AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene60543

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60543.t1 MTR_1g091047 93.151 73 5 0 7 79 1 73 4.79e-43 134
MS.gene60543.t1 MTR_3g006150 64.615 65 21 2 15 78 90 153 4.04e-18 73.6
MS.gene60543.t1 MTR_1g109550 55.882 68 28 2 11 78 12 77 6.49e-18 72.8
MS.gene60543.t1 MTR_8g062700 53.846 65 29 1 14 78 41 104 7.10e-18 76.6
MS.gene60543.t1 MTR_8g062700 53.846 65 29 1 14 78 41 104 7.10e-18 76.6
MS.gene60543.t1 MTR_5g036670 52.308 65 30 1 14 78 42 105 6.48e-17 73.6
MS.gene60543.t1 MTR_3g006065 63.077 65 22 2 15 78 90 153 7.36e-17 71.2
MS.gene60543.t1 MTR_1g105010 51.515 66 31 1 14 79 15 79 2.48e-16 68.2
MS.gene60543.t1 MTR_1g105960 54.839 62 27 1 17 78 3 63 3.04e-16 67.8
MS.gene60543.t1 MTR_1g105955 46.377 69 36 1 10 78 90 157 7.42e-15 65.9
MS.gene60543.t1 MTR_1g105955 48.387 62 31 1 17 78 18 78 2.47e-13 61.6
MS.gene60543.t1 MTR_1g100260 56.061 66 26 1 16 78 25 90 1.27e-14 63.9
MS.gene60543.t1 MTR_6g008970 47.692 65 33 1 14 78 62 125 5.16e-14 65.5
MS.gene60543.t1 MTR_3g006185 53.846 65 28 2 15 78 98 161 8.28e-14 62.8
MS.gene60543.t1 MTR_3g006185 52.703 74 32 3 7 79 1 72 2.53e-13 61.6
MS.gene60543.t1 MTR_3g006125 51.899 79 35 3 2 79 77 153 9.69e-14 63.9
MS.gene60543.t1 MTR_3g006125 50.769 65 30 2 15 78 180 243 1.39e-12 60.8
MS.gene60543.t1 MTR_5g073430 57.627 59 23 2 20 77 17 74 1.50e-13 60.8
MS.gene60543.t1 MTR_1g093310 51.562 64 24 2 14 77 8 64 1.90e-13 59.7
MS.gene60543.t1 MTR_7g013410 46.667 60 31 1 19 78 2 60 3.86e-13 60.5
MS.gene60543.t1 MTR_3g006105 51.351 74 33 3 7 79 1 72 1.06e-12 60.1
MS.gene60543.t1 MTR_3g006105 50.000 64 30 2 15 77 99 161 7.71e-12 57.8
MS.gene60543.t1 MTR_8g062350 46.970 66 34 1 14 79 13 77 1.33e-12 60.1
MS.gene60543.t1 MTR_3g006010 49.315 73 34 3 7 78 1 71 2.35e-12 60.8
MS.gene60543.t1 MTR_1g104940 44.444 72 38 2 9 79 7 77 7.94e-12 56.6
MS.gene60543.t1 MTR_6g008995 45.312 64 34 1 15 78 37 99 9.23e-12 58.9
MS.gene60543.t1 MTR_4g133470 50.794 63 30 1 16 78 173 234 8.41e-11 55.8
MS.gene60543.t1 MTR_1g104960 50.769 65 31 1 14 78 12 75 8.74e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene60543.t1 AT1G24190 52.308 65 30 1 14 78 13 76 4.82e-17 74.3
MS.gene60543.t1 AT1G24190 52.308 65 30 1 14 78 13 76 5.42e-17 73.9
MS.gene60543.t1 AT1G24190 52.308 65 30 1 14 78 13 76 5.92e-17 73.9
MS.gene60543.t1 AT1G70060 52.308 65 30 1 14 78 13 76 3.10e-16 72.0
MS.gene60543.t1 AT1G70060 52.308 65 30 1 14 78 13 76 3.10e-16 72.0
MS.gene60543.t1 AT1G59890 53.125 64 29 1 15 78 45 107 3.54e-16 71.6
MS.gene60543.t1 AT1G59890 53.125 64 29 1 15 78 45 107 3.76e-16 71.6
MS.gene60543.t1 AT1G59890 53.125 64 29 1 15 78 45 107 3.83e-16 71.6
MS.gene60543.t1 AT1G59890 53.125 64 29 1 15 78 45 107 3.83e-16 71.6
MS.gene60543.t1 AT5G15020 50.769 65 31 1 14 78 51 114 1.94e-15 69.7
MS.gene60543.t1 AT5G15020 50.769 65 31 1 14 78 51 114 2.18e-15 69.3
MS.gene60543.t1 AT3G01320 49.231 65 32 1 14 78 56 119 4.95e-15 68.6
MS.gene60543.t1 AT3G01320 49.231 65 32 1 14 78 56 119 5.30e-15 68.2
MS.gene60543.t1 AT1G10450 51.562 64 30 1 15 78 33 95 1.44e-14 67.0
MS.gene60543.t1 AT1G10450 51.562 64 30 1 15 78 33 95 1.44e-14 67.0
MS.gene60543.t1 AT1G10450 51.562 64 30 1 15 78 84 146 1.62e-14 67.0
MS.gene60543.t1 AT5G15025 49.231 65 32 1 14 78 46 109 1.37e-13 61.2
MS.gene60543.t1 AT1G24200 48.485 66 33 1 14 79 13 77 3.16e-13 61.6
MS.gene60543.t1 AT1G27250 46.154 65 34 1 14 78 20 83 3.77e-13 60.5
MS.gene60543.t1 AT1G24210 43.284 67 37 1 14 80 13 78 1.22e-12 59.7
MS.gene60543.t1 AT1G70030 46.154 65 34 1 15 79 22 85 1.59e-12 58.5
MS.gene60543.t1 AT1G27220 43.077 65 36 1 14 78 13 76 1.89e-12 59.7
MS.gene60543.t1 AT1G24250 48.438 64 32 1 14 77 119 181 2.13e-12 60.5
MS.gene60543.t1 AT1G70030 46.154 65 34 1 15 79 11 74 4.26e-12 58.2
MS.gene60543.t1 AT1G70030 46.154 65 34 1 15 79 22 85 4.35e-12 57.8
MS.gene60543.t1 AT1G23810 45.312 64 34 1 14 77 108 170 7.01e-12 58.9
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.74e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 241 301 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT4G12020 47.619 63 31 2 15 77 308 368 5.78e-11 57.0
MS.gene60543.t1 AT1G27280 41.538 65 37 1 14 78 80 143 9.78e-11 55.5

Find 15 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCAGCCCTCAAATCTTTC+AGG 0.146764 1.2:-68721788 None:intergenic
AGGACATACAGATTTAATTC+TGG 0.289730 1.2:+68721860 MS.gene60543:CDS
GGACATACAGATTTAATTCT+GGG 0.368970 1.2:+68721861 MS.gene60543:CDS
TAAAACTCCTGAAAGATTTG+AGG 0.415830 1.2:+68721781 MS.gene60543:CDS
AAAACTCCTGAAAGATTTGA+GGG 0.424484 1.2:+68721782 MS.gene60543:CDS
CGAATCGGCGACGATAAACT+AGG 0.434109 1.2:+68721699 MS.gene60543:CDS
CTAGTTTATCGTCGCCGATT+CGG 0.442166 1.2:-68721698 None:intergenic
CTCCTGAAAGATTTGAGGGC+TGG 0.459564 1.2:+68721786 MS.gene60543:CDS
AACTATGCAAATCAGTTCAA+TGG 0.478283 1.2:+68721549 None:intergenic
GGAAGAAGAATTGATATAAG+AGG 0.508673 1.2:+68721807 MS.gene60543:CDS
AAGATGAAGAATTTCCGAAT+CGG 0.560007 1.2:+68721684 MS.gene60543:intron
AGAGTGAAGAAGCTGTTGAA+AGG 0.582834 1.2:+68721840 MS.gene60543:CDS
GTAGTAACTAACCAGTTGGA+AGG 0.611566 1.2:-68721896 None:intergenic
GAATCGGCGACGATAAACTA+GGG 0.619068 1.2:+68721700 MS.gene60543:CDS
CGATAAACTAGGGTTTCTCA+AGG 0.627978 1.2:+68721710 MS.gene60543:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTATGTCTATTATTTATG+TGG + chr1.2:68722071-68722090 MS.gene60543:intron 15.0%
!!! TTGGTTTTATTATTTTGAAT+TGG + chr1.2:68721607-68721626 MS.gene60543:intron 15.0%
!!! TTTTAACAAAATAGTTTTAG+AGG + chr1.2:68722005-68722024 MS.gene60543:intron 15.0%
AAAACTCCTGAAAGATTTGA+GGG + chr1.2:68721782-68721801 MS.gene60543:CDS 30.0%
AAAAGTAGTAACTAACCAGT+TGG - chr1.2:68721903-68721922 None:intergenic 30.0%
AAGATGAAGAATTTCCGAAT+CGG + chr1.2:68721684-68721703 MS.gene60543:intron 30.0%
AGGACATACAGATTTAATTC+TGG + chr1.2:68721860-68721879 MS.gene60543:CDS 30.0%
GGAAGAAGAATTGATATAAG+AGG + chr1.2:68721807-68721826 MS.gene60543:CDS 30.0%
GGACATACAGATTTAATTCT+GGG + chr1.2:68721861-68721880 MS.gene60543:CDS 30.0%
TAAAACTCCTGAAAGATTTG+AGG + chr1.2:68721781-68721800 MS.gene60543:CDS 30.0%
TAACATGATGAACAACTACA+TGG - chr1.2:68722106-68722125 None:intergenic 30.0%
! TTCAAAATTTTCCTTCCAAC+TGG + chr1.2:68721885-68721904 MS.gene60543:CDS 30.0%
AGAAATAAATCGAGTGAAGG+AGG - chr1.2:68721588-68721607 None:intergenic 35.0%
CCAAGAAATAAATCGAGTGA+AGG - chr1.2:68721591-68721610 None:intergenic 35.0%
TGAACAAATGTGAAGTGCAA+TGG - chr1.2:68721927-68721946 None:intergenic 35.0%
! CCTTCACTCGATTTATTTCT+TGG + chr1.2:68721588-68721607 MS.gene60543:intron 35.0%
AATCGAGTGAAGGAGGATTA+AGG - chr1.2:68721581-68721600 None:intergenic 40.0%
AGAGTGAAGAAGCTGTTGAA+AGG + chr1.2:68721840-68721859 MS.gene60543:CDS 40.0%
CGATAAACTAGGGTTTCTCA+AGG + chr1.2:68721710-68721729 MS.gene60543:CDS 40.0%
GTAGTAACTAACCAGTTGGA+AGG - chr1.2:68721899-68721918 None:intergenic 40.0%
GAATCGGCGACGATAAACTA+GGG + chr1.2:68721700-68721719 MS.gene60543:CDS 45.0%
TTCCAGCCCTCAAATCTTTC+AGG - chr1.2:68721791-68721810 None:intergenic 45.0%
! CTAGTTTATCGTCGCCGATT+CGG - chr1.2:68721701-68721720 None:intergenic 45.0%
CGAATCGGCGACGATAAACT+AGG + chr1.2:68721699-68721718 MS.gene60543:CDS 50.0%
CTCCTGAAAGATTTGAGGGC+TGG + chr1.2:68721786-68721805 MS.gene60543:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 68721553 68722194 68721553 ID=MS.gene60543
chr1.2 mRNA 68721553 68722194 68721553 ID=MS.gene60543.t1;Parent=MS.gene60543
chr1.2 exon 68721553 68721570 68721553 ID=MS.gene60543.t1.exon1;Parent=MS.gene60543.t1
chr1.2 CDS 68721553 68721570 68721553 ID=cds.MS.gene60543.t1;Parent=MS.gene60543.t1
chr1.2 exon 68721687 68721906 68721687 ID=MS.gene60543.t1.exon2;Parent=MS.gene60543.t1
chr1.2 CDS 68721687 68721906 68721687 ID=cds.MS.gene60543.t1;Parent=MS.gene60543.t1
chr1.2 exon 68722190 68722194 68722190 ID=MS.gene60543.t1.exon3;Parent=MS.gene60543.t1
chr1.2 CDS 68722190 68722194 68722190 ID=cds.MS.gene60543.t1;Parent=MS.gene60543.t1
Gene Sequence

>MS.gene60543

ATGCAAATCAGTTCAATGGTATGCACCTTAATCCTCCTTCACTCGATTTATTTCTTGGTTTTATTATTTTGAATTGGAATTAGTAGTTCTTAAACTGAATAATAATAATAATAATAATTTTGTGAACAATAAAGATGAAGAATTTCCGAATCGGCGACGATAAACTAGGGTTTCTCAAGGCAGTGAAAGCTGCATTTGAATATAACAGAATAAAGTATCATCAGTTTTTAAAACTCCTGAAAGATTTGAGGGCTGGAAGAAGAATTGATATAAGAGGTGTCATGACTAGAGTGAAGAAGCTGTTGAAAGGACATACAGATTTAATTCTGGGATTCAAAATTTTCCTTCCAACTGGTTAGTTACTACTTTTTCCATTGCACTTCACATTTGTTCACACTTTTCTGTTGTTTTTTCTTTGCTATATGCTTCTACATTATATCTTTATCTGCATCTTTTAACAAAATAGTTTTAGAGGAGCATTTTATATGTGTAGTTATATTACTTACATTTGTTGAAATATTTATGTCTATTATTTATGTGGTTTAACGAACCATGTAGTTGTTCATCATGTTAGTTTATATACGTATTGTATTGCTGTGATCATTGAAGATATTTCTTTTTTCTTTTCTCTTTTTAGTGTGA
Protein sequence

>MS.gene60543.t1

MQISSMMKNFRIGDDKLGFLKAVKAAFEYNRIKYHQFLKLLKDLRAGRRIDIRGVMTRVKKLLKGHTDLILGFKIFLPTV