AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0720350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0720350 MtrunA17_Chr8g0339011 56.069 173 36 3 7 140 874 1045 4.49e-53 180
Msa0720350 MtrunA17_Chr8g0338901 54.913 173 38 3 7 140 901 1072 4.19e-51 174
Msa0720350 MtrunA17_Chr8g0370511 54.749 179 32 4 1 140 874 1042 9.77e-50 170
Msa0720350 MtrunA17_Chr8g0338981 49.000 200 30 4 12 140 883 1081 2.35e-44 155
Msa0720350 MtrunA17_Chr5g0414761 53.939 165 36 3 15 140 673 836 7.08e-43 150
Msa0720350 MtrunA17_Chr5g0420341 48.824 170 64 3 1 148 875 1043 3.10e-42 149
Msa0720350 MtrunA17_Chr8g0339031 47.337 169 57 3 3 140 882 1049 2.64e-38 137
Msa0720350 MtrunA17_Chr3g0114381 43.750 176 59 2 3 139 110 284 2.85e-38 131
Msa0720350 MtrunA17_Chr3g0085731 46.552 174 53 2 3 137 883 1055 9.90e-38 136
Msa0720350 MtrunA17_Chr8g0338931 43.889 180 61 2 1 141 11 189 2.54e-37 129
Msa0720350 MtrunA17_Chr3g0085531 44.706 170 54 2 10 140 80 248 3.47e-37 130
Msa0720350 MtrunA17_Chr8g0339021 45.294 170 70 2 1 148 864 1032 9.37e-37 133
Msa0720350 MtrunA17_Chr5g0430541 44.253 174 58 1 7 141 389 562 1.15e-36 132
Msa0720350 MtrunA17_Chr5g0420331 48.667 150 54 3 1 128 875 1023 9.73e-36 130
Msa0720350 MtrunA17_Chr2g0296451 44.720 161 65 2 3 139 394 554 4.11e-35 127
Msa0720350 MtrunA17_Chr8g0352221 41.667 180 64 3 3 142 791 969 2.55e-34 126
Msa0720350 MtrunA17_Chr7g0223531 42.262 168 67 2 3 140 891 1058 2.26e-32 120
Msa0720350 MtrunA17_Chr8g0338881 66.279 86 28 1 3 87 905 990 6.82e-32 119
Msa0720350 MtrunA17_Chr8g0338841 41.420 169 58 2 1 130 317 483 4.42e-30 113
Msa0720350 MtrunA17_Chr8g0352211 62.791 86 32 0 3 88 805 890 1.43e-29 112
Msa0720350 MtrunA17_Chr8g0338801 35.870 184 61 4 15 142 85 267 1.75e-23 93.6
Msa0720350 MtrunA17_Chr6g0455131 38.739 111 64 1 1 107 976 1086 7.48e-20 85.1
Msa0720350 MtrunA17_Chr7g0257531 37.838 111 64 2 1 107 532 641 1.26e-19 84.3
Msa0720350 MtrunA17_Chr6g0455221 38.739 111 63 2 1 107 988 1097 2.95e-19 83.6
Msa0720350 MtrunA17_Chr6g0454911 38.739 111 63 2 1 107 110 219 3.05e-19 81.3
Msa0720350 MtrunA17_Chr3g0135571 38.776 98 55 2 14 107 10 106 6.86e-19 78.6
Msa0720350 MtrunA17_Chr4g0009401 42.056 107 56 3 5 105 1378 1484 6.99e-18 79.3
Msa0720350 MtrunA17_Chr5g0411061 94.737 38 2 0 103 140 1 38 7.90e-18 72.8
Msa0720350 MtrunA17_Chr4g0009041 42.708 96 51 1 14 105 1395 1490 7.93e-18 79.3
Msa0720350 MtrunA17_Chr3g0135511 37.755 98 56 2 14 107 10 106 8.16e-18 75.9
Msa0720350 MtrunA17_Chr6g0455251 39.640 111 59 3 1 107 1000 1106 1.59e-17 78.6
Msa0720350 MtrunA17_Chr3g0135541 38.776 98 55 2 14 107 162 258 1.65e-17 77.4
Msa0720350 MtrunA17_Chr6g0455191 36.036 111 66 2 1 107 1200 1309 3.56e-17 77.4
Msa0720350 MtrunA17_Chr6g0454961 34.234 111 69 1 1 107 919 1029 4.02e-17 77.4
Msa0720350 MtrunA17_Chr6g0454971 38.739 111 63 2 1 107 915 1024 4.16e-17 77.0
Msa0720350 MtrunA17_Chr4g0009361 46.341 82 43 1 7 87 395 476 5.32e-17 77.0
Msa0720350 MtrunA17_Chr4g0014821 40.206 97 52 4 15 107 7 101 5.86e-17 73.6
Msa0720350 MtrunA17_Chr4g0005891 42.697 89 48 3 1 88 932 1018 7.73e-17 76.3
Msa0720350 MtrunA17_Chr6g0454951 35.780 109 65 2 1 105 969 1076 8.79e-17 76.3
Msa0720350 MtrunA17_Chr4g0009141 42.574 101 53 2 10 105 1402 1502 2.49e-16 75.1
Msa0720350 MtrunA17_Chr6g0455211 37.838 111 64 2 1 107 917 1026 2.60e-16 75.1
Msa0720350 MtrunA17_Chr7g0234901 44.828 87 45 2 1 87 409 492 4.78e-16 73.9
Msa0720350 MtrunA17_Chr6g0455551 35.714 98 59 1 14 107 980 1077 6.72e-16 73.6
Msa0720350 MtrunA17_Chr8g0343781 74.419 43 11 0 45 87 1 43 8.22e-16 68.2
Msa0720350 MtrunA17_Chr4g0005851 43.182 88 48 2 2 88 918 1004 9.31e-16 73.2
Msa0720350 MtrunA17_Chr6g0454851 35.135 111 67 2 1 107 975 1084 1.54e-15 72.8
Msa0720350 MtrunA17_Chr4g0005591 37.778 90 55 1 1 90 960 1048 1.56e-15 72.8
Msa0720350 MtrunA17_Chr4g0009241 40.385 104 56 3 5 102 1400 1503 5.00e-15 71.2
Msa0720350 MtrunA17_Chr7g0255681 42.529 87 47 2 1 87 1901 1984 1.43e-14 70.1
Msa0720350 MtrunA17_Chr4g0010711 43.373 83 44 2 1 83 1394 1473 5.61e-14 68.2
Msa0720350 MtrunA17_Chr4g0005871 40.964 83 47 2 7 88 1013 1094 7.39e-14 67.8
Msa0720350 MtrunA17_Chr4g0009101 36.735 98 56 2 12 105 1423 1518 9.94e-13 64.7
Msa0720350 MtrunA17_Chr6g0454831 33.019 106 66 2 1 102 890 994 9.95e-13 64.7
Msa0720350 MtrunA17_Chr6g0454821 35.789 95 57 1 17 107 940 1034 1.28e-12 64.3
Msa0720350 MtrunA17_Chr4g0009301 40.404 99 53 3 12 105 1425 1522 2.12e-12 63.5
Msa0720350 MtrunA17_Chr4g0009171 37.113 97 57 1 13 105 1611 1707 2.40e-12 63.5
Msa0720350 MtrunA17_Chr6g0455031 35.135 111 55 3 13 107 904 1013 5.58e-12 62.4
Msa0720350 MtrunA17_Chr4g0009011 38.776 98 54 2 12 105 175 270 6.78e-12 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCAGGGGTTGGCAATTTC+TGG 0.137983 5_1:-16302543 None:intergenic
TGATGTTCCTTCACATTTAT+AGG 0.202253 5_1:-16302611 None:intergenic
CTGTGTCTTGCTTGTAAATC+TGG 0.264591 5_1:-16302774 None:intergenic
CGGGCGACAATTATCCTTCT+TGG 0.279147 5_1:+16302584 Msa0720350:CDS
ACATAAAATCATTCCCTTCA+TGG 0.316491 5_1:-16302668 None:intergenic
ACTTCCTCCATCATATTTGA+TGG 0.351281 5_1:-16302939 None:intergenic
AGAAAAGAATCTCTAGAATC+AGG 0.353994 5_1:-16302559 None:intergenic
TGTACTTCCTCTTCAGCTGA+TGG 0.430305 5_1:-16303038 None:intergenic
TGCACTTCCACTTCATGTAA+TGG 0.431239 5_1:-16302990 None:intergenic
TTTCCGTTTGGCTTCAGTAA+TGG 0.461310 5_1:-16303091 None:intergenic
CAAGACACAGTGACTAAGAT+TGG 0.472059 5_1:+16302787 Msa0720350:CDS
ATATGACTAGTCGAATGCTT+TGG 0.472120 5_1:+16302908 Msa0720350:intron
AATTGAGCCATTACATGAAG+TGG 0.472186 5_1:+16302983 Msa0720350:CDS
GAAAAGAATCTCTAGAATCA+GGG 0.487299 5_1:-16302558 None:intergenic
ACCATCACCAAATGTGAAAA+CGG 0.490531 5_1:+16303013 Msa0720350:CDS
TAGGGAAACATTCGATTGCC+AGG 0.493291 5_1:-16302717 None:intergenic
TTCATCAACATCTGAAAACC+TGG 0.501296 5_1:+16302699 Msa0720350:CDS
AATCACTATTATCGGGCACT+TGG 0.501628 5_1:-16302642 None:intergenic
AATTGAGCCATCAAATATGA+TGG 0.522488 5_1:+16302932 Msa0720350:CDS
CATTTATAGGCTAACCAAGA+AGG 0.525338 5_1:-16302598 None:intergenic
AACGGAGCCATCAGCTGAAG+AGG 0.549662 5_1:+16303031 Msa0720350:CDS
CAAGAAGGATAATTGTCGCC+CGG 0.561804 5_1:-16302583 None:intergenic
TGGTTAGCCTATAAATGTGA+AGG 0.579037 5_1:+16302604 Msa0720350:CDS
GAATCTCTAGAATCAGGGGT+TGG 0.584728 5_1:-16302553 None:intergenic
TAATTAATGATCAAGACACT+AGG 0.592041 5_1:-16302736 None:intergenic
CACAGTGACTAAGATTGGCA+AGG 0.622378 5_1:+16302792 Msa0720350:CDS
AATTAATGATCAAGACACTA+GGG 0.625643 5_1:-16302735 None:intergenic
AAAAGAATCTCTAGAATCAG+GGG 0.626080 5_1:-16302557 None:intergenic
TGAGCCATCAAATATGATGG+AGG 0.653957 5_1:+16302935 Msa0720350:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CAAGGTTTAATATCAAATTT+TGG + chr5_1:16302810-16302829 Msa0720350:intron 20.0%
!!! TTTTTTTTTACAGTAAGTGA+TGG - chr5_1:16303066-16303085 None:intergenic 20.0%
! ATGGAAAAATCACTATTATC+GGG - chr5_1:16302652-16302671 None:intergenic 25.0%
! CATGGAAAAATCACTATTAT+CGG - chr5_1:16302653-16302672 None:intergenic 25.0%
!! TAATAGTGATTTTTCCATGA+AGG + chr5_1:16302654-16302673 Msa0720350:CDS 25.0%
!! AATAGTGATTTTTCCATGAA+GGG + chr5_1:16302655-16302674 Msa0720350:CDS 25.0%
! AATTAATGATCAAGACACTA+GGG - chr5_1:16302738-16302757 None:intergenic 25.0%
! TAATTAATGATCAAGACACT+AGG - chr5_1:16302739-16302758 None:intergenic 25.0%
!! GGTTTAATATCAAATTTTGG+AGG + chr5_1:16302813-16302832 Msa0720350:intron 25.0%
!!! TCAATTTTTTTATCAGTCGA+CGG - chr5_1:16302969-16302988 None:intergenic 25.0%
!! AAAAGAATCTCTAGAATCAG+GGG - chr5_1:16302560-16302579 None:intergenic 30.0%
!! GAAAAGAATCTCTAGAATCA+GGG - chr5_1:16302561-16302580 None:intergenic 30.0%
!! AGAAAAGAATCTCTAGAATC+AGG - chr5_1:16302562-16302581 None:intergenic 30.0%
!! TTCTAGAGATTCTTTTCTTC+CGG + chr5_1:16302564-16302583 Msa0720350:CDS 30.0%
TGATGTTCCTTCACATTTAT+AGG - chr5_1:16302614-16302633 None:intergenic 30.0%
ACATAAAATCATTCCCTTCA+TGG - chr5_1:16302671-16302690 None:intergenic 30.0%
AATTGAGCCATCAAATATGA+TGG + chr5_1:16302932-16302951 Msa0720350:CDS 30.0%
!!! CAATTTTTTTATCAGTCGAC+GGG - chr5_1:16302968-16302987 None:intergenic 30.0%
! TCTAGAGATTCTTTTCTTCC+GGG + chr5_1:16302565-16302584 Msa0720350:CDS 35.0%
CATTTATAGGCTAACCAAGA+AGG - chr5_1:16302601-16302620 None:intergenic 35.0%
!! TGGTTAGCCTATAAATGTGA+AGG + chr5_1:16302604-16302623 Msa0720350:CDS 35.0%
TTCATCAACATCTGAAAACC+TGG + chr5_1:16302699-16302718 Msa0720350:CDS 35.0%
! ATTTTCGTAGCTATTGGACA+TGG + chr5_1:16302852-16302871 Msa0720350:intron 35.0%
! ATATGACTAGTCGAATGCTT+TGG + chr5_1:16302908-16302927 Msa0720350:intron 35.0%
ACTTCCTCCATCATATTTGA+TGG - chr5_1:16302942-16302961 None:intergenic 35.0%
AATTGAGCCATTACATGAAG+TGG + chr5_1:16302983-16303002 Msa0720350:CDS 35.0%
ACCATCACCAAATGTGAAAA+CGG + chr5_1:16303013-16303032 Msa0720350:CDS 35.0%
AATCACTATTATCGGGCACT+TGG - chr5_1:16302645-16302664 None:intergenic 40.0%
CTGTGTCTTGCTTGTAAATC+TGG - chr5_1:16302777-16302796 None:intergenic 40.0%
CAAGACACAGTGACTAAGAT+TGG + chr5_1:16302787-16302806 Msa0720350:CDS 40.0%
!! TTTTGGAGGTTGTGACAATG+TGG + chr5_1:16302827-16302846 Msa0720350:intron 40.0%
! GTGGAGATTTTCGTAGCTAT+TGG + chr5_1:16302846-16302865 Msa0720350:intron 40.0%
! TTGGACATGGACTGACTATT+AGG + chr5_1:16302865-16302884 Msa0720350:intron 40.0%
! TGGACATGGACTGACTATTA+GGG + chr5_1:16302866-16302885 Msa0720350:intron 40.0%
TGAGCCATCAAATATGATGG+AGG + chr5_1:16302935-16302954 Msa0720350:CDS 40.0%
TGCACTTCCACTTCATGTAA+TGG - chr5_1:16302993-16303012 None:intergenic 40.0%
!! TCCGTTTTCACATTTGGTGA+TGG - chr5_1:16303017-16303036 None:intergenic 40.0%
! AATCAGGGGTTGGCAATTTC+TGG - chr5_1:16302546-16302565 None:intergenic 45.0%
!! GAATCTCTAGAATCAGGGGT+TGG - chr5_1:16302556-16302575 None:intergenic 45.0%
CAAGAAGGATAATTGTCGCC+CGG - chr5_1:16302586-16302605 None:intergenic 45.0%
TAGGGAAACATTCGATTGCC+AGG - chr5_1:16302720-16302739 None:intergenic 45.0%
CACAGTGACTAAGATTGGCA+AGG + chr5_1:16302792-16302811 Msa0720350:CDS 45.0%
GGACTGACTATTAGGGAAAC+AGG + chr5_1:16302873-16302892 Msa0720350:intron 45.0%
! GATGGCTCCGTTTTCACATT+TGG - chr5_1:16303023-16303042 None:intergenic 45.0%
TGTACTTCCTCTTCAGCTGA+TGG - chr5_1:16303041-16303060 None:intergenic 45.0%
CGGGCGACAATTATCCTTCT+TGG + chr5_1:16302584-16302603 Msa0720350:CDS 50.0%
AACGGAGCCATCAGCTGAAG+AGG + chr5_1:16303031-16303050 Msa0720350:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 16302538 16303100 16302538 ID=Msa0720350;Name=Msa0720350
chr5_1 mRNA 16302538 16303100 16302538 ID=Msa0720350-mRNA-1;Parent=Msa0720350;Name=Msa0720350-mRNA-1;_AED=0.14;_eAED=0.25;_QI=0|0|0|1|1|1|2|0|152
chr5_1 exon 16302538 16302813 16302538 ID=Msa0720350-mRNA-1:exon:6240;Parent=Msa0720350-mRNA-1
chr5_1 exon 16302918 16303100 16302918 ID=Msa0720350-mRNA-1:exon:6241;Parent=Msa0720350-mRNA-1
chr5_1 CDS 16302538 16302813 16302538 ID=Msa0720350-mRNA-1:cds;Parent=Msa0720350-mRNA-1
chr5_1 CDS 16302918 16303100 16302918 ID=Msa0720350-mRNA-1:cds;Parent=Msa0720350-mRNA-1
Gene Sequence

>Msa0720350

ATGATCCAGAAATTGCCAACCCCTGATTCTAGAGATTCTTTTCTTCCGGGCGACAATTATCCTTCTTGGTTAGCCTATAAATGTGAAGGAACATCAGTACTTCTCCAAGTGCCCGATAATAGTGATTTTTCCATGAAGGGAATGATTTTATGTGTTCTTTATTCATCAACATCTGAAAACCTGGCAATCGAATGTTTCCCTAGTGTCTTGATCATTAATTACACAAAATTCACTATCCAGATTTACAAGCAAGACACAGTGACTAAGATTGGCAAGTCGAATGCTTTGGAAATTGAGCCATCAAATATGATGGAGGAAGTTGACCCGTCGACTGATAAAAAAATTGAGCCATTACATGAAGTGGAAGTGCAACCATCACCAAATGTGAAAACGGAGCCATCAGCTGAAGAGGAAGTACAAACCATCACTTACTGTAAAAAAAAAATGAGCCATTACTGA
Protein sequence

>Msa0720350

MIQKLPTPDSRDSFLPGDNYPSWLAYKCEGTSVLLQVPDNSDFSMKGMILCVLYSSTSENLAIECFPSVLIINYTKFTIQIYKQDTVTKIGKSNALEIEPSNMMEEVDPSTDKKIEPLHEVEVQPSPNVKTEPSAEEEVQTITYCKKKMSHY*