AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene94620

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene94620.t1 MTR_2g084510 86.420 243 32 1 5 247 1 242 2.15e-157 436
MS.gene94620.t1 MTR_2g084525 87.295 244 30 1 4 247 1 243 1.73e-143 401
MS.gene94620.t1 MTR_2g084495 60.246 244 83 4 4 247 1 230 3.26e-92 271
MS.gene94620.t1 MTR_2g060540 73.793 145 37 1 2 146 5 148 3.39e-75 225
MS.gene94620.t1 MTR_2g060500 74.648 142 35 1 2 143 5 145 8.39e-75 224
MS.gene94620.t1 MTR_1g062160 37.600 250 102 9 2 246 1 201 1.33e-43 146
MS.gene94620.t1 MTR_7g102790 38.866 247 104 8 2 246 1 202 7.08e-41 139
MS.gene94620.t1 MTR_4g078170 33.878 245 104 7 8 246 16 208 1.04e-33 121
MS.gene94620.t1 MTR_5g030130 44.056 143 69 4 8 150 36 167 1.06e-33 122
MS.gene94620.t1 MTR_5g007230 34.310 239 104 7 8 246 22 207 1.22e-33 121
MS.gene94620.t1 MTR_5g030130 44.604 139 66 4 8 146 36 163 2.86e-33 119
MS.gene94620.t1 MTR_8g066820 43.478 138 67 4 8 145 34 160 2.35e-30 113
MS.gene94620.t1 MTR_4g094680 29.583 240 142 7 9 247 24 237 8.83e-25 98.6
MS.gene94620.t1 MTR_2g083710 65.079 63 21 1 2 64 1 62 1.25e-23 90.9
MS.gene94620.t1 MTR_4g116300 35.915 142 80 4 8 149 6 136 2.16e-21 90.1
MS.gene94620.t1 MTR_2g055210 27.451 255 154 9 7 246 101 339 1.10e-20 89.7
MS.gene94620.t1 MTR_2g083720 42.276 123 32 2 2 124 1 84 3.29e-20 82.4
MS.gene94620.t1 MTR_8g105930 32.692 156 87 5 9 151 15 165 2.75e-18 81.3
MS.gene94620.t1 MTR_2g036170 34.459 148 79 6 9 156 39 168 5.52e-17 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene94620.t1 AT1G43000 36.032 247 120 8 3 246 12 223 2.37e-37 131
MS.gene94620.t1 AT1G43000 36.032 247 120 8 3 246 5 216 3.47e-37 130
MS.gene94620.t1 AT1G21000 34.677 248 145 8 3 246 12 246 3.68e-37 131
MS.gene94620.t1 AT1G21000 34.677 248 145 8 3 246 9 243 4.13e-37 131
MS.gene94620.t1 AT1G76590 33.745 243 141 8 8 246 19 245 5.73e-37 130
MS.gene94620.t1 AT1G32700 35.714 238 108 7 9 246 14 206 8.58e-32 116
MS.gene94620.t1 AT4G17900 46.763 139 62 5 8 145 35 162 8.70e-31 114
MS.gene94620.t1 AT4G17900 46.763 139 62 5 8 145 21 148 2.21e-30 112
MS.gene94620.t1 AT2G27930 44.604 139 74 3 9 146 6 142 4.87e-30 110
MS.gene94620.t1 AT2G27930 44.604 139 74 3 9 146 6 142 4.87e-30 110
MS.gene94620.t1 AT2G27930 44.853 136 72 3 9 143 6 139 1.23e-29 110
MS.gene94620.t1 AT2G27930 44.853 136 72 3 9 143 6 139 1.23e-29 110
MS.gene94620.t1 AT1G32700 35.238 210 92 6 37 246 2 167 2.07e-26 101
MS.gene94620.t1 AT1G31040 27.888 251 139 8 9 246 21 242 1.46e-24 98.2
MS.gene94620.t1 AT2G01818 31.276 243 130 10 9 247 13 222 1.70e-22 92.4
MS.gene94620.t1 AT2G12646 37.589 141 76 5 9 149 8 136 5.53e-22 91.7
MS.gene94620.t1 AT2G12646 37.589 141 76 5 9 149 8 136 5.53e-22 91.7
MS.gene94620.t1 AT2G12646 37.589 141 76 5 9 149 5 133 5.69e-22 91.7
MS.gene94620.t1 AT5G46710 32.365 241 115 10 9 246 30 225 2.36e-21 89.4
MS.gene94620.t1 AT5G46710 32.365 241 115 10 9 246 14 209 2.55e-21 89.0
MS.gene94620.t1 AT5G46710 41.176 136 68 5 9 143 30 154 1.36e-20 85.9
MS.gene94620.t1 AT3G60670 37.226 137 74 5 9 145 9 133 1.06e-18 82.8
MS.gene94620.t1 AT2G27930 46.341 82 43 1 63 143 61 142 3.25e-15 72.0
MS.gene94620.t1 AT2G27930 46.341 82 43 1 63 143 61 142 3.25e-15 72.0

Find 25 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATTTCTTCCATCTCTTT+TGG 0.137837 2.4:-14915539 None:intergenic
CCAGTTTGCGTTTATCAAAA+AGG 0.264489 2.4:+14915496 MS.gene94620:intron
TCTATACAAGATTCACAAAA+TGG 0.271078 2.4:-14914637 None:intergenic
CGCTAGAATTGATGAGAAAA+AGG 0.285964 2.4:+14915652 MS.gene94620:CDS
GAGATGTGATATATATCTTA+TGG 0.328572 2.4:+14915033 MS.gene94620:CDS
CCCAAAAGAGATGGAAGAAA+TGG 0.335283 2.4:+14915538 MS.gene94620:CDS
CAATGTTGAACCTCTTAGAT+TGG 0.356311 2.4:-14914976 None:intergenic
AAGAATGCTTTCTCTGTCAT+TGG 0.368617 2.4:-14915711 None:intergenic
ACCTTGGCTTGTAAACTTGC+TGG 0.395128 2.4:+14914522 MS.gene94620:CDS
AAAGAAAGGGAATAGCTCAT+AGG 0.424904 2.4:+14915777 MS.gene94620:CDS
TGAAGCCGATGAGCGATTAA+CGG 0.434087 2.4:-14915735 None:intergenic
AATGTTGAACCTCTTAGATT+GGG 0.435133 2.4:-14914975 None:intergenic
GAAGCCGATGAGCGATTAAC+GGG 0.442394 2.4:-14915734 None:intergenic
AAGAAAGGGAATAGCTCATA+GGG 0.490291 2.4:+14915778 MS.gene94620:CDS
ACTAGAGCTATTAATGACAT+AGG 0.514121 2.4:-14914924 None:intergenic
GCCAGCAAGTTTACAAGCCA+AGG 0.514131 2.4:-14914523 None:intergenic
GAGCTCATGCCCAATCTAAG+AGG 0.532616 2.4:+14914966 MS.gene94620:CDS
TCTTCCCGTTAATCGCTCAT+CGG 0.540242 2.4:+14915730 MS.gene94620:CDS
AGGATATGATGTGTGTACCT+TGG 0.542052 2.4:+14914506 MS.gene94620:intron
TTTCGTAAACCCAAAAGAGA+TGG 0.546273 2.4:+14915529 MS.gene94620:CDS
ATATCTAGAGCAATCAATCA+AGG 0.554194 2.4:+14915565 MS.gene94620:CDS
TACAAACATGTAGACATCCT+CGG 0.578107 2.4:+14914893 MS.gene94620:CDS
TGACATAGGTTTGAATTCCG+AGG 0.586337 2.4:-14914910 None:intergenic
CAATCTAAGAGGTTCAACAT+TGG 0.620728 2.4:+14914977 MS.gene94620:CDS
CAATGATAAATCAGATAAGG+AGG 0.638313 2.4:+14914834 MS.gene94620:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATATAAAAAAAATATAAT+AGG - chr2.4:14915106-14915125 None:intergenic 0.0%
!!! ATTTTTTAATTTTGTTTCTT+AGG + chr2.4:14914486-14914505 MS.gene94620:intron 10.0%
!! GAAAAAAAATACAAAGAATT+AGG - chr2.4:14914458-14914477 None:intergenic 15.0%
!!! AGTTAAATTTGCTTATATTT+AGG + chr2.4:14915283-14915302 MS.gene94620:intron 15.0%
!!! ATAAGCAAATTTAACTTTTT+AGG - chr2.4:14915279-14915298 None:intergenic 15.0%
!!! TCAAATTTGCTTATATATTT+AGG - chr2.4:14915184-14915203 None:intergenic 15.0%
!! ATTAATAGTAATAAAAGGAG+TGG - chr2.4:14915331-14915350 None:intergenic 20.0%
!! CATTTAATTAATGATGTATG+TGG - chr2.4:14915254-14915273 None:intergenic 20.0%
!!! TCCTTTTATTACTATTAATC+CGG + chr2.4:14915332-14915351 MS.gene94620:intron 20.0%
! AAGCCAAATTCAAAAAGAAA+GGG + chr2.4:14915764-14915783 MS.gene94620:CDS 25.0%
! CATTCAATTAATGATGTATG+TGG + chr2.4:14915215-14915234 MS.gene94620:intron 25.0%
! GAGATGTGATATATATCTTA+TGG + chr2.4:14915033-14915052 MS.gene94620:CDS 25.0%
! TCCGGATTAATAGTAATAAA+AGG - chr2.4:14915336-14915355 None:intergenic 25.0%
! TCTATACAAGATTCACAAAA+TGG - chr2.4:14914640-14914659 None:intergenic 25.0%
! TTGATTACTAGATCTTATCT+AGG + chr2.4:14914707-14914726 MS.gene94620:intron 25.0%
! TTGCAATGATAAATCAGATA+AGG + chr2.4:14914831-14914850 MS.gene94620:intron 25.0%
!! AATTTGCTTATATTTAGGAC+CGG + chr2.4:14915288-14915307 MS.gene94620:intron 25.0%
!! ATTCCCTTTCTTTTTGAATT+TGG - chr2.4:14915770-14915789 None:intergenic 25.0%
!! TTTGCTTATATATTTAGGAC+CGG - chr2.4:14915179-14915198 None:intergenic 25.0%
!!! ATTTTGTTTGCTGCATTTTT+TGG - chr2.4:14915612-14915631 None:intergenic 25.0%
AAGTACAATAACTGGTATTC+TGG - chr2.4:14915419-14915438 None:intergenic 30.0%
AATAACTGGTATTCTGGTAA+TGG - chr2.4:14915413-14915432 None:intergenic 30.0%
AATGTTGAACCTCTTAGATT+GGG - chr2.4:14914978-14914997 None:intergenic 30.0%
AATTGATGAGAAAAAGGAAG+AGG + chr2.4:14915658-14915677 MS.gene94620:CDS 30.0%
ACTAGAGCTATTAATGACAT+AGG - chr2.4:14914927-14914946 None:intergenic 30.0%
AGGTTCAACATTGGAAAAAT+CGG + chr2.4:14914986-14915005 MS.gene94620:CDS 30.0%
ATCAACGTAAGTACAATAAC+TGG - chr2.4:14915427-14915446 None:intergenic 30.0%
CAAATTAAACAACACTCACT+TGG - chr2.4:14914690-14914709 None:intergenic 30.0%
CAAGCCAAATTCAAAAAGAA+AGG + chr2.4:14915763-14915782 MS.gene94620:CDS 30.0%
CAATGATAAATCAGATAAGG+AGG + chr2.4:14914834-14914853 MS.gene94620:intron 30.0%
GATGTATGTGGTTCATATTA+TGG - chr2.4:14915242-14915261 None:intergenic 30.0%
GTAGAAAAAGAAATGGAAGA+AGG + chr2.4:14915686-14915705 MS.gene94620:CDS 30.0%
TTTGCGTTTATCAAAAAGGA+TGG + chr2.4:14915500-14915519 MS.gene94620:CDS 30.0%
! ATATCTAGAGCAATCAATCA+AGG + chr2.4:14915565-14915584 MS.gene94620:CDS 30.0%
!! ATTTTTGGACTTGTTTGGAT+GGG - chr2.4:14914578-14914597 None:intergenic 30.0%
!! TTTTTGGCCTTCTCTTTTTT+AGG - chr2.4:14915596-14915615 None:intergenic 30.0%
AAAGAAAGGGAATAGCTCAT+AGG + chr2.4:14915777-14915796 MS.gene94620:CDS 35.0%
AAGAAAGGGAATAGCTCATA+GGG + chr2.4:14915778-14915797 MS.gene94620:CDS 35.0%
AAGAATGCTTTCTCTGTCAT+TGG - chr2.4:14915714-14915733 None:intergenic 35.0%
ACTATTAATCCGGAGATTGA+AGG + chr2.4:14915342-14915361 MS.gene94620:intron 35.0%
CAAACAAGTCCAAAAATGAG+CGG + chr2.4:14914581-14914600 MS.gene94620:CDS 35.0%
CAATCTAAGAGGTTCAACAT+TGG + chr2.4:14914977-14914996 MS.gene94620:CDS 35.0%
CAATGTTGAACCTCTTAGAT+TGG - chr2.4:14914979-14914998 None:intergenic 35.0%
CCAGTTTGCGTTTATCAAAA+AGG + chr2.4:14915496-14915515 MS.gene94620:intron 35.0%
CGCTAGAATTGATGAGAAAA+AGG + chr2.4:14915652-14915671 MS.gene94620:CDS 35.0%
GGAAGACGTAGAAAAAGAAA+TGG + chr2.4:14915679-14915698 MS.gene94620:CDS 35.0%
GGAATAAAATATACTCCCTC+CGG - chr2.4:14915310-14915329 None:intergenic 35.0%
TACAAACATGTAGACATCCT+CGG + chr2.4:14914893-14914912 MS.gene94620:CDS 35.0%
TTTCGTAAACCCAAAAGAGA+TGG + chr2.4:14915529-14915548 MS.gene94620:CDS 35.0%
! CCATTTCTTCCATCTCTTTT+GGG - chr2.4:14915541-14915560 None:intergenic 35.0%
! CCTTTTTGATAAACGCAAAC+TGG - chr2.4:14915499-14915518 None:intergenic 35.0%
! CTTATATATTTAGGACCGGA+GGG - chr2.4:14915175-14915194 None:intergenic 35.0%
! GATTTTCAATATTGCAGTCG+AGG - chr2.4:14914618-14914637 None:intergenic 35.0%
! TAGCATGCAAGGTGAATTTT+TGG + chr2.4:14915077-14915096 MS.gene94620:intron 35.0%
! TCCATTTCTTCCATCTCTTT+TGG - chr2.4:14915542-14915561 None:intergenic 35.0%
!! CATTTTTGGACTTGTTTGGA+TGG - chr2.4:14914579-14914598 None:intergenic 35.0%
AGGATATGATGTGTGTACCT+TGG + chr2.4:14914506-14914525 MS.gene94620:intron 40.0%
CATTACATGCCTTCAATCTC+CGG - chr2.4:14915354-14915373 None:intergenic 40.0%
CCCAAAAGAGATGGAAGAAA+TGG + chr2.4:14915538-14915557 MS.gene94620:CDS 40.0%
GCGTTTATCAAAAAGGATGG+AGG + chr2.4:14915503-14915522 MS.gene94620:CDS 40.0%
TGAAAAACTAGTACTCCCTC+CGG + chr2.4:14915157-14915176 MS.gene94620:intron 40.0%
TGACATAGGTTTGAATTCCG+AGG - chr2.4:14914913-14914932 None:intergenic 40.0%
TGGAAAAATCGGTCACAGTA+GGG + chr2.4:14914997-14915016 MS.gene94620:CDS 40.0%
TTGGAAAAATCGGTCACAGT+AGG + chr2.4:14914996-14915015 MS.gene94620:CDS 40.0%
! CTTTTGCTCTTTAGCATGCA+AGG + chr2.4:14915066-14915085 MS.gene94620:CDS 40.0%
! GCTTATATATTTAGGACCGG+AGG - chr2.4:14915176-14915195 None:intergenic 40.0%
! TGCTTATATTTAGGACCGGA+GGG + chr2.4:14915292-14915311 MS.gene94620:intron 40.0%
! TTGCTTATATTTAGGACCGG+AGG + chr2.4:14915291-14915310 MS.gene94620:intron 40.0%
!! CGCTCATTTTTGGACTTGTT+TGG - chr2.4:14914583-14914602 None:intergenic 40.0%
!! GAACTTGTTCCGCTCATTTT+TGG - chr2.4:14914593-14914612 None:intergenic 40.0%
GGAAAAATCGGTCACAGTAG+GGG + chr2.4:14914998-14915017 MS.gene94620:CDS 45.0%
GGCATCGCCTAAAAAAGAGA+AGG + chr2.4:14915586-14915605 MS.gene94620:CDS 45.0%
TCTTCCCGTTAATCGCTCAT+CGG + chr2.4:14915730-14915749 MS.gene94620:CDS 45.0%
TGAAGCCGATGAGCGATTAA+CGG - chr2.4:14915738-14915757 None:intergenic 45.0%
! CGGAGATTGAAGGCATGTAA+TGG + chr2.4:14915352-14915371 MS.gene94620:intron 45.0%
!! ACCTTGGCTTGTAAACTTGC+TGG + chr2.4:14914522-14914541 MS.gene94620:CDS 45.0%
!!! TTTTTATATTATGTTTTAAA+CGG + chr2.4:14915115-14915134 MS.gene94620:intron 5.0%
GAAGCCGATGAGCGATTAAC+GGG - chr2.4:14915737-14915756 None:intergenic 50.0%
GAGCTCATGCCCAATCTAAG+AGG + chr2.4:14914966-14914985 MS.gene94620:CDS 50.0%
GCCAGCAAGTTTACAAGCCA+AGG - chr2.4:14914526-14914545 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 14914416 14915814 14914416 ID=MS.gene94620
chr2.4 mRNA 14914416 14915814 14914416 ID=MS.gene94620.t1;Parent=MS.gene94620
chr2.4 exon 14914416 14914421 14914416 ID=MS.gene94620.t1.exon1;Parent=MS.gene94620.t1
chr2.4 CDS 14914416 14914421 14914416 ID=cds.MS.gene94620.t1;Parent=MS.gene94620.t1
chr2.4 exon 14914508 14914690 14914508 ID=MS.gene94620.t1.exon2;Parent=MS.gene94620.t1
chr2.4 CDS 14914508 14914690 14914508 ID=cds.MS.gene94620.t1;Parent=MS.gene94620.t1
chr2.4 exon 14914848 14915087 14914848 ID=MS.gene94620.t1.exon3;Parent=MS.gene94620.t1
chr2.4 CDS 14914848 14915087 14914848 ID=cds.MS.gene94620.t1;Parent=MS.gene94620.t1
chr2.4 exon 14915500 14915814 14915500 ID=MS.gene94620.t1.exon4;Parent=MS.gene94620.t1
chr2.4 CDS 14915500 14915814 14915500 ID=cds.MS.gene94620.t1;Parent=MS.gene94620.t1
Gene Sequence

>MS.gene94620

ATGATGGTAATATCTATGCATTTTAATTATAATGTCAAGCCTAATTCTTTGTATTTTTTTTCTTAATGCAATTTTTTAATTTTGTTTCTTAGGATATGATGTGTGTACCTTGGCTTGTAAACTTGCTGGCAATCACTTCGTTTTTCACAACATGTGAAACCCATCCAAACAAGTCCAAAAATGAGCGGAACAAGTTCTGCCTCGACTGCAATATTGAAAATCCATTTTGTGAATCTTGTATAGAATCTCGTCACAAAGATCATCAAATAATCCAAGTGAGTGTTGTTTAATTTGATTACTAGATCTTATCTAGGTATCTGTGTTGTATCTCTTTCTCTTCGATTTTGTTTTTGTTACACTTAAGCAATTTTAATTAATTTTTTTTACTATGTTATGTAAATATGAATTCTTATATTTGCAATGATAAATCAGATAAGGAGGTCATCATATAATGAAGTAGTGAAGACTAGTGAAATTTACAAACATGTAGACATCCTCGGAATTCAAACCTATGTCATTAATAGCTCTAGTGTTGTATACTTAAACAAGAGAGCTCATGCCCAATCTAAGAGGTTCAACATTGGAAAAATCGGTCACAGTAGGGGAGCTTTTTGTAAGAGATGTGATATATATCTTATGGACTCTACTCACTTTTGCTCTTTAGCATGCAAGGTGAATTTTTGGTCTCCTATTATATTTTTTTTATATTATGTTTTAAACGGTAAAAAAAAGTTCAATATATGAAAAACTAGTACTCCCTCCGGTCCTAAATATATAAGCAAATTTGACTTTTTAGATTCATTCAATTAATGATGTATGTGGTCCATAATATGAACCACATACATCATTAATTAAATGAACCTAAAAAGTTAAATTTGCTTATATTTAGGACCGGAGGGAGTATATTTTATTCCACTCCTTTTATTACTATTAATCCGGAGATTGAAGGCATGTAATGGATATTATAAGTTTATAACTTATACTTTTCTTTCAACCATTACCAGAATACCAGTTATTGTACTTACGTTGATTTTCTTTTCTTTTTGAAAGAATGATTAATTAATGTTGCATTATATGATACCAGTTTGCGTTTATCAAAAAGGATGGAGGCTTTTTCGTAAACCCAAAAGAGATGGAAGAAATGGAAAGATATCTAGAGCAATCAATCAAGGCATCGCCTAAAAAAGAGAAGGCCAAAAAATGCAGCAAACAAAATCTGAAACGAAAATTAGAAGACGCTAGAATTGATGAGAAAAAGGAAGAGGAAGACGTAGAAAAAGAAATGGAAGAAGGCGCCAATGACAGAGAAAGCATTCTTCCCGTTAATCGCTCATCGGCTTCACTTCGCAAGCCAAATTCAAAAAGAAAGGGAATAGCTCATAGGGCACCTTTTTTTTAA
Protein sequence

>MS.gene94620.t1

MMDMMCVPWLVNLLAITSFFTTCETHPNKSKNERNKFCLDCNIENPFCESCIESRHKDHQIIQIRRSSYNEVVKTSEIYKHVDILGIQTYVINSSSVVYLNKRAHAQSKRFNIGKIGHSRGAFCKRCDIYLMDSTHFCSLACKFAFIKKDGGFFVNPKEMEEMERYLEQSIKASPKKEKAKKCSKQNLKRKLEDARIDEKKEEEDVEKEMEEGANDRESILPVNRSSASLRKPNSKRKGIAHRAPFF