AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0455630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0455630 MtrunA17_Chr3g0102571 59.777 179 31 2 1 138 238 416 4.92e-65 203
Msa0455630 MtrunA17_Chr3g0102601 55.866 179 38 2 1 138 76 254 8.54e-61 187
Msa0455630 MtrunA17_Chr8g0378831 52.222 180 43 5 1 138 190 368 8.66e-49 160
Msa0455630 MtrunA17_Chr3g0141871 45.455 176 53 4 1 134 190 364 1.71e-40 138
Msa0455630 MtrunA17_Chr8g0378871 42.143 140 46 4 33 138 15 153 1.44e-23 89.7
Msa0455630 MtrunA17_Chr5g0397261 35.429 175 69 6 1 132 198 371 2.17e-23 93.6
Msa0455630 MtrunA17_Chr4g0030151 34.463 177 72 6 1 134 196 371 1.61e-22 90.9
Msa0455630 MtrunA17_Chr7g0248461 32.955 176 72 5 1 132 195 368 5.84e-22 89.7
Msa0455630 MtrunA17_Chr8g0387401 33.333 177 70 6 1 132 209 382 8.83e-22 89.4
Msa0455630 MtrunA17_Chr4g0045841 32.000 175 74 6 1 132 212 384 5.57e-21 87.0
Msa0455630 MtrunA17_Chr4g0030231 33.714 175 72 6 1 132 197 370 2.22e-20 85.1
Msa0455630 MtrunA17_Chr8g0348481 31.250 176 75 5 1 132 194 367 2.48e-20 85.1
Msa0455630 MtrunA17_Chr5g0443351 30.114 176 78 6 2 132 184 359 1.62e-18 80.5
Msa0455630 MtrunA17_Chr4g0030241 55.072 69 21 2 1 59 58 126 1.10e-17 75.1
Msa0455630 MtrunA17_Chr3g0096631 29.545 176 79 6 2 132 187 362 1.86e-17 77.4
Msa0455630 MtrunA17_Chr2g0287271 27.273 176 83 6 2 132 187 362 2.11e-15 71.6
Msa0455630 MtrunA17_Chr6g0482681 27.684 177 81 6 2 132 251 426 3.17e-14 68.2
Msa0455630 MtrunA17_Chr8g0392811 27.841 176 82 6 2 132 279 454 1.87e-13 66.2
Msa0455630 MtrunA17_Chr5g0396361 37.719 114 59 3 1 102 297 410 4.04e-13 65.1
Msa0455630 MtrunA17_Chr8g0390341 47.619 63 24 1 1 54 284 346 6.99e-12 61.6
Msa0455630 MtrunA17_Chr2g0293491 31.298 131 50 3 1 91 160 290 1.41e-11 60.5
Msa0455630 MtrunA17_Chr6g0486031 46.032 63 25 1 1 54 271 333 1.60e-11 60.5
Msa0455630 MtrunA17_Chr8g0383451 44.776 67 28 1 1 58 155 221 1.76e-11 60.5
Msa0455630 MtrunA17_Chr7g0273601 47.619 63 24 1 1 54 264 326 2.33e-11 60.1
Msa0455630 MtrunA17_Chr2g0324461 43.284 67 29 1 1 58 298 364 2.71e-11 60.1
Msa0455630 MtrunA17_Chr2g0317501 43.284 67 29 1 1 58 291 357 4.24e-11 59.3
Msa0455630 MtrunA17_Chr2g0286421 43.284 67 29 1 1 58 259 325 5.29e-11 58.9
Msa0455630 MtrunA17_Chr3g0102581 60.714 56 12 2 15 60 114 169 9.50e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0455630 AT1G10210.2 47.727 176 49 4 1 134 190 364 2.32e-42 144
Msa0455630 AT1G10210.3 47.727 176 49 4 1 134 190 364 2.32e-42 144
Msa0455630 AT1G10210.1 47.727 176 49 4 1 134 190 364 2.32e-42 144
Msa0455630 AT2G18170.1 48.000 175 48 5 1 133 190 363 2.17e-41 141
Msa0455630 AT1G59580.2 46.667 180 51 6 1 136 190 368 3.62e-36 127
Msa0455630 AT1G59580.1 46.667 180 51 6 1 136 190 368 3.62e-36 127
Msa0455630 AT4G36450.1 45.506 178 49 6 1 133 187 361 1.46e-35 125
Msa0455630 AT3G59790.1 31.285 179 74 6 1 134 217 391 2.76e-22 90.9
Msa0455630 AT1G07880.2 34.104 173 68 6 1 129 190 360 2.98e-22 90.5
Msa0455630 AT3G45640.1 35.593 177 64 7 1 131 195 367 5.61e-22 90.1
Msa0455630 AT4G01370.1 32.386 176 73 6 1 132 200 373 1.33e-20 86.3
Msa0455630 AT4G11330.1 32.759 174 73 5 1 131 200 372 3.99e-20 85.1
Msa0455630 AT2G43790.1 29.714 175 78 5 1 132 220 392 2.31e-19 82.8
Msa0455630 AT1G01560.2 30.682 176 74 5 1 131 197 369 3.87e-18 79.3
Msa0455630 AT2G01450.3 29.775 178 76 5 2 132 178 353 4.65e-17 76.6
Msa0455630 AT2G01450.1 29.775 178 76 5 2 132 178 353 4.65e-17 76.6
Msa0455630 AT2G01450.2 29.775 178 76 5 2 132 178 353 4.65e-17 76.6
Msa0455630 AT2G01450.4 29.775 178 76 5 2 132 178 353 4.65e-17 76.6
Msa0455630 AT2G46070.2 50.000 70 26 1 1 61 198 267 5.63e-17 75.9
Msa0455630 AT2G46070.1 50.000 70 26 1 1 61 198 267 6.04e-17 76.3
Msa0455630 AT2G46070.3 50.000 70 26 1 1 61 232 301 6.79e-17 76.3
Msa0455630 AT2G42880.1 29.545 176 79 6 2 132 187 362 2.06e-16 75.1
Msa0455630 AT2G42880.2 29.545 176 79 6 2 132 187 362 2.27e-16 74.7
Msa0455630 AT1G53510.1 29.545 176 79 6 2 132 187 362 7.68e-16 73.2
Msa0455630 AT3G14720.1 27.624 181 76 6 2 132 187 362 9.65e-16 73.2
Msa0455630 AT3G14720.2 27.624 181 76 6 2 132 187 362 1.01e-15 72.8
Msa0455630 AT3G14720.3 27.624 181 76 6 2 132 187 362 1.01e-15 72.8
Msa0455630 AT1G01560.3 50.794 63 22 1 1 54 197 259 2.51e-15 71.6
Msa0455630 AT5G19010.1 26.705 176 84 5 2 132 187 362 3.43e-14 68.6
Msa0455630 AT1G01560.4 51.667 60 20 1 1 51 197 256 3.46e-14 67.8
Msa0455630 AT1G01560.1 51.667 60 20 1 1 51 197 256 3.46e-14 67.8
Msa0455630 AT1G07880.1 53.333 60 19 1 1 51 190 249 3.67e-14 67.4
Msa0455630 AT5G63370.5 46.774 62 24 1 2 54 459 520 6.96e-13 64.7
Msa0455630 AT5G63370.10 46.774 62 24 1 2 54 459 520 6.96e-13 64.7
Msa0455630 AT5G63370.9 46.774 62 24 1 2 54 325 386 7.02e-13 64.7
Msa0455630 AT5G63370.2 46.774 62 24 1 2 54 325 386 7.83e-13 64.7
Msa0455630 AT5G63370.3 46.774 62 24 1 2 54 325 386 7.83e-13 64.7
Msa0455630 AT5G63370.7 46.774 62 24 1 2 54 459 520 8.11e-13 64.7
Msa0455630 AT5G63370.8 46.774 62 24 1 2 54 459 520 8.11e-13 64.7
Msa0455630 AT5G63370.4 46.774 62 24 1 2 54 459 520 8.11e-13 64.7
Msa0455630 AT5G63370.6 46.774 62 24 1 2 54 459 520 8.11e-13 64.7
Msa0455630 AT5G63370.1 46.774 62 24 1 2 54 459 520 8.11e-13 64.7
Msa0455630 AT3G48750.1 32.824 131 48 3 1 91 160 290 1.65e-12 63.2
Msa0455630 AT4G10010.1 37.500 112 50 3 1 103 133 233 2.09e-12 63.5
Msa0455630 AT4G10010.2 37.500 112 50 3 1 103 313 413 2.84e-12 63.2
Msa0455630 AT1G71530.2 38.235 102 44 2 1 93 304 395 4.52e-12 62.4
Msa0455630 AT1G71530.3 38.235 102 44 2 1 93 304 395 6.17e-12 62.0
Msa0455630 AT1G71530.1 38.235 102 44 2 1 93 304 395 8.08e-12 62.0
Msa0455630 AT1G33770.1 45.588 68 28 1 1 59 298 365 1.03e-11 61.6
Msa0455630 AT5G10270.1 45.588 68 28 1 1 59 197 264 1.34e-11 61.2
Msa0455630 AT1G54610.1 36.842 95 49 2 1 84 275 369 1.48e-11 60.8
Msa0455630 AT1G54610.3 36.842 95 49 2 1 84 275 369 1.48e-11 60.8
Msa0455630 AT1G54610.2 36.842 95 49 2 1 84 275 369 1.48e-11 60.8
Msa0455630 AT4G22940.2 43.284 67 29 1 1 58 261 327 4.11e-11 59.7
Msa0455630 AT4G22940.1 43.284 67 29 1 1 58 261 327 4.58e-11 59.7
Msa0455630 AT5G64960.2 39.796 98 45 4 1 85 144 240 4.72e-11 59.7
Msa0455630 AT1G03740.2 44.444 63 26 1 1 54 370 432 4.72e-11 59.7
Msa0455630 AT1G03740.1 44.444 63 26 1 1 54 370 432 4.85e-11 59.7
Msa0455630 AT5G64960.1 39.796 98 45 4 1 85 197 293 5.01e-11 59.3
Msa0455630 AT5G50860.1 44.444 63 26 1 1 54 271 333 6.77e-11 59.3
Msa0455630 AT5G50860.2 44.444 63 26 1 1 54 271 333 9.14e-11 58.9

Find 27 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTCACATTGATGAAAAT+TGG 0.148851 3_3:+48628548 Msa0455630:CDS
AAACTAATTAGAAGTGTTCT+TGG 0.263161 3_3:+48628314 Msa0455630:CDS
ATCGATGGAGGTTCCGTAAT+TGG 0.270595 3_3:-48628208 None:intergenic
TCACATAGATCAGCCATATA+TGG 0.351435 3_3:-48628487 None:intergenic
CACTTCTAATTAGTTTCATC+TGG 0.365659 3_3:-48628307 None:intergenic
TCTTCACATTGATGAAAATT+GGG 0.390420 3_3:+48628549 Msa0455630:CDS
AGCACTCCGACATCCATATA+TGG 0.426106 3_3:+48628474 Msa0455630:CDS
GGCAGAAAGCCAATCTTCCC+TGG 0.432334 3_3:+48628269 Msa0455630:intron
GCAATGACAAAAGCAGCTTC+AGG 0.435785 3_3:-48628622 None:intergenic
TAACTGTCCTCCTCAAGTTC+CGG 0.454540 3_3:+48628522 Msa0455630:CDS
GCATATCCTAAAAGAAGGTC+TGG 0.454898 3_3:-48628186 None:intergenic
TCATCAATGTGAAGATTGAC+CGG 0.493486 3_3:-48628541 None:intergenic
TTAACTCAAGATCAGACTCT+TGG 0.514842 3_3:-48628340 None:intergenic
TCCATCGATGTGTGGTCCGT+AGG 0.525304 3_3:+48628222 Msa0455630:CDS
CCATCGATGTGTGGTCCGTA+GGG 0.537547 3_3:+48628223 Msa0455630:CDS
AATTGGCATATCCTAAAAGA+AGG 0.544656 3_3:-48628191 None:intergenic
GCAGAAAGCCAATCTTCCCT+GGG 0.574723 3_3:+48628270 Msa0455630:intron
CTGATCTATGTGATGATCAA+TGG 0.582595 3_3:+48628497 Msa0455630:CDS
CTGAGTATGTTGTCACGCGC+TGG 0.586534 3_3:+48628154 Msa0455630:CDS
TGAAGATTGACCGGAACTTG+AGG 0.588250 3_3:-48628532 None:intergenic
GATCAGCCATATATGGATGT+CGG 0.608682 3_3:-48628480 None:intergenic
CCCTACGGACCACACATCGA+TGG 0.617558 3_3:-48628223 None:intergenic
AAATGATTAGAGAAATGATG+TGG 0.617892 3_3:+48628578 Msa0455630:CDS
TGACAAAAGCAGCTTCAGGA+TGG 0.629134 3_3:-48628618 None:intergenic
AGATTGACCGGAACTTGAGG+AGG 0.650608 3_3:-48628529 None:intergenic
ACGGAACCTCCATCGATGTG+TGG 0.655065 3_3:+48628214 Msa0455630:CDS
TACGGACCACACATCGATGG+AGG 0.663564 3_3:-48628220 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAACTAATTAGAAGTGTTCT+TGG + chr3_3:48628314-48628333 Msa0455630:CDS 25.0%
! AATAGTTAATCCAAAAACCA+AGG + chr3_3:48628361-48628380 Msa0455630:intron 25.0%
!! TGATGTAGTAATTCTTTTAG+TGG - chr3_3:48628452-48628471 None:intergenic 25.0%
! ATCTTCACATTGATGAAAAT+TGG + chr3_3:48628548-48628567 Msa0455630:CDS 25.0%
! TCTTCACATTGATGAAAATT+GGG + chr3_3:48628549-48628568 Msa0455630:CDS 25.0%
! AAATGATTAGAGAAATGATG+TGG + chr3_3:48628578-48628597 Msa0455630:CDS 25.0%
AATTGGCATATCCTAAAAGA+AGG - chr3_3:48628194-48628213 None:intergenic 30.0%
!!! CTTTTAGGATATGCCAATTA+CGG + chr3_3:48628195-48628214 Msa0455630:CDS 30.0%
! CATTTTTGTTGAGATATGCT+TGG + chr3_3:48628248-48628267 Msa0455630:intron 30.0%
! CACTTCTAATTAGTTTCATC+TGG - chr3_3:48628310-48628329 None:intergenic 30.0%
!! TTGATAAATGCCTTGGTTTT+TGG - chr3_3:48628374-48628393 None:intergenic 30.0%
AAGTGATTTGATAAATGCCT+TGG - chr3_3:48628381-48628400 None:intergenic 30.0%
! AAATTTTTCCCAGGGAAGAT+TGG - chr3_3:48628281-48628300 None:intergenic 35.0%
TTAACTCAAGATCAGACTCT+TGG - chr3_3:48628343-48628362 None:intergenic 35.0%
AAATCACTTCCCTATACAGA+GGG + chr3_3:48628392-48628411 Msa0455630:intron 35.0%
TCACATAGATCAGCCATATA+TGG - chr3_3:48628490-48628509 None:intergenic 35.0%
CTGATCTATGTGATGATCAA+TGG + chr3_3:48628497-48628516 Msa0455630:CDS 35.0%
TCATCAATGTGAAGATTGAC+CGG - chr3_3:48628544-48628563 None:intergenic 35.0%
GCATATCCTAAAAGAAGGTC+TGG - chr3_3:48628189-48628208 None:intergenic 40.0%
CTCAACAAAAATGCACCCTA+CGG - chr3_3:48628241-48628260 None:intergenic 40.0%
! GGTGCATCAAATTTTTCCCA+GGG - chr3_3:48628289-48628308 None:intergenic 40.0%
! TGGTGCATCAAATTTTTCCC+AGG - chr3_3:48628290-48628309 None:intergenic 40.0%
CAAATCACTTCCCTATACAG+AGG + chr3_3:48628391-48628410 Msa0455630:intron 40.0%
AATCACTTCCCTATACAGAG+GGG + chr3_3:48628393-48628412 Msa0455630:intron 40.0%
AATTGTGTCCCCTCTGTATA+GGG - chr3_3:48628404-48628423 None:intergenic 40.0%
!! TCTTTTAGTGGATCTGCTTG+TGG - chr3_3:48628440-48628459 None:intergenic 40.0%
GATCAGCCATATATGGATGT+CGG - chr3_3:48628483-48628502 None:intergenic 40.0%
ATCGATGGAGGTTCCGTAAT+TGG - chr3_3:48628211-48628230 None:intergenic 45.0%
GAATTGTGTCCCCTCTGTAT+AGG - chr3_3:48628405-48628424 None:intergenic 45.0%
AGCACTCCGACATCCATATA+TGG + chr3_3:48628474-48628493 Msa0455630:CDS 45.0%
TAACTGTCCTCCTCAAGTTC+CGG + chr3_3:48628522-48628541 Msa0455630:CDS 45.0%
TGAAGATTGACCGGAACTTG+AGG - chr3_3:48628535-48628554 None:intergenic 45.0%
TGACAAAAGCAGCTTCAGGA+TGG - chr3_3:48628621-48628640 None:intergenic 45.0%
GCAATGACAAAAGCAGCTTC+AGG - chr3_3:48628625-48628644 None:intergenic 45.0%
! CGAGCTCCAGACCTTCTTTT+AGG + chr3_3:48628180-48628199 Msa0455630:CDS 50.0%
GCAGAAAGCCAATCTTCCCT+GGG + chr3_3:48628270-48628289 Msa0455630:intron 50.0%
AGATTGACCGGAACTTGAGG+AGG - chr3_3:48628532-48628551 None:intergenic 50.0%
CTGAGTATGTTGTCACGCGC+TGG + chr3_3:48628154-48628173 Msa0455630:CDS 55.0%
ACGGAACCTCCATCGATGTG+TGG + chr3_3:48628214-48628233 Msa0455630:CDS 55.0%
TACGGACCACACATCGATGG+AGG - chr3_3:48628223-48628242 None:intergenic 55.0%
TCCATCGATGTGTGGTCCGT+AGG + chr3_3:48628222-48628241 Msa0455630:CDS 55.0%
CCATCGATGTGTGGTCCGTA+GGG + chr3_3:48628223-48628242 Msa0455630:CDS 55.0%
GGCAGAAAGCCAATCTTCCC+TGG + chr3_3:48628269-48628288 Msa0455630:intron 55.0%
CCCTACGGACCACACATCGA+TGG - chr3_3:48628226-48628245 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 48628150 48628648 48628150 ID=Msa0455630;Name=Msa0455630
chr3_3 mRNA 48628150 48628648 48628150 ID=Msa0455630-mRNA-1;Parent=Msa0455630;Name=Msa0455630-mRNA-1;_AED=0.41;_eAED=0.42;_QI=0|0|0|1|0|0.33|3|0|138
chr3_3 exon 48628150 48628244 48628150 ID=Msa0455630-mRNA-1:exon:9073;Parent=Msa0455630-mRNA-1
chr3_3 exon 48628274 48628357 48628274 ID=Msa0455630-mRNA-1:exon:9074;Parent=Msa0455630-mRNA-1
chr3_3 exon 48628411 48628648 48628411 ID=Msa0455630-mRNA-1:exon:9075;Parent=Msa0455630-mRNA-1
chr3_3 CDS 48628150 48628244 48628150 ID=Msa0455630-mRNA-1:cds;Parent=Msa0455630-mRNA-1
chr3_3 CDS 48628274 48628357 48628274 ID=Msa0455630-mRNA-1:cds;Parent=Msa0455630-mRNA-1
chr3_3 CDS 48628411 48628648 48628411 ID=Msa0455630-mRNA-1:cds;Parent=Msa0455630-mRNA-1
Gene Sequence

>Msa0455630

ATGACTGAGTATGTTGTCACGCGCTGGTATCGAGCTCCAGACCTTCTTTTAGGATATGCCAATTACGGAACCTCCATCGATGTGTGGTCCGTAGGAAAGCCAATCTTCCCTGGGAAAAATTTGATGCACCAGATGAAACTAATTAGAAGTGTTCTTGGAAGCCAAGAGTCTGATCTTGAAGGGGACACAATTCTCTCAGCTATAACCACAAGCAGATCCACTAAAAGAATTACTACATCAGAAGCACTCCGACATCCATATATGGCTGATCTATGTGATGATCAATGGCGTAACTGTCCTCCTCAAGTTCCGGTCAATCTTCACATTGATGAAAATTGGGATAACAAAATGATTAGAGAAATGATGTGGAATGAGATGCTTCATTACCATCCTGAAGCTGCTTTTGTCATTGCATAG
Protein sequence

>Msa0455630

MTEYVVTRWYRAPDLLLGYANYGTSIDVWSVGKPIFPGKNLMHQMKLIRSVLGSQESDLEGDTILSAITTSRSTKRITTSEALRHPYMADLCDDQWRNCPPQVPVNLHIDENWDNKMIREMMWNEMLHYHPEAAFVIA*