AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene88100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88100.t1 MTR_4g032620 75.431 232 56 1 1 232 1 231 7.63e-128 360
MS.gene88100.t1 MTR_8g036130 58.065 248 87 4 1 232 1 247 4.31e-87 258
MS.gene88100.t1 MTR_4g031910 55.172 232 101 2 1 232 1 229 2.74e-77 233
MS.gene88100.t1 MTR_4g032290 52.245 245 90 4 1 232 1 231 5.43e-70 214
MS.gene88100.t1 MTR_4g032260 64.744 156 55 0 1 156 1 156 9.76e-60 186
MS.gene88100.t1 MTR_3g065100 48.707 232 110 4 1 224 1 231 1.42e-57 183
MS.gene88100.t1 MTR_3g466980 41.905 210 110 2 1 199 1 209 2.96e-52 169
MS.gene88100.t1 MTR_2g035610 66.116 121 41 0 1 121 1 121 5.52e-46 149
MS.gene88100.t1 MTR_3g466830 45.399 163 84 2 3 163 2 161 4.51e-45 148
MS.gene88100.t1 MTR_5g047580 42.308 156 88 2 1 156 1 154 3.16e-41 138
MS.gene88100.t1 MTR_1g090697 41.139 158 91 2 1 158 1 156 1.25e-38 131
MS.gene88100.t1 MTR_3g466890 42.949 156 88 1 3 158 2 156 7.33e-38 130
MS.gene88100.t1 MTR_4g063790 41.935 155 90 0 1 155 1 155 1.41e-37 129
MS.gene88100.t1 MTR_1g077390 39.744 156 92 2 1 156 1 154 9.70e-37 127
MS.gene88100.t1 MTR_1g090710 39.241 158 95 1 1 158 1 157 9.81e-37 127
MS.gene88100.t1 MTR_3g031100 38.788 165 101 0 1 165 1 165 3.35e-35 125
MS.gene88100.t1 MTR_1g084950 42.949 156 87 2 1 156 1 154 3.50e-35 122
MS.gene88100.t1 MTR_2g016210 37.805 164 102 0 1 164 1 164 6.14e-35 125
MS.gene88100.t1 MTR_7g011950 41.026 156 90 2 1 156 1 154 3.95e-34 120
MS.gene88100.t1 MTR_4g028800 79.167 72 13 1 1 72 1 70 4.80e-34 117
MS.gene88100.t1 MTR_1g090783 39.610 154 91 2 3 156 2 153 5.11e-34 120
MS.gene88100.t1 MTR_3g467080 37.179 156 98 0 1 156 1 156 7.23e-34 119
MS.gene88100.t1 MTR_4g028720 41.667 156 89 2 1 156 1 154 7.45e-33 117
MS.gene88100.t1 MTR_5g075380 38.961 154 93 1 1 154 1 153 2.00e-32 115
MS.gene88100.t1 MTR_3g031240 32.099 162 110 0 1 162 1 162 9.43e-30 109
MS.gene88100.t1 MTR_1g077320 36.538 156 97 2 1 156 1 154 3.54e-28 105
MS.gene88100.t1 MTR_7g055800 47.059 119 35 2 1 119 1 91 2.56e-26 98.2
MS.gene88100.t1 MTR_3g465410 39.683 126 76 0 29 154 1 126 8.10e-26 98.6
MS.gene88100.t1 MTR_1g077300 38.462 156 92 2 1 156 1 152 1.23e-25 98.2
MS.gene88100.t1 MTR_3g466900 37.795 127 78 1 32 158 2 127 1.77e-25 97.1
MS.gene88100.t1 MTR_3g466930 39.844 128 74 3 32 158 2 127 1.86e-25 97.1
MS.gene88100.t1 MTR_5g047560 35.256 156 83 3 1 156 1 138 3.36e-25 96.7
MS.gene88100.t1 MTR_2g035580 35.256 156 100 1 1 156 1 155 1.09e-23 93.2
MS.gene88100.t1 MTR_4g032270 49.000 100 45 4 135 232 36 131 3.71e-21 85.9
MS.gene88100.t1 MTR_7g106510 31.875 160 105 2 1 157 4 162 1.30e-20 90.1
MS.gene88100.t1 MTR_4g019670 35.897 117 75 0 3 119 6 122 1.40e-20 90.1
MS.gene88100.t1 MTR_7g055940 45.714 105 29 2 1 105 1 77 2.67e-20 82.0
MS.gene88100.t1 MTR_7g055790 45.455 110 42 1 1 110 59 150 3.15e-19 81.3
MS.gene88100.t1 MTR_3g093900 34.127 126 81 2 1 125 4 128 1.36e-16 78.6
MS.gene88100.t1 MTR_6g018920 30.000 160 97 6 1 154 1 151 5.52e-14 70.5
MS.gene88100.t1 MTR_1g114730 33.333 117 63 4 1 103 1 116 1.98e-12 65.9
MS.gene88100.t1 MTR_6g005450 35.593 118 61 5 1 104 1 117 9.00e-12 63.9
MS.gene88100.t1 MTR_2g035590 45.977 87 47 0 74 160 1 87 1.03e-11 60.1
MS.gene88100.t1 MTR_6g005440 36.441 118 60 5 1 104 1 117 1.52e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene88100.t1 AT5G48670 53.750 160 73 1 1 160 1 159 1.94e-49 164
MS.gene88100.t1 AT5G26630 39.267 191 114 2 1 190 1 190 4.39e-36 127
MS.gene88100.t1 AT1G65300 42.484 153 87 1 3 155 2 153 1.69e-35 127
MS.gene88100.t1 AT5G26650 40.523 153 90 1 4 156 2 153 1.39e-33 124
MS.gene88100.t1 AT5G27810 47.788 113 59 0 29 141 1 113 2.35e-33 117
MS.gene88100.t1 AT5G27960 46.610 118 63 0 4 121 2 119 4.41e-33 122
MS.gene88100.t1 AT3G05860 40.000 150 89 1 1 150 1 149 1.31e-32 117
MS.gene88100.t1 AT1G65330 39.205 176 94 3 3 173 2 169 1.98e-32 119
MS.gene88100.t1 AT3G05860 40.000 150 89 1 1 150 1 149 4.78e-32 117
MS.gene88100.t1 AT3G05860 40.000 150 89 1 1 150 1 149 5.54e-32 117
MS.gene88100.t1 AT1G31630 32.759 174 113 3 3 176 2 171 1.16e-28 110
MS.gene88100.t1 AT2G28700 36.184 152 92 2 1 150 1 149 1.36e-27 107
MS.gene88100.t1 AT1G31640 34.437 151 97 2 3 153 2 150 5.44e-27 108
MS.gene88100.t1 AT1G22590 30.769 156 104 1 1 156 1 152 2.15e-24 95.5
MS.gene88100.t1 AT5G26580 34.839 155 86 2 1 155 1 140 2.86e-23 96.3
MS.gene88100.t1 AT5G06500 36.364 154 96 1 1 154 1 152 1.78e-22 92.4
MS.gene88100.t1 AT2G40210 41.176 119 70 0 1 119 1 119 9.00e-20 87.0
MS.gene88100.t1 AT5G58890 38.384 99 53 3 1 92 1 98 4.07e-13 67.8
MS.gene88100.t1 AT5G55690 26.702 191 105 5 1 184 1 163 7.21e-13 66.6
MS.gene88100.t1 AT5G55690 26.702 191 105 5 1 184 1 163 7.21e-13 66.6

Find 59 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAGCTTGTGCCATAGTTTA+TGG 0.132446 4.4:+71946852 MS.gene88100:CDS
CACAACAATGACTAGGAAAA+AGG 0.228363 4.4:+71946722 None:intergenic
TCTTCATTACTGAATGTAAA+TGG 0.245246 4.4:-71947242 None:intergenic
TTCATTTAAGGTAGTAGATT+TGG 0.253282 4.4:-71947410 None:intergenic
TCATTGTCGATGATGATTCT+AGG 0.260008 4.4:+71946757 MS.gene88100:CDS
ATGTAAATGGTGGTGGTATT+TGG 0.308969 4.4:-71947229 None:intergenic
TACATTCAGTAATGAAGAAA+TGG 0.368381 4.4:+71947247 MS.gene88100:CDS
TACCAACCTCCTTCAATTTG+TGG 0.372241 4.4:-71947160 None:intergenic
ATGTTGTCGCCATTATTCAT+AGG 0.380827 4.4:-71947302 None:intergenic
GGAAAGCAACATACAATAGA+AGG 0.409123 4.4:+71946778 MS.gene88100:CDS
TAATGAAGAAATGGCAATGA+TGG 0.426450 4.4:+71947256 MS.gene88100:CDS
GGAGATGAGTCGGTGCCATT+TGG 0.429830 4.4:+71947365 MS.gene88100:CDS
TGTGGTGACGGCCAGATCTC+TGG 0.431268 4.4:-71946891 None:intergenic
AATTGAAGGAGGTTGGTAGA+AGG 0.442772 4.4:+71947165 MS.gene88100:CDS
GAAGGAGGTTGGTAGAAGGT+TGG 0.444882 4.4:+71947169 MS.gene88100:CDS
GGAATGCCGCCTATGAATAA+TGG 0.453131 4.4:+71947293 MS.gene88100:CDS
TATGCTGAATAATTTGTCAT+TGG 0.454426 4.4:+71947106 MS.gene88100:CDS
TGGTAGAAGGTTGGAAGCAG+AGG 0.457415 4.4:+71947178 MS.gene88100:CDS
GTTGATTGACCACAAATTGA+AGG 0.458305 4.4:+71947151 MS.gene88100:CDS
AGAGATCTGGCCGTCACCAC+AGG 0.458628 4.4:+71946893 MS.gene88100:CDS
ATCTCTGGTTGAGGCTCGTA+GGG 0.464949 4.4:-71946876 None:intergenic
TTGATTCAAAACATCTTTGT+TGG 0.470119 4.4:+71947129 MS.gene88100:CDS
ACGAGCCTCAACCAGAGATC+TGG 0.471522 4.4:+71946880 MS.gene88100:CDS
CATGAACGAAAGGGTTCTAA+AGG 0.484653 4.4:+71946995 MS.gene88100:CDS
CTCGTAGGGTCCATAAACTA+TGG 0.509841 4.4:-71946862 None:intergenic
CTAGGATCGACTTCGCCAAA+TGG 0.512642 4.4:-71947380 None:intergenic
AGTAGATTTGGCAAAACTCT+AGG 0.518146 4.4:-71947398 None:intergenic
GACCACAAATTGAAGGAGGT+TGG 0.522187 4.4:+71947158 MS.gene88100:CDS
GATCTCTGGTTGAGGCTCGT+AGG 0.522551 4.4:-71946877 None:intergenic
GACGGCCAGATCTCTGGTTG+AGG 0.531549 4.4:-71946885 None:intergenic
ATGATGGGTCCTAGCCATGC+TGG 0.537310 4.4:+71947272 MS.gene88100:CDS
AAAATTCAGAACAATGAATG+TGG 0.538041 4.4:+71946935 MS.gene88100:CDS
GCGGAAGGGTCTACTGAAGA+AGG 0.542122 4.4:+71946800 MS.gene88100:CDS
AGAATCATCATCGACAATGA+AGG 0.542377 4.4:-71946754 None:intergenic
CATGTAAGTCTCTTGATCAA+CGG 0.549961 4.4:-71946976 None:intergenic
AAATTCAGAACAATGAATGT+GGG 0.550450 4.4:+71946936 MS.gene88100:CDS
AAGGCATGATAACAAGGAGA+TGG 0.564923 4.4:+71947040 MS.gene88100:CDS
AACATACAATAGAAGGCGGA+AGG 0.566279 4.4:+71946785 MS.gene88100:CDS
AATGAAGAAATGGCAATGAT+GGG 0.575476 4.4:+71947257 MS.gene88100:CDS
AAGAGACTTACATGAACGAA+AGG 0.579981 4.4:+71946985 MS.gene88100:CDS
GTTTGGACTCCCTGTGGTGA+CGG 0.587157 4.4:-71946903 None:intergenic
GATACAAAGGCATGATAACA+AGG 0.593660 4.4:+71947034 MS.gene88100:CDS
AAGAGAAACTAAAGATACAA+AGG 0.596350 4.4:+71947021 MS.gene88100:CDS
GGCGGCATTCCAGCATGGCT+AGG 0.600043 4.4:-71947281 None:intergenic
AATTCAGAACAATGAATGTG+GGG 0.603139 4.4:+71946937 MS.gene88100:CDS
AGAGACTTACATGAACGAAA+GGG 0.604276 4.4:+71946986 MS.gene88100:CDS
GGCTTGATGATGAATAGTAA+TGG 0.609105 4.4:+71947344 MS.gene88100:CDS
TCATAGGCGGCATTCCAGCA+TGG 0.625874 4.4:-71947286 None:intergenic
TTACTGAATGTAAATGGTGG+TGG 0.629493 4.4:-71947236 None:intergenic
GATTGACCACAAATTGAAGG+AGG 0.630849 4.4:+71947154 MS.gene88100:CDS
GAGATCTGGCCGTCACCACA+GGG 0.642312 4.4:+71946894 MS.gene88100:CDS
TTGTCGCCATTATTCATAGG+CGG 0.647988 4.4:-71947299 None:intergenic
ATTCAGAACAATGAATGTGG+GGG 0.650757 4.4:+71946938 MS.gene88100:CDS
GAATAGTAATGGAGATGAGT+CGG 0.650993 4.4:+71947355 MS.gene88100:CDS
AGCACTGTTTGGACTCCCTG+TGG 0.665566 4.4:-71946909 None:intergenic
ACATACAATAGAAGGCGGAA+GGG 0.677825 4.4:+71946786 MS.gene88100:CDS
AAGCAACATACAATAGAAGG+CGG 0.694844 4.4:+71946781 MS.gene88100:CDS
TATGAACTAAGCACTCTGTG+TGG 0.701795 4.4:+71946825 MS.gene88100:CDS
TCATTACTGAATGTAAATGG+TGG 0.709945 4.4:-71947239 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTGAAAGTCAATCTTTTAT+GGG + chr4.4:71947323-71947342 MS.gene88100:CDS 20.0%
! AAAATTCAGAACAATGAATG+TGG + chr4.4:71946935-71946954 MS.gene88100:CDS 25.0%
! AAATTCAGAACAATGAATGT+GGG + chr4.4:71946936-71946955 MS.gene88100:CDS 25.0%
! AAGAGAAACTAAAGATACAA+AGG + chr4.4:71947021-71947040 MS.gene88100:CDS 25.0%
! TACATTCAGTAATGAAGAAA+TGG + chr4.4:71947247-71947266 MS.gene88100:CDS 25.0%
! TCTTCATTACTGAATGTAAA+TGG - chr4.4:71947245-71947264 None:intergenic 25.0%
! TTGATTCAAAACATCTTTGT+TGG + chr4.4:71947129-71947148 MS.gene88100:CDS 25.0%
!! CATTGAAAGTCAATCTTTTA+TGG + chr4.4:71947322-71947341 MS.gene88100:CDS 25.0%
!! TATGCTGAATAATTTGTCAT+TGG + chr4.4:71947106-71947125 MS.gene88100:CDS 25.0%
AATGAAGAAATGGCAATGAT+GGG + chr4.4:71947257-71947276 MS.gene88100:CDS 30.0%
AATTCAGAACAATGAATGTG+GGG + chr4.4:71946937-71946956 MS.gene88100:CDS 30.0%
TAATGAAGAAATGGCAATGA+TGG + chr4.4:71947256-71947275 MS.gene88100:CDS 30.0%
TCATTACTGAATGTAAATGG+TGG - chr4.4:71947242-71947261 None:intergenic 30.0%
AAGAGACTTACATGAACGAA+AGG + chr4.4:71946985-71947004 MS.gene88100:CDS 35.0%
AAGCAACATACAATAGAAGG+CGG + chr4.4:71946781-71946800 MS.gene88100:CDS 35.0%
AGAATCATCATCGACAATGA+AGG - chr4.4:71946757-71946776 None:intergenic 35.0%
AGAGACTTACATGAACGAAA+GGG + chr4.4:71946986-71947005 MS.gene88100:CDS 35.0%
AGTAGATTTGGCAAAACTCT+AGG - chr4.4:71947401-71947420 None:intergenic 35.0%
ATGTTGTCGCCATTATTCAT+AGG - chr4.4:71947305-71947324 None:intergenic 35.0%
ATTCAGAACAATGAATGTGG+GGG + chr4.4:71946938-71946957 MS.gene88100:CDS 35.0%
CATGTAAGTCTCTTGATCAA+CGG - chr4.4:71946979-71946998 None:intergenic 35.0%
GGAAAGCAACATACAATAGA+AGG + chr4.4:71946778-71946797 MS.gene88100:CDS 35.0%
GTTGATTGACCACAAATTGA+AGG + chr4.4:71947151-71947170 MS.gene88100:CDS 35.0%
TCATTGTCGATGATGATTCT+AGG + chr4.4:71946757-71946776 MS.gene88100:CDS 35.0%
TTACTGAATGTAAATGGTGG+TGG - chr4.4:71947239-71947258 None:intergenic 35.0%
! ATAGCTTGTGCCATAGTTTA+TGG + chr4.4:71946852-71946871 MS.gene88100:CDS 35.0%
! GAATAGTAATGGAGATGAGT+CGG + chr4.4:71947355-71947374 MS.gene88100:CDS 35.0%
! GATACAAAGGCATGATAACA+AGG + chr4.4:71947034-71947053 MS.gene88100:CDS 35.0%
!! ATGTAAATGGTGGTGGTATT+TGG - chr4.4:71947232-71947251 None:intergenic 35.0%
!! GGCTTGATGATGAATAGTAA+TGG + chr4.4:71947344-71947363 MS.gene88100:CDS 35.0%
!!! TGAATTTTGAGAGCACTGTT+TGG - chr4.4:71946923-71946942 None:intergenic 35.0%
AACATACAATAGAAGGCGGA+AGG + chr4.4:71946785-71946804 MS.gene88100:CDS 40.0%
AAGGCATGATAACAAGGAGA+TGG + chr4.4:71947040-71947059 MS.gene88100:CDS 40.0%
ACATACAATAGAAGGCGGAA+GGG + chr4.4:71946786-71946805 MS.gene88100:CDS 40.0%
GATTGACCACAAATTGAAGG+AGG + chr4.4:71947154-71947173 MS.gene88100:CDS 40.0%
TACCAACCTCCTTCAATTTG+TGG - chr4.4:71947163-71947182 None:intergenic 40.0%
TATGAACTAAGCACTCTGTG+TGG + chr4.4:71946825-71946844 MS.gene88100:CDS 40.0%
TTGTCGCCATTATTCATAGG+CGG - chr4.4:71947302-71947321 None:intergenic 40.0%
! CATGAACGAAAGGGTTCTAA+AGG + chr4.4:71946995-71947014 MS.gene88100:CDS 40.0%
!! AATTGAAGGAGGTTGGTAGA+AGG + chr4.4:71947165-71947184 MS.gene88100:CDS 40.0%
CTCGTAGGGTCCATAAACTA+TGG - chr4.4:71946865-71946884 None:intergenic 45.0%
GACCACAAATTGAAGGAGGT+TGG + chr4.4:71947158-71947177 MS.gene88100:CDS 45.0%
GGAATGCCGCCTATGAATAA+TGG + chr4.4:71947293-71947312 MS.gene88100:CDS 45.0%
ATCTCTGGTTGAGGCTCGTA+GGG - chr4.4:71946879-71946898 None:intergenic 50.0%
TGGTAGAAGGTTGGAAGCAG+AGG + chr4.4:71947178-71947197 MS.gene88100:CDS 50.0%
! CTAGGATCGACTTCGCCAAA+TGG - chr4.4:71947383-71947402 None:intergenic 50.0%
!! GAAGGAGGTTGGTAGAAGGT+TGG + chr4.4:71947169-71947188 MS.gene88100:CDS 50.0%
ACGAGCCTCAACCAGAGATC+TGG + chr4.4:71946880-71946899 MS.gene88100:CDS 55.0%
AGCACTGTTTGGACTCCCTG+TGG - chr4.4:71946912-71946931 None:intergenic 55.0%
GATCTCTGGTTGAGGCTCGT+AGG - chr4.4:71946880-71946899 None:intergenic 55.0%
GCGGAAGGGTCTACTGAAGA+AGG + chr4.4:71946800-71946819 MS.gene88100:CDS 55.0%
GTTTGGACTCCCTGTGGTGA+CGG - chr4.4:71946906-71946925 None:intergenic 55.0%
TCATAGGCGGCATTCCAGCA+TGG - chr4.4:71947289-71947308 None:intergenic 55.0%
!! ATGATGGGTCCTAGCCATGC+TGG + chr4.4:71947272-71947291 MS.gene88100:CDS 55.0%
!! GGAGATGAGTCGGTGCCATT+TGG + chr4.4:71947365-71947384 MS.gene88100:CDS 55.0%
AGAGATCTGGCCGTCACCAC+AGG + chr4.4:71946893-71946912 MS.gene88100:CDS 60.0%
GACGGCCAGATCTCTGGTTG+AGG - chr4.4:71946888-71946907 None:intergenic 60.0%
GAGATCTGGCCGTCACCACA+GGG + chr4.4:71946894-71946913 MS.gene88100:CDS 60.0%
!! TGTGGTGACGGCCAGATCTC+TGG - chr4.4:71946894-71946913 None:intergenic 60.0%
GGCGGCATTCCAGCATGGCT+AGG - chr4.4:71947284-71947303 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 71946729 71947427 71946729 ID=MS.gene88100
chr4.4 mRNA 71946729 71947427 71946729 ID=MS.gene88100.t1;Parent=MS.gene88100
chr4.4 exon 71946729 71947427 71946729 ID=MS.gene88100.t1.exon1;Parent=MS.gene88100.t1
chr4.4 CDS 71946729 71947427 71946729 ID=cds.MS.gene88100.t1;Parent=MS.gene88100.t1
Gene Sequence

>MS.gene88100

ATGACTAGGAAAAAGGTGAAACTTGCCTTCATTGTCGATGATGATTCTAGGAAAGCAACATACAATAGAAGGCGGAAGGGTCTACTGAAGAAGGTTTATGAACTAAGCACTCTGTGTGGAGTTATAGCTTGTGCCATAGTTTATGGACCCTACGAGCCTCAACCAGAGATCTGGCCGTCACCACAGGGAGTCCAAACAGTGCTCTCAAAATTCAGAACAATGAATGTGGGGGAGAAGAGCAACAAAACCGTTGATCAAGAGACTTACATGAACGAAAGGGTTCTAAAGGCTAAAGAGAAACTAAAGATACAAAGGCATGATAACAAGGAGATGGAGATGACAATGCTCATGATTCAATGTCTTTTTGACAATAAATTTATGCTGAATAATTTGTCATTGGTTGATTCAAAACATCTTTGTTGGTTGATTGACCACAAATTGAAGGAGGTTGGTAGAAGGTTGGAAGCAGAGGATAATAGTAGTCAACATCAAATTCAACTCCAAATACCACCACCATTTACATTCAGTAATGAAGAAATGGCAATGATGGGTCCTAGCCATGCTGGAATGCCGCCTATGAATAATGGCGACAACATTGAAAGTCAATCTTTTATGGGCTTGATGATGAATAGTAATGGAGATGAGTCGGTGCCATTTGGCGAAGTCGATCCTAGAGTTTTGCCAAATCTACTACCTTAA
Protein sequence

>MS.gene88100.t1

MTRKKVKLAFIVDDDSRKATYNRRRKGLLKKVYELSTLCGVIACAIVYGPYEPQPEIWPSPQGVQTVLSKFRTMNVGEKSNKTVDQETYMNERVLKAKEKLKIQRHDNKEMEMTMLMIQCLFDNKFMLNNLSLVDSKHLCWLIDHKLKEVGRRLEAEDNSSQHQIQLQIPPPFTFSNEEMAMMGPSHAGMPPMNNGDNIESQSFMGLMMNSNGDESVPFGEVDPRVLPNLLP