AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0244080

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0244080 MtrunA17_Chr2g0303381 87.946 224 24 2 1 223 89 310 4.94e-144 404
Msa0244080 MtrunA17_Chr2g0303401 87.946 224 24 2 1 223 89 310 4.94e-144 404
Msa0244080 MtrunA17_Chr2g0297811 56.195 226 91 5 1 223 89 309 5.24e-67 208
Msa0244080 MtrunA17_Chr2g0297801 56.195 226 91 5 1 223 89 309 5.24e-67 208
Msa0244080 MtrunA17_Chr2g0297791 56.195 226 91 5 1 223 89 309 5.24e-67 208
Msa0244080 MtrunA17_Chr2g0297731 45.455 231 104 6 1 220 78 297 4.63e-60 190
Msa0244080 MtrunA17_Chr8g0350511 47.111 225 102 4 1 222 89 299 5.18e-60 190
Msa0244080 MtrunA17_Chr8g0350521 47.111 225 102 4 1 222 89 299 5.18e-60 190
Msa0244080 MtrunA17_Chr8g0350541 47.111 225 102 4 1 222 89 299 5.18e-60 190
Msa0244080 MtrunA17_Chr8g0350501 47.111 225 102 4 1 222 89 299 5.18e-60 190
Msa0244080 MtrunA17_Chr8g0350531 47.111 225 102 4 1 222 353 563 2.14e-57 190
Msa0244080 MtrunA17_Chr8g0350531 44.595 222 92 5 1 216 89 285 1.42e-47 164
Msa0244080 MtrunA17_Chr2g0297761 45.022 231 103 9 1 220 78 295 4.92e-53 172
Msa0244080 MtrunA17_Chr2g0297771 45.022 231 103 9 1 220 78 295 4.92e-53 172
Msa0244080 MtrunA17_Chr2g0297781 45.022 231 103 9 1 220 78 295 4.92e-53 172
Msa0244080 MtrunA17_Chr8g0350551 43.556 225 96 4 1 222 89 285 3.82e-52 169
Msa0244080 MtrunA17_Chr8g0350441 40.090 222 115 5 1 221 87 291 5.07e-47 157
Msa0244080 MtrunA17_Chr8g0350431 40.367 218 112 5 1 217 87 287 3.30e-44 149
Msa0244080 MtrunA17_Chr8g0350421 40.367 218 112 5 1 217 87 287 3.30e-44 149
Msa0244080 MtrunA17_Chr8g0350411 40.367 218 112 5 1 217 87 287 3.30e-44 149
Msa0244080 MtrunA17_Chr8g0350451 40.179 224 101 5 1 223 87 278 1.57e-42 145
Msa0244080 MtrunA17_Chr8g0350461 40.179 224 101 5 1 223 87 278 1.57e-42 145
Msa0244080 MtrunA17_Chr8g0350471 40.179 224 101 5 1 223 87 278 1.57e-42 145
Msa0244080 MtrunA17_Chr2g0327611 31.633 196 112 7 1 191 99 277 1.49e-22 92.8
Msa0244080 MtrunA17_Chr6g0481561 30.732 205 114 6 1 199 106 288 8.09e-22 91.3
Msa0244080 MtrunA17_Chr2g0327601 31.068 206 112 7 1 199 103 285 1.82e-18 82.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 49 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCACTACCACAAATTGTTT+TGG 0.245343 2_2:-22075803 Msa0244080:CDS
TGTAGCTAGTAATCAATTAT+TGG 0.249179 2_2:+22075470 None:intergenic
ATTCAATCCTAAGGAGAAAA+AGG 0.297710 2_2:-22076087 Msa0244080:CDS
GGACACATATTCCATGGATT+TGG 0.302531 2_2:+22075851 None:intergenic
TTACGGTGAGCTTAAACTTT+TGG 0.347612 2_2:-22075679 Msa0244080:CDS
GATATGTCTGATCGAGCTTA+TGG 0.361529 2_2:+22076049 None:intergenic
CCCAAAACAATTTGTGGTAG+TGG 0.365132 2_2:+22075802 None:intergenic
TACCTTGTCAATGATGATTC+TGG 0.380807 2_2:-22076008 Msa0244080:CDS
ACAATTTGTGGTAGTGGGCT+TGG 0.408360 2_2:+22075808 None:intergenic
CACTGCACTAGCATAATTGA+TGG 0.434540 2_2:-22075978 Msa0244080:CDS
AATCAACTAATAACGGATTA+CGG 0.451454 2_2:-22075696 Msa0244080:CDS
ATCATCAAACTCATCCTTTG+AGG 0.453286 2_2:+22075725 None:intergenic
CGGTTCATCTTAGTATCAGC+TGG 0.454457 2_2:+22075639 None:intergenic
AGCATTTCCTCCAAGATGTA+AGG 0.467593 2_2:+22075507 None:intergenic
TGTGGTCCCAAAACAATTTG+TGG 0.468651 2_2:+22075796 None:intergenic
TATATCGATTCTAGTGTGAC+TGG 0.486159 2_2:-22075936 Msa0244080:CDS
GATGTCATTGCTCGGTGGGT+TGG 0.490586 2_2:+22075533 None:intergenic
AACCGAGAGGTGTTCATTGA+GGG 0.499384 2_2:-22075621 Msa0244080:CDS
CGCCCTCAATGAACACCTCT+CGG 0.504404 2_2:+22075619 None:intergenic
TGACATCGAGCCTTACATCT+TGG 0.507062 2_2:-22075517 Msa0244080:CDS
TCTCTACAATCAACTAATAA+CGG 0.510522 2_2:-22075703 Msa0244080:CDS
CCAAAACAATTTGTGGTAGT+GGG 0.514829 2_2:+22075803 None:intergenic
CTAGTAATCAATTATTGGTA+AGG 0.518596 2_2:+22075475 None:intergenic
ATCAACAGCAAATCACTCCT+TGG 0.519679 2_2:-22075585 Msa0244080:CDS
TAAATATCCATTCAATCCTA+AGG 0.520789 2_2:-22076096 Msa0244080:CDS
GCTGACTTCTCCAACTGCAT+TGG 0.521072 2_2:-22075912 Msa0244080:CDS
AATAACTTGTCCAATGCAGT+TGG 0.521593 2_2:+22075902 None:intergenic
ATTTGTGGTAGTGGGCTTGG+AGG 0.527426 2_2:+22075811 None:intergenic
GCTCGATGTCATTGCTCGGT+GGG 0.532171 2_2:+22075529 None:intergenic
GAGGAGCTCTGTCGGAGCAA+TGG 0.538177 2_2:+22075830 None:intergenic
ATGAAGGTTATGATAACTAT+CGG 0.552996 2_2:-22076131 Msa0244080:CDS
CATCGAGCCTTACATCTTGG+AGG 0.554478 2_2:-22075514 Msa0244080:CDS
TAAGCATGTATCCAAATCCA+TGG 0.557313 2_2:-22075862 Msa0244080:CDS
CATCTTAGTATCAGCTGGAT+CGG 0.557541 2_2:+22075644 None:intergenic
TGAATGGATATTTAGTGCCA+TGG 0.560003 2_2:+22076105 None:intergenic
GAACCGAGAGGTGTTCATTG+AGG 0.566347 2_2:-22075622 Msa0244080:CDS
CAATCAAACTATATCCTCAA+AGG 0.567378 2_2:-22075739 Msa0244080:CDS
AGCAATGGACACATATTCCA+TGG 0.567858 2_2:+22075845 None:intergenic
GGCTCGATGTCATTGCTCGG+TGG 0.574776 2_2:+22075528 None:intergenic
ATATCGATTCTAGTGTGACT+GGG 0.576037 2_2:-22075935 Msa0244080:CDS
TGGGCTTGGAGGAGCTCTGT+CGG 0.577415 2_2:+22075822 None:intergenic
ATGATAACTATCGGAGGCCA+TGG 0.579102 2_2:-22076122 Msa0244080:CDS
TAAGGCTCGATGTCATTGCT+CGG 0.600452 2_2:+22075525 None:intergenic
AGTTATTAAACATCTCAAGA+AGG 0.601516 2_2:-22075886 Msa0244080:CDS
TACCAGAATCATCATTGACA+AGG 0.665409 2_2:+22076006 None:intergenic
CATCAATTATGCTAGTGCAG+TGG 0.677859 2_2:+22075979 None:intergenic
AAGGTTATGATAACTATCGG+AGG 0.701816 2_2:-22076128 Msa0244080:CDS
TATCGATTCTAGTGTGACTG+GGG 0.708158 2_2:-22075934 Msa0244080:CDS
TGATACTAAGATGAACCGAG+AGG 0.777827 2_2:-22075634 Msa0244080:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGAAGGTTATGATAACTAT+CGG - chr2_2:22075482-22075501 Msa0244080:CDS 25.0%
! TAAATATCCATTCAATCCTA+AGG - chr2_2:22075517-22075536 Msa0244080:CDS 25.0%
! AGTTATTAAACATCTCAAGA+AGG - chr2_2:22075727-22075746 Msa0244080:CDS 25.0%
! TCTCTACAATCAACTAATAA+CGG - chr2_2:22075910-22075929 Msa0244080:CDS 25.0%
!!! AATCAACTAATAACGGATTA+CGG - chr2_2:22075917-22075936 Msa0244080:CDS 25.0%
! TTTTTCTCCTTAGGATTGAA+TGG + chr2_2:22075527-22075546 None:intergenic 30.0%
ATTCAATCCTAAGGAGAAAA+AGG - chr2_2:22075526-22075545 Msa0244080:CDS 30.0%
!! CATAGTTGATATCCATTTTG+TGG + chr2_2:22075838-22075857 None:intergenic 30.0%
CAATCAAACTATATCCTCAA+AGG - chr2_2:22075874-22075893 Msa0244080:CDS 30.0%
AAGGTTATGATAACTATCGG+AGG - chr2_2:22075485-22075504 Msa0244080:CDS 35.0%
TGAATGGATATTTAGTGCCA+TGG + chr2_2:22075511-22075530 None:intergenic 35.0%
ATCCTAAGGAGAAAAAGGTA+TGG - chr2_2:22075531-22075550 Msa0244080:CDS 35.0%
! ATCCATACCTTTTTCTCCTT+AGG + chr2_2:22075536-22075555 None:intergenic 35.0%
TACCTTGTCAATGATGATTC+TGG - chr2_2:22075605-22075624 Msa0244080:CDS 35.0%
TACCAGAATCATCATTGACA+AGG + chr2_2:22075610-22075629 None:intergenic 35.0%
!! TATATCGATTCTAGTGTGAC+TGG - chr2_2:22075677-22075696 Msa0244080:CDS 35.0%
!! ATATCGATTCTAGTGTGACT+GGG - chr2_2:22075678-22075697 Msa0244080:CDS 35.0%
! AATAACTTGTCCAATGCAGT+TGG + chr2_2:22075714-22075733 None:intergenic 35.0%
TAAGCATGTATCCAAATCCA+TGG - chr2_2:22075751-22075770 Msa0244080:CDS 35.0%
CCAAAACAATTTGTGGTAGT+GGG + chr2_2:22075813-22075832 None:intergenic 35.0%
! CCACTACCACAAATTGTTTT+GGG - chr2_2:22075811-22075830 Msa0244080:CDS 35.0%
!!! ATTGTTTTGGGACCACAAAA+TGG - chr2_2:22075823-22075842 Msa0244080:CDS 35.0%
ATCATCAAACTCATCCTTTG+AGG + chr2_2:22075891-22075910 None:intergenic 35.0%
! TTACGGTGAGCTTAAACTTT+TGG - chr2_2:22075934-22075953 Msa0244080:CDS 35.0%
GATATGTCTGATCGAGCTTA+TGG + chr2_2:22075567-22075586 None:intergenic 40.0%
CATCAATTATGCTAGTGCAG+TGG + chr2_2:22075637-22075656 None:intergenic 40.0%
CACTGCACTAGCATAATTGA+TGG - chr2_2:22075635-22075654 Msa0244080:CDS 40.0%
!! TATCGATTCTAGTGTGACTG+GGG - chr2_2:22075679-22075698 Msa0244080:CDS 40.0%
GGACACATATTCCATGGATT+TGG + chr2_2:22075765-22075784 None:intergenic 40.0%
AGCAATGGACACATATTCCA+TGG + chr2_2:22075771-22075790 None:intergenic 40.0%
! CCCACTACCACAAATTGTTT+TGG - chr2_2:22075810-22075829 Msa0244080:CDS 40.0%
CCCAAAACAATTTGTGGTAG+TGG + chr2_2:22075814-22075833 None:intergenic 40.0%
TGTGGTCCCAAAACAATTTG+TGG + chr2_2:22075820-22075839 None:intergenic 40.0%
CATCTTAGTATCAGCTGGAT+CGG + chr2_2:22075972-22075991 None:intergenic 40.0%
TGATACTAAGATGAACCGAG+AGG - chr2_2:22075979-22075998 Msa0244080:CDS 40.0%
ATCAACAGCAAATCACTCCT+TGG - chr2_2:22076028-22076047 Msa0244080:CDS 40.0%
! CACTCCTTGGACTTTTTGTT+TGG - chr2_2:22076041-22076060 Msa0244080:CDS 40.0%
CACTCCAAACAAAAAGTCCA+AGG + chr2_2:22076048-22076067 None:intergenic 40.0%
AGCATTTCCTCCAAGATGTA+AGG + chr2_2:22076109-22076128 None:intergenic 40.0%
ATGATAACTATCGGAGGCCA+TGG - chr2_2:22075491-22075510 Msa0244080:CDS 45.0%
!! ACAATTTGTGGTAGTGGGCT+TGG + chr2_2:22075808-22075827 None:intergenic 45.0%
! GGTGAGCTTAAACTTTTGGC+AGG - chr2_2:22075938-22075957 Msa0244080:CDS 45.0%
CGGTTCATCTTAGTATCAGC+TGG + chr2_2:22075977-22075996 None:intergenic 45.0%
!! AACCGAGAGGTGTTCATTGA+GGG - chr2_2:22075992-22076011 Msa0244080:CDS 45.0%
TAAGGCTCGATGTCATTGCT+CGG + chr2_2:22076091-22076110 None:intergenic 45.0%
TGACATCGAGCCTTACATCT+TGG - chr2_2:22076096-22076115 Msa0244080:CDS 45.0%
! GCTGACTTCTCCAACTGCAT+TGG - chr2_2:22075701-22075720 Msa0244080:CDS 50.0%
!! ATTTGTGGTAGTGGGCTTGG+AGG + chr2_2:22075805-22075824 None:intergenic 50.0%
!! GAACCGAGAGGTGTTCATTG+AGG - chr2_2:22075991-22076010 Msa0244080:CDS 50.0%
CATCGAGCCTTACATCTTGG+AGG - chr2_2:22076099-22076118 Msa0244080:CDS 50.0%
CGCCCTCAATGAACACCTCT+CGG + chr2_2:22075997-22076016 None:intergenic 55.0%
! GATGTCATTGCTCGGTGGGT+TGG + chr2_2:22076083-22076102 None:intergenic 55.0%
GCTCGATGTCATTGCTCGGT+GGG + chr2_2:22076087-22076106 None:intergenic 55.0%
GAGGAGCTCTGTCGGAGCAA+TGG + chr2_2:22075786-22075805 None:intergenic 60.0%
TGGGCTTGGAGGAGCTCTGT+CGG + chr2_2:22075794-22075813 None:intergenic 60.0%
GGCTCGATGTCATTGCTCGG+TGG + chr2_2:22076088-22076107 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 22075482 22076153 22075482 ID=Msa0244080;Name=Msa0244080
chr2_2 mRNA 22075482 22076153 22075482 ID=Msa0244080-mRNA-1;Parent=Msa0244080;Name=Msa0244080-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|-1|0|1|-1|1|1|0|223
chr2_2 exon 22075482 22076153 22075482 ID=Msa0244080-mRNA-1:exon:8564;Parent=Msa0244080-mRNA-1
chr2_2 CDS 22075482 22076153 22075482 ID=Msa0244080-mRNA-1:cds;Parent=Msa0244080-mRNA-1
Gene Sequence

>Msa0244080

ATGAAGGTTATGATAACTATCGGAGGCCATGGCACTAAATATCCATTCAATCCTAAGGAGAAAAAGGTATGGATTTTCAATGCCATAAGCTCGATCAGACATATCATTCAAGACTATGAGAACTACCTTGTCAATGATGATTCTGGTAGCTGCCACTGCACTAGCATAATTGATGGTATTGATATTAACTATGAGTATATCGATTCTAGTGTGACTGGGGCTGACTTCTCCAACTGCATTGGACAAGTTATTAAACATCTCAAGAAGGATAAGCATGTATCCAAATCCATGGAATATGTGTCCATTGCTCCGACAGAGCTCCTCCAAGCCCACTACCACAAATTGTTTTGGGACCACAAAATGGATATCAACTATGTTGACTACAAGTTCTACAATCAAACTATATCCTCAAAGGATGAGTTTGATGATCTCTACAATCAACTAATAACGGATTACGGTGAGCTTAAACTTTTGGCAGGTGTTAGTACCGATCCAGCTGATACTAAGATGAACCGAGAGGTGTTCATTGAGGGCGTCACAAGACTGATCAACAGCAAATCACTCCTTGGACTTTTTGTTTGGAGTGCTAATGACTCTACCAACCCACCGAGCAATGACATCGAGCCTTACATCTTGGAGGAAATGCTACAAGATCTCCTTACCAATAATTGA
Protein sequence

>Msa0244080

MKVMITIGGHGTKYPFNPKEKKVWIFNAISSIRHIIQDYENYLVNDDSGSCHCTSIIDGIDINYEYIDSSVTGADFSNCIGQVIKHLKKDKHVSKSMEYVSIAPTELLQAHYHKLFWDHKMDINYVDYKFYNQTISSKDEFDDLYNQLITDYGELKLLAGVSTDPADTKMNREVFIEGVTRLINSKSLLGLFVWSANDSTNPPSNDIEPYILEEMLQDLLTNN*