AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0667340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0667340 MtrunA17_Chr4g0005891 87.786 131 16 0 1 131 980 1110 1.29e-65 214
Msa0667340 MtrunA17_Chr4g0005851 76.336 131 30 1 1 130 966 1096 4.12e-60 199
Msa0667340 MtrunA17_Chr4g0005591 76.154 130 30 1 1 130 1008 1136 1.44e-59 197
Msa0667340 MtrunA17_Chr4g0005871 74.809 131 29 2 1 130 1056 1183 2.13e-57 191
Msa0667340 MtrunA17_Chr3g0135571 54.962 131 58 1 1 130 45 175 7.86e-42 136
Msa0667340 MtrunA17_Chr3g0135541 54.962 131 58 1 1 130 197 327 8.24e-41 138
Msa0667340 MtrunA17_Chr3g0135511 54.198 131 59 1 1 130 45 175 1.25e-40 133
Msa0667340 MtrunA17_Chr6g0454821 51.316 152 48 1 3 128 975 1126 1.39e-40 143
Msa0667340 MtrunA17_Chr7g0257531 65.455 110 36 2 1 108 580 689 3.07e-38 136
Msa0667340 MtrunA17_Chr6g0454961 50.336 149 51 2 5 130 972 1120 1.39e-36 132
Msa0667340 MtrunA17_Chr6g0454951 52.308 130 61 1 1 129 1017 1146 5.36e-36 130
Msa0667340 MtrunA17_Chr6g0454861 51.938 129 38 1 1 129 2 106 1.02e-35 119
Msa0667340 MtrunA17_Chr4g0014821 49.600 125 62 1 1 124 40 164 7.96e-34 116
Msa0667340 MtrunA17_Chr6g0454971 50.769 130 52 2 1 129 963 1081 3.54e-33 122
Msa0667340 MtrunA17_Chr6g0454911 51.163 129 39 1 1 129 158 262 3.88e-33 117
Msa0667340 MtrunA17_Chr6g0455191 51.938 129 48 1 1 129 1248 1362 1.63e-32 120
Msa0667340 MtrunA17_Chr4g0010711 57.944 107 43 2 1 105 1440 1546 2.31e-32 120
Msa0667340 MtrunA17_Chr6g0454851 59.596 99 40 0 1 99 1023 1121 2.74e-32 119
Msa0667340 MtrunA17_Chr6g0455251 51.538 130 51 2 1 129 1045 1163 3.21e-32 119
Msa0667340 MtrunA17_Chr6g0455551 59.048 105 41 1 5 107 1020 1124 4.04e-32 119
Msa0667340 MtrunA17_Chr7g0234901 57.009 107 44 2 1 105 455 561 1.01e-31 117
Msa0667340 MtrunA17_Chr6g0455221 51.538 130 51 2 1 129 1036 1154 2.06e-31 117
Msa0667340 MtrunA17_Chr4g0009241 47.458 118 51 1 1 107 1447 1564 7.73e-31 115
Msa0667340 MtrunA17_Chr4g0009011 46.610 118 58 3 3 118 213 327 1.09e-30 112
Msa0667340 MtrunA17_Chr4g0009171 49.057 106 53 1 1 105 1648 1753 1.11e-30 115
Msa0667340 MtrunA17_Chr4g0009141 54.945 91 41 0 1 91 1443 1533 2.50e-30 114
Msa0667340 MtrunA17_Chr4g0008981 48.113 106 54 1 1 105 11 116 8.79e-30 105
Msa0667340 MtrunA17_Chr6g0455131 67.500 80 26 0 3 82 1027 1106 1.35e-29 112
Msa0667340 MtrunA17_Chr4g0009041 54.945 91 41 0 1 91 1431 1521 2.41e-29 111
Msa0667340 MtrunA17_Chr6g0455211 55.670 97 43 0 1 97 965 1061 2.97e-29 110
Msa0667340 MtrunA17_Chr4g0009101 49.524 105 52 1 3 106 1461 1565 4.37e-29 110
Msa0667340 MtrunA17_Chr7g0255681 59.000 100 40 1 1 99 1947 2046 8.59e-29 109
Msa0667340 MtrunA17_Chr4g0009401 50.943 106 51 1 1 105 1425 1530 1.68e-28 108
Msa0667340 MtrunA17_Chr4g0009211 44.262 122 52 1 1 106 11 132 3.45e-27 98.2
Msa0667340 MtrunA17_Chr4g0009301 45.217 115 52 1 3 106 1465 1579 1.08e-26 103
Msa0667340 MtrunA17_Chr6g0454831 56.842 95 41 0 3 97 940 1034 6.86e-26 101
Msa0667340 MtrunA17_Chr8g0352211 53.933 89 41 0 1 89 852 940 1.14e-24 97.8
Msa0667340 MtrunA17_Chr6g0454881 55.172 87 37 2 24 108 4 90 2.65e-24 89.4
Msa0667340 MtrunA17_Chr8g0352221 46.667 90 48 0 1 90 839 928 2.46e-22 91.3
Msa0667340 MtrunA17_Chr5g0414761 46.067 89 48 0 1 89 708 796 4.01e-22 90.5
Msa0667340 MtrunA17_Chr8g0370511 47.561 82 43 0 1 82 922 1003 1.06e-20 86.7
Msa0667340 MtrunA17_Chr8g0338981 45.238 84 46 0 1 84 921 1004 1.66e-20 85.9
Msa0667340 MtrunA17_Chr6g0455031 40.845 142 60 4 1 129 940 1070 2.23e-20 85.9
Msa0667340 MtrunA17_Chr3g0085531 46.341 82 44 0 1 82 120 201 2.49e-20 84.7
Msa0667340 MtrunA17_Chr2g0296451 50.000 82 41 0 1 82 441 522 8.48e-20 84.0
Msa0667340 MtrunA17_Chr8g0339011 46.341 82 44 0 1 82 917 998 9.28e-20 84.0
Msa0667340 MtrunA17_Chr3g0114381 43.678 87 49 0 4 90 160 246 1.77e-19 81.6
Msa0667340 MtrunA17_Chr8g0343781 50.000 76 38 0 1 76 6 81 1.90e-19 76.6
Msa0667340 MtrunA17_Chr4g0009361 51.250 80 39 0 1 80 439 518 2.17e-19 82.8
Msa0667340 MtrunA17_Chr8g0339021 45.783 83 45 0 1 83 912 994 4.45e-19 82.0
Msa0667340 MtrunA17_Chr5g0420341 44.578 83 46 0 1 83 923 1005 6.24e-19 81.6
Msa0667340 MtrunA17_Chr8g0338931 42.222 90 52 0 1 90 60 149 6.32e-19 80.1
Msa0667340 MtrunA17_Chr5g0420331 44.578 83 46 0 1 83 923 1005 8.42e-19 81.3
Msa0667340 MtrunA17_Chr3g0085731 45.122 82 45 0 1 82 930 1011 9.73e-19 80.9
Msa0667340 MtrunA17_Chr8g0338841 44.944 89 49 0 1 89 366 454 1.04e-18 80.9
Msa0667340 MtrunA17_Chr7g0223531 48.780 82 42 0 1 82 938 1019 1.65e-18 80.5
Msa0667340 MtrunA17_Chr8g0338801 43.820 89 49 1 3 90 122 210 3.15e-18 78.6
Msa0667340 MtrunA17_Chr8g0338901 46.341 82 44 0 1 82 944 1025 3.70e-18 79.3
Msa0667340 MtrunA17_Chr8g0339031 43.902 82 46 0 1 82 929 1010 4.75e-18 79.0
Msa0667340 MtrunA17_Chr8g0338881 40.000 90 53 1 1 89 952 1041 4.83e-18 79.0
Msa0667340 MtrunA17_Chr6g0455141 47.436 78 40 1 53 129 1 78 3.37e-17 70.9
Msa0667340 MtrunA17_Chr5g0430541 42.683 82 47 0 1 82 432 513 5.47e-16 73.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATCTGATGTTATGTCATT+TGG 0.253045 4_4:-7573350 None:intergenic
CATCTGATGTTATGTCATTT+GGG 0.315870 4_4:-7573349 None:intergenic
GCAGAGAGTTGTATCAAATA+TGG 0.344964 4_4:+7573463 Msa0667340:CDS
CCAACAATAACATTCTTATC+TGG 0.418980 4_4:-7573605 None:intergenic
GATGGCCTTCAAAATGTGTT+GGG 0.431104 4_4:+7573368 Msa0667340:CDS
AGTGGAGATAGTTGTTGTTA+TGG 0.439065 4_4:+7573499 Msa0667340:CDS
CTCTCTCTTATAAAGTTGAA+TGG 0.502684 4_4:-7573411 None:intergenic
GTTATCGTCCTTTGAAAATG+AGG 0.514834 4_4:+7573436 Msa0667340:CDS
CCAGATAAGAATGTTATTGT+TGG 0.523029 4_4:+7573605 Msa0667340:CDS
GATAAGAATGTTATTGTTGG+TGG 0.523427 4_4:+7573608 Msa0667340:CDS
AGATGGCCTTCAAAATGTGT+TGG 0.529571 4_4:+7573367 Msa0667340:CDS
CCAAATGACATAACATCAGA+TGG 0.573044 4_4:+7573350 Msa0667340:CDS
ACTATCTCCACTTTGTCACC+AGG 0.590758 4_4:-7573488 None:intergenic
CATTCAACTTTATAAGAGAG+AGG 0.597882 4_4:+7573412 Msa0667340:CDS
TATGGAACCTGGTGACAAAG+TGG 0.605786 4_4:+7573481 Msa0667340:CDS
TCTTTGATTAGAATCATCTG+TGG 0.613273 4_4:-7573678 None:intergenic
AAAATGAATGCTCTTCCAAG+AGG 0.621913 4_4:+7573636 Msa0667340:CDS
TCATCTGTGGACTCTACTTG+AGG 0.622210 4_4:-7573665 None:intergenic
GTTGTATCAAATATGGAACC+TGG 0.628393 4_4:+7573470 Msa0667340:CDS
TCTTATCTGGTGCATCACAA+TGG 0.636991 4_4:-7573592 None:intergenic
ATGGCCTTCAAAATGTGTTG+GGG 0.652462 4_4:+7573369 Msa0667340:CDS
CGTCCTTTGAAAATGAGGAG+TGG 0.657389 4_4:+7573441 Msa0667340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CATCTGATGTTATGTCATTT+GGG - chr4_4:7573352-7573371 None:intergenic 30.0%
CTCTCTCTTATAAAGTTGAA+TGG - chr4_4:7573414-7573433 None:intergenic 30.0%
CATTCAACTTTATAAGAGAG+AGG + chr4_4:7573412-7573431 Msa0667340:CDS 30.0%
TGAACCAATTGACGAAAAAA+TGG + chr4_4:7573568-7573587 Msa0667340:CDS 30.0%
CCAACAATAACATTCTTATC+TGG - chr4_4:7573608-7573627 None:intergenic 30.0%
CCAGATAAGAATGTTATTGT+TGG + chr4_4:7573605-7573624 Msa0667340:CDS 30.0%
GATAAGAATGTTATTGTTGG+TGG + chr4_4:7573608-7573627 Msa0667340:CDS 30.0%
TCTTTGATTAGAATCATCTG+TGG - chr4_4:7573681-7573700 None:intergenic 30.0%
CCATCTGATGTTATGTCATT+TGG - chr4_4:7573353-7573372 None:intergenic 35.0%
CCAAATGACATAACATCAGA+TGG + chr4_4:7573350-7573369 Msa0667340:CDS 35.0%
! TTATCCCCAACACATTTTGA+AGG - chr4_4:7573376-7573395 None:intergenic 35.0%
! GTTATCGTCCTTTGAAAATG+AGG + chr4_4:7573436-7573455 Msa0667340:CDS 35.0%
GCAGAGAGTTGTATCAAATA+TGG + chr4_4:7573463-7573482 Msa0667340:CDS 35.0%
GTTGTATCAAATATGGAACC+TGG + chr4_4:7573470-7573489 Msa0667340:CDS 35.0%
! AGTGGAGATAGTTGTTGTTA+TGG + chr4_4:7573499-7573518 Msa0667340:CDS 35.0%
!!! TGGTCCATTTTTTCGTCAAT+TGG - chr4_4:7573575-7573594 None:intergenic 35.0%
AAAATGAATGCTCTTCCAAG+AGG + chr4_4:7573636-7573655 Msa0667340:CDS 35.0%
TACTTGAGGAAAAATCCTCT+TGG - chr4_4:7573654-7573673 None:intergenic 35.0%
AGATGGCCTTCAAAATGTGT+TGG + chr4_4:7573367-7573386 Msa0667340:CDS 40.0%
GATGGCCTTCAAAATGTGTT+GGG + chr4_4:7573368-7573387 Msa0667340:CDS 40.0%
ATGGCCTTCAAAATGTGTTG+GGG + chr4_4:7573369-7573388 Msa0667340:CDS 40.0%
TCTTATCTGGTGCATCACAA+TGG - chr4_4:7573595-7573614 None:intergenic 40.0%
! CGTCCTTTGAAAATGAGGAG+TGG + chr4_4:7573441-7573460 Msa0667340:CDS 45.0%
! CTGCCACTCCTCATTTTCAA+AGG - chr4_4:7573447-7573466 None:intergenic 45.0%
TATGGAACCTGGTGACAAAG+TGG + chr4_4:7573481-7573500 Msa0667340:CDS 45.0%
ACTATCTCCACTTTGTCACC+AGG - chr4_4:7573491-7573510 None:intergenic 45.0%
TCATCTGTGGACTCTACTTG+AGG - chr4_4:7573668-7573687 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 7573326 7573721 7573326 ID=Msa0667340;Name=Msa0667340
chr4_4 mRNA 7573326 7573721 7573326 ID=Msa0667340-mRNA-1;Parent=Msa0667340;Name=Msa0667340-mRNA-1;_AED=0.42;_eAED=0.43;_QI=0|-1|0|1|-1|1|1|0|131
chr4_4 exon 7573326 7573721 7573326 ID=Msa0667340-mRNA-1:exon:2495;Parent=Msa0667340-mRNA-1
chr4_4 CDS 7573326 7573721 7573326 ID=Msa0667340-mRNA-1:cds;Parent=Msa0667340-mRNA-1
Gene Sequence

>Msa0667340

ATGTTCATTGTCTATTCTTCAAGCCCAAATGACATAACATCAGATGGCCTTCAAAATGTGTTGGGGATAAATCACACAAAGATCACCATTCAACTTTATAAGAGAGAGGCGTTATCGTCCTTTGAAAATGAGGAGTGGCAGAGAGTTGTATCAAATATGGAACCTGGTGACAAAGTGGAGATAGTTGTTGTTATGGTGAACAATGTCATTGTGACGAAGACAGCAGTTTATCTCATATATGATGAACCAATTGACGAAAAAATGGACCATTGTGATGCACCAGATAAGAATGTTATTGTTGGTGGTGATGAAAATGAATGCTCTTCCAAGAGGATTTTTCCTCAAGTAGAGTCCACAGATGATTCTAATCAAAGACAAAAAAGAAGAAAACACTAG
Protein sequence

>Msa0667340

MFIVYSSSPNDITSDGLQNVLGINHTKITIQLYKREALSSFENEEWQRVVSNMEPGDKVEIVVVMVNNVIVTKTAVYLIYDEPIDEKMDHCDAPDKNVIVGGDENECSSKRIFPQVESTDDSNQRQKRRKH*