AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene62747

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene62747.t1 MTR_3g107120 43.204 206 110 4 11 215 79 278 1.16e-37 135
MS.gene62747.t1 MTR_3g107160 40.092 217 123 5 2 215 58 270 2.42e-35 129
MS.gene62747.t1 MTR_3g107100 42.654 211 110 6 9 215 67 270 2.79e-34 126
MS.gene62747.t1 MTR_1g053025 41.892 222 105 10 10 213 60 275 7.93e-31 117
MS.gene62747.t1 MTR_2g007450 39.431 246 110 11 2 212 63 304 6.38e-30 115
MS.gene62747.t1 MTR_3g107140 47.020 151 73 4 4 153 52 196 9.93e-30 110
MS.gene62747.t1 MTR_4g098590 38.073 218 115 9 9 212 55 266 1.90e-28 110
MS.gene62747.t1 MTR_2g007400 40.654 214 112 9 10 211 69 279 1.01e-27 108
MS.gene62747.t1 MTR_1g041245 36.792 212 111 7 11 214 66 262 2.35e-22 94.0
MS.gene62747.t1 MTR_2g007500 38.889 180 92 7 48 212 91 267 5.98e-22 92.4
MS.gene62747.t1 MTR_7g034090 55.670 97 34 3 4 99 60 148 1.53e-21 92.0
MS.gene62747.t1 MTR_2g008320 35.885 209 121 6 10 211 109 311 7.19e-19 84.7
MS.gene62747.t1 MTR_3g108150 33.962 212 115 7 11 213 68 263 2.04e-18 83.2
MS.gene62747.t1 MTR_2g008310 36.667 210 114 8 10 211 59 257 6.45e-18 81.6
MS.gene62747.t1 MTR_2g005990 33.937 221 127 7 10 217 63 277 2.23e-17 80.1
MS.gene62747.t1 MTR_5g083890 35.426 223 115 9 11 211 64 279 2.55e-17 80.5
MS.gene62747.t1 MTR_4g039440 31.250 224 136 8 6 220 82 296 5.67e-17 79.0
MS.gene62747.t1 MTR_5g012840 30.811 185 108 5 11 188 44 215 1.78e-16 77.0
MS.gene62747.t1 MTR_3g026920 32.800 250 111 10 2 213 66 296 1.86e-15 74.7
MS.gene62747.t1 MTR_7g055943 31.401 207 131 7 10 213 97 295 2.29e-15 74.3
MS.gene62747.t1 MTR_7g075820 34.821 224 114 10 11 211 64 278 3.36e-15 73.9
MS.gene62747.t1 MTR_7g098570 35.266 207 121 6 11 214 75 271 7.22e-15 73.2
MS.gene62747.t1 MTR_3g040700 33.796 216 103 9 10 213 97 284 1.16e-14 72.4
MS.gene62747.t1 MTR_3g450920 38.000 150 71 7 15 158 73 206 1.35e-14 70.5
MS.gene62747.t1 MTR_6g011460 32.701 211 118 7 10 212 103 297 3.09e-14 71.2
MS.gene62747.t1 MTR_7g088260 30.288 208 123 6 11 212 146 337 3.56e-14 71.2
MS.gene62747.t1 MTR_6g022500 30.693 202 129 6 12 212 164 355 4.60e-14 70.9
MS.gene62747.t1 MTR_5g058100 34.831 178 105 6 10 185 66 234 1.08e-13 69.7
MS.gene62747.t1 MTR_3g023630 32.093 215 118 9 11 216 63 258 1.12e-13 69.3
MS.gene62747.t1 MTR_7g098510 38.060 134 73 5 11 141 73 199 3.93e-13 67.8
MS.gene62747.t1 MTR_6g045333 35.829 187 107 8 2 185 112 288 4.96e-13 67.8
MS.gene62747.t1 MTR_7g115270 34.659 176 93 6 11 170 67 236 5.33e-13 67.4
MS.gene62747.t1 MTR_7g098480 35.961 203 115 8 15 214 77 267 6.14e-13 67.4
MS.gene62747.t1 MTR_7g083740 30.493 223 102 10 1 211 65 246 7.40e-13 67.0
MS.gene62747.t1 MTR_3g095600 35.106 188 85 9 2 185 55 209 1.42e-12 65.9
MS.gene62747.t1 MTR_0543s0010 37.778 135 73 4 10 144 140 263 2.46e-12 65.9
MS.gene62747.t1 MTR_0492s0020 33.010 206 116 8 10 213 140 325 2.67e-12 65.5
MS.gene62747.t1 MTR_3g087260 34.177 158 97 5 56 213 181 331 3.42e-12 65.5
MS.gene62747.t1 MTR_7g034120 32.673 202 117 8 19 212 1 191 3.51e-12 64.7
MS.gene62747.t1 MTR_3g082890 30.357 224 121 9 15 216 73 283 3.56e-12 65.1
MS.gene62747.t1 MTR_3g109982 37.778 135 77 3 9 143 66 193 3.99e-12 65.5
MS.gene62747.t1 MTR_3g110010 37.778 135 77 3 9 143 66 193 4.09e-12 65.5
MS.gene62747.t1 MTR_3g082890 30.357 224 121 9 15 216 153 363 4.58e-12 65.1
MS.gene62747.t1 MTR_3g108560 28.638 213 123 6 9 213 73 264 6.75e-12 63.9
MS.gene62747.t1 MTR_3g108560 28.638 213 123 6 9 213 73 264 7.38e-12 64.3
MS.gene62747.t1 MTR_7g032370 31.250 208 111 8 11 212 45 226 9.17e-12 63.9
MS.gene62747.t1 MTR_1g066830 32.569 218 127 8 10 217 65 272 1.77e-11 63.2
MS.gene62747.t1 MTR_7g007370 36.486 148 85 5 75 220 93 233 8.17e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene62747.t1 AT3G54160 36.496 137 77 5 11 142 46 177 1.36e-11 63.5
MS.gene62747.t1 AT4G14103 36.111 144 84 6 4 146 63 199 5.29e-11 61.6
MS.gene62747.t1 AT4G14103 36.111 144 84 6 4 146 63 199 5.29e-11 61.6
MS.gene62747.t1 AT4G14103 35.862 145 85 6 3 146 62 199 6.02e-11 61.6

Find 46 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTCTCAAAACTCTTCATT+TGG 0.264967 7.3:-65376452 MS.gene62747:CDS
AAGCGATCCCTCACGATTAA+AGG 0.277121 7.3:+65376336 None:intergenic
CCTGCATGTTAAAATTCTAA+TGG 0.310426 7.3:+65376540 None:intergenic
ATTTGGAACAGATTCGGTTT+TGG 0.340854 7.3:-65376435 MS.gene62747:CDS
TTGAGACGGAAAGTCTTAAT+AGG 0.377890 7.3:+65376691 None:intergenic
TTACTCGGGCAGTGAAGTTC+AGG 0.379273 7.3:+65376652 None:intergenic
CTCTTCATTTGGAACAGATT+CGG 0.384063 7.3:-65376441 MS.gene62747:CDS
TCTGAGCTTTGAGTTTGATC+AGG 0.390769 7.3:-65376209 MS.gene62747:intron
CTGCATGTTAAAATTCTAAT+GGG 0.416885 7.3:+65376541 None:intergenic
GTGAGTAAATTCTCAAGGAT+TGG 0.417544 7.3:+65376370 None:intergenic
AGCACAAAGTTGAGCCATAT+GGG 0.457271 7.3:+65376622 None:intergenic
TGAGTAAATTCTCAAGGATT+GGG 0.457540 7.3:+65376371 None:intergenic
AATAGGAAGTGCAGCATCTC+GGG 0.459627 7.3:+65376708 None:intergenic
TAGCACAAAGTTGAGCCATA+TGG 0.461051 7.3:+65376621 None:intergenic
ACATTGCGAACTGCTTTCAA+TGG 0.466186 7.3:+65376238 None:intergenic
CTCTGTCCACATAGAGATGA+AGG 0.476912 7.3:+65376581 None:intergenic
AGCGATCCCTCACGATTAAA+GGG 0.477909 7.3:+65376337 None:intergenic
CGAGTAACAGTATCCCCATA+TGG 0.479391 7.3:-65376636 MS.gene62747:CDS
ATATGGGGATACTGTTACTC+GGG 0.479941 7.3:+65376638 None:intergenic
CGGGTCAAATTATGAAAAGT+AGG 0.496081 7.3:+65376075 None:intergenic
TACGAGAAGTAAACTCCAGC+CGG 0.498764 7.3:+65376055 None:intergenic
TATTAAGACTTTCCGTCTCA+AGG 0.504509 7.3:-65376689 MS.gene62747:CDS
CATATGGGGATACTGTTACT+CGG 0.513430 7.3:+65376637 None:intergenic
CAAGCGGATATTGATTGTGT+TGG 0.526450 7.3:-65376271 MS.gene62747:CDS
AGAGAAGGAAGTAGAACCGA+AGG 0.527419 7.3:+65376469 None:intergenic
AAGGAAAACCCTTGTCCATA+CGG 0.534697 7.3:+65376488 None:intergenic
TTCATCTCTATGTGGACAGA+GGG 0.536682 7.3:-65376579 MS.gene62747:CDS
GATCGCTTACCTCTGAAGAA+TGG 0.546125 7.3:-65376321 MS.gene62747:CDS
TAATAGGAAGTGCAGCATCT+CGG 0.546702 7.3:+65376707 None:intergenic
CATCTCTATGTGGACAGAGG+GGG 0.550500 7.3:-65376577 MS.gene62747:CDS
CTTAAATAACTTGATCCAAG+CGG 0.552272 7.3:-65376287 MS.gene62747:CDS
TCAAATTATGAAAAGTAGGA+AGG 0.561424 7.3:+65376079 None:intergenic
CAACACAATCAATATCCGCT+TGG 0.576658 7.3:+65376272 None:intergenic
ATTAACAGACGGACATAGCA+TGG 0.602363 7.3:-65375869 MS.gene62747:intron
ACGAGAAGTAAACTCCAGCC+GGG 0.610447 7.3:+65376056 None:intergenic
TTTGGTTTCCGTATGGACAA+GGG 0.612583 7.3:-65376496 MS.gene62747:CDS
CATATGTGAGTAAATTCTCA+AGG 0.612617 7.3:+65376365 None:intergenic
AATCATATAGCGCCTTGAGA+CGG 0.613866 7.3:+65376677 None:intergenic
TGATGTGCCCTTTAATCGTG+AGG 0.616906 7.3:-65376344 MS.gene62747:CDS
TGAAAACCTTCATCTCTATG+TGG 0.619909 7.3:-65376587 MS.gene62747:CDS
GGAAGGCAATCTTTACAGCA+AGG 0.629622 7.3:+65376096 None:intergenic
GCACAAAGTTGAGCCATATG+GGG 0.663457 7.3:+65376623 None:intergenic
GATGTGCCCTTTAATCGTGA+GGG 0.664869 7.3:-65376343 MS.gene62747:CDS
TCATCTCTATGTGGACAGAG+GGG 0.666250 7.3:-65376578 MS.gene62747:CDS
CTCAACTTTGTGCTACCACG+CGG 0.671498 7.3:-65376613 MS.gene62747:CDS
CTTCATCTCTATGTGGACAG+AGG 0.679618 7.3:-65376580 MS.gene62747:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAATTAAAACACATAA+AGG + chr7.3:65376734-65376753 None:intergenic 10.0%
!! AAGACAAATTGTTAGAAATA+AGG + chr7.3:65376500-65376519 None:intergenic 20.0%
!! TACTTACTATAGAATTGAAT+TGG - chr7.3:65376458-65376477 MS.gene62747:CDS 20.0%
!!! AGATTTTATGTCATTTCTAA+AGG - chr7.3:65376235-65376254 MS.gene62747:CDS 20.0%
!!! GATTTTATGTCATTTCTAAA+GGG - chr7.3:65376236-65376255 MS.gene62747:CDS 20.0%
! AGATATTATCCTTAACAAAC+CGG + chr7.3:65376660-65376679 None:intergenic 25.0%
! CTGCATGTTAAAATTCTAAT+GGG + chr7.3:65376095-65376114 None:intergenic 25.0%
! TCAAATTATGAAAAGTAGGA+AGG + chr7.3:65376557-65376576 None:intergenic 25.0%
! TTTGTCTTTGTACATATTCT+AGG - chr7.3:65376512-65376531 MS.gene62747:CDS 25.0%
!! TTTTGTGCATTATTAACAGA+CGG - chr7.3:65376753-65376772 MS.gene62747:CDS 25.0%
ATTTATTTATTCGTCCAGTG+TGG - chr7.3:65376693-65376712 MS.gene62747:CDS 30.0%
CATATGTGAGTAAATTCTCA+AGG + chr7.3:65376271-65376290 None:intergenic 30.0%
CCTGCATGTTAAAATTCTAA+TGG + chr7.3:65376096-65376115 None:intergenic 30.0%
CTTAAATAACTTGATCCAAG+CGG - chr7.3:65376346-65376365 MS.gene62747:CDS 30.0%
TCAAAATCTTGACATTGATC+CGG - chr7.3:65376638-65376657 MS.gene62747:CDS 30.0%
TGAGTAAATTCTCAAGGATT+GGG + chr7.3:65376265-65376284 None:intergenic 30.0%
TTCTCTCAAAACTCTTCATT+TGG - chr7.3:65376181-65376200 MS.gene62747:intron 30.0%
TTTATTTATTCGTCCAGTGT+GGG - chr7.3:65376694-65376713 MS.gene62747:CDS 30.0%
!! CCATTAGAATTTTAACATGC+AGG - chr7.3:65376093-65376112 MS.gene62747:CDS 30.0%
!! CTACTTTTCATAATTTGACC+CGG - chr7.3:65376559-65376578 MS.gene62747:CDS 30.0%
!!! AAATGAAGAGTTTTGAGAGA+AGG + chr7.3:65376182-65376201 None:intergenic 30.0%
!!! AATGTCAAGATTTTGAAGCT+TGG + chr7.3:65376634-65376653 None:intergenic 30.0%
!!! ATGTCAAGATTTTGAAGCTT+GGG + chr7.3:65376633-65376652 None:intergenic 30.0%
CGGGTCAAATTATGAAAAGT+AGG + chr7.3:65376561-65376580 None:intergenic 35.0%
GTGAGTAAATTCTCAAGGAT+TGG + chr7.3:65376266-65376285 None:intergenic 35.0%
TATTAAGACTTTCCGTCTCA+AGG - chr7.3:65375944-65375963 MS.gene62747:intron 35.0%
TGAAAACCTTCATCTCTATG+TGG - chr7.3:65376046-65376065 MS.gene62747:intron 35.0%
TTGAGACGGAAAGTCTTAAT+AGG + chr7.3:65375945-65375964 None:intergenic 35.0%
! AAAGCTTTTCCATTCTTCAG+AGG + chr7.3:65376324-65376343 None:intergenic 35.0%
! CTCTTCATTTGGAACAGATT+CGG - chr7.3:65376192-65376211 MS.gene62747:intron 35.0%
!! ATTTGGAACAGATTCGGTTT+TGG - chr7.3:65376198-65376217 MS.gene62747:intron 35.0%
!!! CTTGTTGTTCTCAAGCTTTT+TGG - chr7.3:65376119-65376138 MS.gene62747:intron 35.0%
!!! TGTCAAGATTTTGAAGCTTG+GGG + chr7.3:65376632-65376651 None:intergenic 35.0%
AAGGAAAACCCTTGTCCATA+CGG + chr7.3:65376148-65376167 None:intergenic 40.0%
AATCATATAGCGCCTTGAGA+CGG + chr7.3:65375959-65375978 None:intergenic 40.0%
ACATTGCGAACTGCTTTCAA+TGG + chr7.3:65376398-65376417 None:intergenic 40.0%
AGCACAAAGTTGAGCCATAT+GGG + chr7.3:65376014-65376033 None:intergenic 40.0%
ATATGGGGATACTGTTACTC+GGG + chr7.3:65375998-65376017 None:intergenic 40.0%
ATTAACAGACGGACATAGCA+TGG - chr7.3:65376764-65376783 MS.gene62747:CDS 40.0%
CAACACAATCAATATCCGCT+TGG + chr7.3:65376364-65376383 None:intergenic 40.0%
CATATGGGGATACTGTTACT+CGG + chr7.3:65375999-65376018 None:intergenic 40.0%
GTATGTTAAAAGTCCCACAC+TGG + chr7.3:65376710-65376729 None:intergenic 40.0%
TAGCACAAAGTTGAGCCATA+TGG + chr7.3:65376015-65376034 None:intergenic 40.0%
TTCATCTCTATGTGGACAGA+GGG - chr7.3:65376054-65376073 MS.gene62747:intron 40.0%
! CAAGCGGATATTGATTGTGT+TGG - chr7.3:65376362-65376381 MS.gene62747:CDS 40.0%
! TAATAGGAAGTGCAGCATCT+CGG + chr7.3:65375929-65375948 None:intergenic 40.0%
! TATGGACAAGGGTTTTCCTT+CGG - chr7.3:65376148-65376167 MS.gene62747:intron 40.0%
! TTTGGTTTCCGTATGGACAA+GGG - chr7.3:65376137-65376156 MS.gene62747:intron 40.0%
! TTTTCATAATTTGACCCGGC+TGG - chr7.3:65376563-65376582 MS.gene62747:CDS 40.0%
!! GACATTGATCCGGTTTGTTA+AGG - chr7.3:65376648-65376667 MS.gene62747:CDS 40.0%
!! TCTGAGCTTTGAGTTTGATC+AGG - chr7.3:65376424-65376443 MS.gene62747:CDS 40.0%
!!! CAAGCTTTTTGGTTTCCGTA+TGG - chr7.3:65376130-65376149 MS.gene62747:intron 40.0%
!!! TTTTGGTTTCCGTATGGACA+AGG - chr7.3:65376136-65376155 MS.gene62747:intron 40.0%
AAGCGATCCCTCACGATTAA+AGG + chr7.3:65376300-65376319 None:intergenic 45.0%
AGAGAAGGAAGTAGAACCGA+AGG + chr7.3:65376167-65376186 None:intergenic 45.0%
AGCGATCCCTCACGATTAAA+GGG + chr7.3:65376299-65376318 None:intergenic 45.0%
CGAGTAACAGTATCCCCATA+TGG - chr7.3:65375997-65376016 MS.gene62747:intron 45.0%
CTCTGTCCACATAGAGATGA+AGG + chr7.3:65376055-65376074 None:intergenic 45.0%
CTTCATCTCTATGTGGACAG+AGG - chr7.3:65376053-65376072 MS.gene62747:intron 45.0%
GATGTGCCCTTTAATCGTGA+GGG - chr7.3:65376290-65376309 MS.gene62747:CDS 45.0%
GCACAAAGTTGAGCCATATG+GGG + chr7.3:65376013-65376032 None:intergenic 45.0%
GGAAGGCAATCTTTACAGCA+AGG + chr7.3:65376540-65376559 None:intergenic 45.0%
TACGAGAAGTAAACTCCAGC+CGG + chr7.3:65376581-65376600 None:intergenic 45.0%
TCATCTCTATGTGGACAGAG+GGG - chr7.3:65376055-65376074 MS.gene62747:intron 45.0%
TGATGTGCCCTTTAATCGTG+AGG - chr7.3:65376289-65376308 MS.gene62747:CDS 45.0%
! AATAGGAAGTGCAGCATCTC+GGG + chr7.3:65375928-65375947 None:intergenic 45.0%
! GATCGCTTACCTCTGAAGAA+TGG - chr7.3:65376312-65376331 MS.gene62747:CDS 45.0%
ACGAGAAGTAAACTCCAGCC+GGG + chr7.3:65376580-65376599 None:intergenic 50.0%
CATCTCTATGTGGACAGAGG+GGG - chr7.3:65376056-65376075 MS.gene62747:intron 50.0%
CTCAACTTTGTGCTACCACG+CGG - chr7.3:65376020-65376039 MS.gene62747:intron 50.0%
TTACTCGGGCAGTGAAGTTC+AGG + chr7.3:65375984-65376003 None:intergenic 50.0%
! TGAAGGTTTTCAACACCGCG+TGG + chr7.3:65376038-65376057 None:intergenic 50.0%
!!! GATTTTGAAGCTTGGGGCAG+TGG + chr7.3:65376626-65376645 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 65375864 65376791 65375864 ID=MS.gene62747
chr7.3 mRNA 65375864 65376791 65375864 ID=MS.gene62747.t1;Parent=MS.gene62747
chr7.3 exon 65376210 65376791 65376210 ID=MS.gene62747.t1.exon1;Parent=MS.gene62747.t1
chr7.3 CDS 65376210 65376791 65376210 ID=cds.MS.gene62747.t1;Parent=MS.gene62747.t1
chr7.3 exon 65376058 65376121 65376058 ID=MS.gene62747.t1.exon2;Parent=MS.gene62747.t1
chr7.3 CDS 65376058 65376121 65376058 ID=cds.MS.gene62747.t1;Parent=MS.gene62747.t1
chr7.3 exon 65375864 65375883 65375864 ID=MS.gene62747.t1.exon3;Parent=MS.gene62747.t1
chr7.3 CDS 65375864 65375883 65375864 ID=cds.MS.gene62747.t1;Parent=MS.gene62747.t1
Gene Sequence

>MS.gene62747

ATGGTGCGCGAGAAAAACATTGAGTTTCGATTTAACGACTTTATATACTCAGTTTTGCTGTCCCGAGATGCTGCACTTCCTATTAAGACTTTCCGTCTCAAGGCGCTATATGATTCTCCTGAACTTCACTGCCCGAGTAACAGTATCCCCATATGGCTCAACTTTGTGCTACCACGCGGTGTTGAAAACCTTCATCTCTATGTGGACAGAGGGGGTTTACAAAAATTACCCATTAGAATTTTAACATGCAGGACGCTTGTTGTTCTCAAGCTTTTTGGTTTCCGTATGGACAAGGGTTTTCCTTCGGTTCTACTTCCTTCTCTCAAAACTCTTCATTTGGAACAGATTCGGTTTTGGTTTCTTGAACTTCGAGATTTTATGTCATTTCTAAAGGGTTGCCCAATCCTTGAGAATTTACTCACATATGATGTGCCCTTTAATCGTGAGGGATCGCTTACCTCTGAAGAATGGAAAAGCTTTTGCTTAAATAACTTGATCCAAGCGGATATTGATTGTGTTGGTTCTTATTTTCCATTGAAAGCAGTTCGCAATGTACTGTCTCTGAGCTTTGAGTTTGATCAGGTCTGTTAATGATACTTACTATAGAATTGAATTGGAAAAAATATACGTTTGCCTTATTTCTAACAATTTGTCTTTGTACATATTCTAGGATCCTTGCTGTAAAGATTGCCTTCCTACTTTTCATAATTTGACCCGGCTGGAGTTTACTTCTCGTAATTTCTTAATAGAAGTTCTGAACCACTGCCCCAAGCTTCAAAATCTTGACATTGATCCGGTTTGTTAAGGATAATATCTTATTTATTTATTTATTTATTTATTCGTCCAGTGTGGGACTTTTAACATACACCTTTATGTGTTTTAATTTATTTTTTGTGCATTATTAACAGACGGACATAGCATGGCCTAG
Protein sequence

>MS.gene62747.t1

MVREKNIEFRFNDFIYSVLLSRDAALPIKTFRLKALYDSPELHCPSNSIPIWLNFVLPRGVENLHLYVDRGGLQKLPIRILTCRTLVVLKLFGFRMDKGFPSVLLPSLKTLHLEQIRFWFLELRDFMSFLKGCPILENLLTYDVPFNREGSLTSEEWKSFCLNNLIQADIDCVGSYFPLKAVRNVLSLSFEFDQDPCCKDCLPTFHNLTRLEFTSHGHSMA