g007900 60.811 74 29 0 23 96 81 154 1.89e-31 108
MS.gene78532.t1 MTR_6g012360 52.577 97 37 1 9 96 11 107 3.85e-31 105
MS.gene78532.t1 MTR_7g010580 51.042 96 38 1 10 96 14 109 5.16e-30 103
MS.gene78532.t1 MTR_5g036860 51.685 89 41 1 10 96 4 92 1.29e-29 101
MS.gene78532.t1 MTR_3g037750 52.688 93 40 1 8 96 11 103 1.62e-29 101
MS.gene78532.t1 MTR_8g085470 61.628 86 33 0 11 96 10 95 1.04e-27 97.1
MS.gene78532.t1 MTR_5g036880 50.562 89 42 1 10 96 4 92 3.24e-26 93.2
MS.gene78532.t1 MTR_5g036720 49.438 89 43 1 10 96 4 92 1.18e-25 91.7
MS.gene78532.t1 MTR_5g036640 46.667 90 40 2 7 96 2 83 2.57e-25 90.5
MS.gene78532.t1 MTR_1g096370 40.449 89 53 0 8 96 7 95 2.33e-18 73.2
MS.gene78532.t1 MTR_1g025220 40.816 98 49 2 8 96 4 101 1.08e-15 66.6
MS.gene78532.t1 MTR_1g025250 49.315 73 36 1 25 96 28 100 1.88e-15 65.9
MS.gene78532.t1 MTR_8g062800 44.872 78 42 1 20 96 35 112 1.01e-14 64.3
MS.gene78532.t1 MTR_3g102660 50.847 59 29 0 38 96 27 85 1.69e-14 63.2
MS.gene78532.t1 MTR_1g106915 46.667 60 32 0 37 96 31 90 7.60e-14 61.6
MS.gene78532.t1 MTR_3g113890 39.362 94 52 2 8 96 10 103 1.42e-13 61.2
MS.gene78532.t1 MTR_4g027870 43.939 66 36 1 8 72 3 68 2.41e-12 57.4
MS.gene78532.t1 MTR_1g018640 41.379 87 51 0 10 96 5 91 1.77e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78532.t1 AT1G74670 58.696 92 34 1 9 96 10 101 5.43e-34 113
MS.gene78532.t1 AT3G02885 71.233 73 21 0 24 96 25 97 5.37e-29 100
MS.gene78532.t1 AT5G15230 51.546 97 38 2 9 96 10 106 6.34e-27 95.5
MS.gene78532.t1 AT2G30810 52.000 100 36 1 9 96 7 106 2.60e-26 94.0
MS.gene78532.t1 AT3G10185 64.000 75 27 0 22 96 48 122 6.67e-25 90.9
MS.gene78532.t1 AT5G15230 54.217 83 35 1 17 96 1 83 7.28e-25 89.4
MS.gene78532.t1 AT2G39540 37.931 87 47 1 10 96 8 87 8.52e-16 66.6
MS.gene78532.t1 AT1G10588 40.909 88 45 2 10 96 9 90 1.48e-14 63.5
MS.gene78532.t1 AT1G22690 48.052 77 38 2 22 96 43 119 2.90e-14 63.5
MS.gene78532.t1 AT1G22690 48.052 77 38 2 22 96 43 119 2.90e-14 63.5
MS.gene78532.t1 AT1G22690 48.052 77 38 2 22 96 43 119 2.90e-14 63.5
MS.gene78532.t1 AT1G10588 39.773 88 45 2 10 96 9 89 5.31e-14 62.0
MS.gene78532.t1 AT4G09600 50.000 60 30 0 37 96 40 99 6.42e-14 62.0
MS.gene78532.t1 AT5G59845 36.364 88 49 2 10 96 8 89 7.36e-13 59.3
MS.gene78532.t1 AT2G18420 50.000 60 30 0 37 96 35 94 9.35e-13 58.9
MS.gene78532.t1 AT2G18420 50.000 60 30 0 37 96 11 70 1.07e-12 58.2
MS.gene78532.t1 AT5G14920 54.098 61 27 1 37 96 215 275 6.48e-12 59.7
MS.gene78532.t1 AT2G14900 34.118 85 45 1 23 96 24 108 2.32e-11 55.8

Find 20 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTCATCTCTTTGCTTCTTT+TGG 0.218438 5.1:-60589178 MS.gene78532:CDS
TTAAGTGCTTAAGGGCATTT+TGG 0.257598 5.1:+60588171 None:intergenic
TGTGTTCCTCCTGGTGTATA+TGG 0.309163 5.1:-60588246 MS.gene78532:CDS
GTGATCCTTGAACAGGCTTA+TGG 0.330002 5.1:-60588987 MS.gene78532:intron
TCATGCCTTTGTGTTCCTCC+TGG 0.416024 5.1:-60588255 MS.gene78532:CDS
TTTGTCCTTGCTACAACAGC+TGG 0.443536 5.1:-60588212 MS.gene78532:CDS
TTGCAATGGCTCCATCTTGG+TGG 0.538056 5.1:-60589199 MS.gene78532:CDS
CAAAGAGATGACCACCAAGA+TGG 0.560846 5.1:+60589188 None:intergenic
CGTGCAAAACTTCGTCCTCA+AGG 0.561656 5.1:-60588963 MS.gene78532:intron
ACGTTGCAATGGCTCCATCT+TGG 0.582831 5.1:-60589202 MS.gene78532:CDS
GTCTTCCAGCTGTTGTAGCA+AGG 0.586689 5.1:+60588207 None:intergenic
TACATTCTCTAATGTAGCTG+AGG 0.595669 5.1:-60589154 MS.gene78532:intron
TGCTTGTTGCCATATACACC+AGG 0.601222 5.1:+60588237 None:intergenic
ACAATGGCAGCACGTTGCAA+TGG 0.611244 5.1:-60589213 MS.gene78532:CDS
CTACAACAGCTGGAAGACAC+AGG 0.616939 5.1:-60588202 MS.gene78532:CDS
GAGCAACGATATGTACACCT+TGG 0.623615 5.1:+60588330 None:intergenic
AACAGCTGGAAGACACAGGA+AGG 0.640099 5.1:-60588198 MS.gene78532:CDS
ATGAAACAGATTGTAAACCA+AGG 0.669189 5.1:-60588347 MS.gene78532:intron
TTGTTGCCATATACACCAGG+AGG 0.729916 5.1:+60588240 None:intergenic
ATACACCAGGAGGAACACAA+AGG 0.753714 5.1:+60588250 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTATAACTTGTTTAAAAAT+TGG - chr5.1:60588677-60588696 MS.gene78532:intron 15.0%
!! AAAACCATTTACTATATGAT+TGG - chr5.1:60588281-60588300 MS.gene78532:CDS 20.0%
!! GTTCTAATATTTCAAAACTT+TGG - chr5.1:60588372-60588391 MS.gene78532:intron 20.0%
!!! ACTGCCAAAATTTATTTTAA+TGG + chr5.1:60588560-60588579 None:intergenic 20.0%
!!! TAAATTTTGGCAGTTTTATA+AGG - chr5.1:60588566-60588585 MS.gene78532:intron 20.0%
!!! TCCTCCATTAAAATAAATTT+TGG - chr5.1:60588553-60588572 MS.gene78532:intron 20.0%
!!! TTTTATAAGGAATTTTTCCT+TGG - chr5.1:60588579-60588598 MS.gene78532:intron 20.0%
! GTATAAGCAACCTAAAATTT+GGG - chr5.1:60588792-60588811 MS.gene78532:intron 25.0%
! TAAATTATTAATGTTGAGCG+AGG + chr5.1:60588619-60588638 None:intergenic 25.0%
! TGATCCAATCATATAGTAAA+TGG + chr5.1:60588288-60588307 None:intergenic 25.0%
! TGTATAAGCAACCTAAAATT+TGG - chr5.1:60588791-60588810 MS.gene78532:intron 25.0%
! TTGCATATATATATACCTTG+AGG + chr5.1:60588444-60588463 None:intergenic 25.0%
!! TGTGTCTATAAGCAAATTTT+GGG - chr5.1:60588488-60588507 MS.gene78532:intron 25.0%
!! TTGTGTCTATAAGCAAATTT+TGG - chr5.1:60588487-60588506 MS.gene78532:intron 25.0%
!!! GCCAAAATTTATTTTAATGG+AGG + chr5.1:60588557-60588576 None:intergenic 25.0%
ATGAAACAGATTGTAAACCA+AGG - chr5.1:60589042-60589061 MS.gene78532:intron 30.0%
TTTCACCACTTATTCAAGAT+CGG + chr5.1:60588868-60588887 None:intergenic 30.0%
! TAGTCCAAATCCCAAATTTT+AGG + chr5.1:60588805-60588824 None:intergenic 30.0%
TACATTCTCTAATGTAGCTG+AGG - chr5.1:60588235-60588254 MS.gene78532:CDS 35.0%
! GCAACCTAAAATTTGGGATT+TGG - chr5.1:60588798-60588817 MS.gene78532:intron 35.0%
! TTTTGGCAGAAAAACATGCA+TGG + chr5.1:60589104-60589123 None:intergenic 35.0%
! TTTTTGTGTGATCCTTGAAC+AGG - chr5.1:60588395-60588414 MS.gene78532:intron 35.0%
!!! AGGACTTTTTTTTACTGCCA+AGG + chr5.1:60588599-60588618 None:intergenic 35.0%
! GGCATGAAGCACAACATTTT+TGG + chr5.1:60589121-60589140 None:intergenic 40.0%
! GGTCATCTCTTTGCTTCTTT+TGG - chr5.1:60588211-60588230 MS.gene78532:CDS 40.0%
ATACACCAGGAGGAACACAA+AGG + chr5.1:60589142-60589161 None:intergenic 45.0%
CAAAGAGATGACCACCAAGA+TGG + chr5.1:60588204-60588223 None:intergenic 45.0%
GAGCAACGATATGTACACCT+TGG + chr5.1:60589062-60589081 None:intergenic 45.0%
GTCGTCCGATCTTGAATAAG+TGG - chr5.1:60588860-60588879 MS.gene78532:intron 45.0%
GTGATCCTTGAACAGGCTTA+TGG - chr5.1:60588402-60588421 MS.gene78532:intron 45.0%
TCTCACTATGTCACGCATCA+TGG + chr5.1:60588751-60588770 None:intergenic 45.0%
TGTGTTCCTCCTGGTGTATA+TGG - chr5.1:60589143-60589162 MS.gene78532:intron 45.0%
TTGTTGCCATATACACCAGG+AGG + chr5.1:60589152-60589171 None:intergenic 45.0%
TTTGTCCTTGCTACAACAGC+TGG - chr5.1:60589177-60589196 MS.gene78532:CDS 45.0%
! TGCTTGTTGCCATATACACC+AGG + chr5.1:60589155-60589174 None:intergenic 45.0%
! TTTGGGATTTGGACTACACG+TGG - chr5.1:60588809-60588828 MS.gene78532:intron 45.0%
AACAGCTGGAAGACACAGGA+AGG - chr5.1:60589191-60589210 MS.gene78532:CDS 50.0%
ACGTTGCAATGGCTCCATCT+TGG - chr5.1:60588187-60588206 MS.gene78532:CDS 50.0%
CACGTCCATAAGCCTGTTCA+AGG + chr5.1:60588410-60588429 None:intergenic 50.0%
CGTGCAAAACTTCGTCCTCA+AGG - chr5.1:60588426-60588445 MS.gene78532:intron 50.0%
CTACAACAGCTGGAAGACAC+AGG - chr5.1:60589187-60589206 MS.gene78532:CDS 50.0%
GTCTTCCAGCTGTTGTAGCA+AGG + chr5.1:60589185-60589204 None:intergenic 50.0%
TCATGCCTTTGTGTTCCTCC+TGG - chr5.1:60589134-60589153 MS.gene78532:intron 50.0%
TTGCAATGGCTCCATCTTGG+TGG - chr5.1:60588190-60588209 MS.gene78532:CDS 50.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 60588179 60589232 60588179 ID=MS.gene78532
chr5.1 mRNA 60588179 60589232 60588179 ID=MS.gene78532.t1;Parent=MS.gene78532
chr5.1 exon 60589155 60589232 60589155 ID=MS.gene78532.t1.exon1;Parent=MS.gene78532.t1
chr5.1 CDS 60589155 60589232 60589155 ID=cds.MS.gene78532.t1;Parent=MS.gene78532.t1
chr5.1 exon 60588964 60588994 60588964 ID=MS.gene78532.t1.exon2;Parent=MS.gene78532.t1
chr5.1 CDS 60588964 60588994 60588964 ID=cds.MS.gene78532.t1;Parent=MS.gene78532.t1
chr5.1 exon 60588179 60588360 60588179 ID=MS.gene78532.t1.exon3;Parent=MS.gene78532.t1
chr5.1 CDS 60588179 60588360 60588179 ID=cds.MS.gene78532.t1;Parent=MS.gene78532.t1
Gene Sequence

>MS.gene78532

ATGGCAGCACGTTGCAATGGCTCCATCTTGGTGGTCATCTCTTTGCTTCTTTTGGTTACATTCTCTAATGTAGCTGAGGTACATTAATTAATAATTATGACAAAAACCATTTACTATATGATTGGATCAATATGATTAATTGATTATCTAGTATGCAATTATCAATTAGTTAACAATGTATACAAGTTCAATTGTTCTAATATTTCAAAACTTTGGTTTTTGTGTGATCCTTGAACAGGCTTATGGACGTGCAAAACTTCGTCCTCAAGGTATATATATATGCAATTGATGTTTTTGTTAATTGTGATTTGTGTCTATAAGCAAATTTTGGGTATTCTATTTTTTGTTTTTGCTAAGAGCAATTTTAGCTCATGTCCTCCATTAAAATAAATTTTGGCAGTTTTATAAGGAATTTTTCCTTGGCAGTAAAAAAAAGTCCTCGCTCAACATTAATAATTTAATTTGAAACAAAACTATGTACAATTAAAAAAGTATAAAAGTATAACTTGTTTAAAAATTGGTTAAAATGTATACTATGACTTTTAGAGAAAATGCTGCTAATCGATAAACCATGATGCGTGACATAGTGAGAGTCACTTACTCACTTAATAGTGTATAAGCAACCTAAAATTTGGGATTTGGACTACACGTGGTTATTGCGTGCTGCAGTTGTTGATTTCAGTCGTCCGATCTTGAATAAGTGGTGAAAATTATTGCGTGCTGCAGTTGTTGATTTCAGTCGTCCGATCTTGAATAAGTGGTGAAAATTATTTAGTAATACTTAGTGAATGTTAATATTAACTATGAATTTTTTTTGTTAATGTTAATTTCTTTGTTGATTTGCTAATAGTGTGAACAAATTAATGAAACAGATTGTAAACCAAGGTGTACATATCGTTGCTCTGCAACTTCACACAAGAAACCATGCATGTTTTTCTGCCAAAAATGTTGTGCTTCATGCCTTTGTGTTCCTCCTGGTGTATATGGCAACAAGCAAGTTTGTCCTTGCTACAACAGCTGGAAGACACAGGAAGGAAAACCAAAATGCCCTTAA
Protein sequence

>MS.gene78532.t1

MAARCNGSILVVISLLLLVTFSNVAEAYGRAKLRPQDCKPRCTYRCSATSHKKPCMFFCQKCCASCLCVPPGVYGNKQVCPCYNSWKTQEGKPKCP