Multiple sequence alignment - TraesCS1A01G407800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G407800 chr1A 100.000 3708 0 0 1 3708 570156537 570152830 0.000000e+00 6848
1 TraesCS1A01G407800 chr1A 78.788 594 87 25 1779 2353 570160249 570160822 2.720000e-96 363
2 TraesCS1A01G407800 chr5D 91.202 2387 135 39 651 2982 545145087 545147453 0.000000e+00 3175
3 TraesCS1A01G407800 chr5D 78.604 1304 194 62 710 1958 545125043 545123770 0.000000e+00 784
4 TraesCS1A01G407800 chr5B 89.625 2429 134 50 661 2982 687745064 687747481 0.000000e+00 2981
5 TraesCS1A01G407800 chr5B 79.630 864 139 27 1513 2353 687739424 687738575 1.480000e-163 586
6 TraesCS1A01G407800 chr5B 85.446 426 37 8 3029 3447 610079536 610079943 1.590000e-113 420
7 TraesCS1A01G407800 chr5B 77.545 717 95 45 710 1409 687740223 687739556 4.520000e-99 372
8 TraesCS1A01G407800 chr5B 87.361 269 27 5 3443 3708 610079906 610080170 6.020000e-78 302
9 TraesCS1A01G407800 chr4A 98.952 1336 10 1 1 1336 624924484 624925815 0.000000e+00 2386
10 TraesCS1A01G407800 chr4A 99.401 835 5 0 2148 2982 624925814 624926648 0.000000e+00 1515
11 TraesCS1A01G407800 chr4A 98.827 682 8 0 3027 3708 47290140 47290821 0.000000e+00 1216
12 TraesCS1A01G407800 chr7A 96.765 680 16 1 3029 3708 715337629 715338302 0.000000e+00 1129
13 TraesCS1A01G407800 chr7A 89.244 688 59 9 3027 3708 28365092 28365770 0.000000e+00 846
14 TraesCS1A01G407800 chr2D 92.868 687 41 6 3027 3708 547032381 547033064 0.000000e+00 990
15 TraesCS1A01G407800 chr2D 83.511 188 25 5 447 629 642259231 642259045 1.770000e-38 171
16 TraesCS1A01G407800 chr2B 90.426 188 18 0 1223 1410 160281053 160281240 7.950000e-62 248
17 TraesCS1A01G407800 chr2A 88.298 188 22 0 1223 1410 107316622 107316809 3.730000e-55 226
18 TraesCS1A01G407800 chr1D 81.667 240 39 5 407 642 456273100 456273338 1.050000e-45 195
19 TraesCS1A01G407800 chr6D 81.735 219 28 11 407 619 469973129 469972917 4.920000e-39 172
20 TraesCS1A01G407800 chr6D 80.349 229 39 4 405 631 361225133 361225357 6.370000e-38 169
21 TraesCS1A01G407800 chr6D 78.899 218 36 8 404 619 298342963 298343172 4.990000e-29 139
22 TraesCS1A01G407800 chr6A 80.349 229 39 5 405 631 502335226 502335450 6.370000e-38 169
23 TraesCS1A01G407800 chr7D 80.569 211 37 4 428 635 100256979 100256770 3.830000e-35 159
24 TraesCS1A01G407800 chr3A 80.000 225 38 6 407 629 225654260 225654041 3.830000e-35 159


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G407800 chr1A 570152830 570156537 3707 True 6848.0 6848 100.0000 1 3708 1 chr1A.!!$R1 3707
1 TraesCS1A01G407800 chr1A 570160249 570160822 573 False 363.0 363 78.7880 1779 2353 1 chr1A.!!$F1 574
2 TraesCS1A01G407800 chr5D 545145087 545147453 2366 False 3175.0 3175 91.2020 651 2982 1 chr5D.!!$F1 2331
3 TraesCS1A01G407800 chr5D 545123770 545125043 1273 True 784.0 784 78.6040 710 1958 1 chr5D.!!$R1 1248
4 TraesCS1A01G407800 chr5B 687745064 687747481 2417 False 2981.0 2981 89.6250 661 2982 1 chr5B.!!$F1 2321
5 TraesCS1A01G407800 chr5B 687738575 687740223 1648 True 479.0 586 78.5875 710 2353 2 chr5B.!!$R1 1643
6 TraesCS1A01G407800 chr5B 610079536 610080170 634 False 361.0 420 86.4035 3029 3708 2 chr5B.!!$F2 679
7 TraesCS1A01G407800 chr4A 624924484 624926648 2164 False 1950.5 2386 99.1765 1 2982 2 chr4A.!!$F2 2981
8 TraesCS1A01G407800 chr4A 47290140 47290821 681 False 1216.0 1216 98.8270 3027 3708 1 chr4A.!!$F1 681
9 TraesCS1A01G407800 chr7A 715337629 715338302 673 False 1129.0 1129 96.7650 3029 3708 1 chr7A.!!$F2 679
10 TraesCS1A01G407800 chr7A 28365092 28365770 678 False 846.0 846 89.2440 3027 3708 1 chr7A.!!$F1 681
11 TraesCS1A01G407800 chr2D 547032381 547033064 683 False 990.0 990 92.8680 3027 3708 1 chr2D.!!$F1 681

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
26 27 0.391661 TTTCGCCTGCCAGATCTCAC 60.392 55.0 0.00 0.00 0.0 3.51 F
146 147 0.532862 CTCCATGCACCGGTGGATAC 60.533 60.0 36.96 20.62 43.2 2.24 F
1533 1624 0.106967 GGGGCTCCATCTTCTCCAAC 60.107 60.0 0.00 0.00 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1602 0.985490 GGAGAAGATGGAGCCCCTGT 60.985 60.000 0.0 0.0 0.00 4.00 R
2051 2176 2.045926 GCCACCTGGTTCATCGCT 60.046 61.111 0.0 0.0 37.57 4.93 R
3403 3608 0.685097 TGCAGCTCCCTAAACTCGTT 59.315 50.000 0.0 0.0 0.00 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.391661 TTTCGCCTGCCAGATCTCAC 60.392 55.000 0.00 0.00 0.00 3.51
146 147 0.532862 CTCCATGCACCGGTGGATAC 60.533 60.000 36.96 20.62 43.20 2.24
197 198 4.202121 GGTTACTAGCCAATCTGACGATCA 60.202 45.833 0.00 0.00 0.00 2.92
275 276 6.091441 CAGTAGTCTGATGCTTAGTGTTTTCC 59.909 42.308 0.00 0.00 43.76 3.13
749 752 3.390135 TCTTTCGTGCACAAGGAACTAG 58.610 45.455 18.64 7.80 38.49 2.57
750 753 1.508632 TTCGTGCACAAGGAACTAGC 58.491 50.000 18.64 0.00 38.49 3.42
751 754 0.679505 TCGTGCACAAGGAACTAGCT 59.320 50.000 18.64 0.00 38.49 3.32
752 755 1.890489 TCGTGCACAAGGAACTAGCTA 59.110 47.619 18.64 0.00 38.49 3.32
961 984 4.481463 CACCTTCTGTTCAAAACGTTTGT 58.519 39.130 15.46 0.75 0.00 2.83
973 996 5.066634 TCAAAACGTTTGTCATTTGAGCCTA 59.933 36.000 15.46 0.00 36.99 3.93
1269 1330 1.802960 GGATCGCGGACTACTTCGATA 59.197 52.381 6.13 0.00 41.11 2.92
1457 1527 7.539712 ACTTTGTATATGTCGTCCATTTCTG 57.460 36.000 0.00 0.00 34.86 3.02
1511 1602 2.171659 TGGATTATTGCGTGGGAAGCTA 59.828 45.455 0.00 0.00 35.28 3.32
1533 1624 0.106967 GGGGCTCCATCTTCTCCAAC 60.107 60.000 0.00 0.00 0.00 3.77
1560 1651 4.074526 GCTCTGGCTCTGGCGACA 62.075 66.667 0.00 0.00 39.81 4.35
1601 1692 0.975556 TACCTCCATTCGCTGCTCCA 60.976 55.000 0.00 0.00 0.00 3.86
1614 1705 3.461773 CTCCATCGGCACCTCGGT 61.462 66.667 0.00 0.00 0.00 4.69
2003 2121 3.068560 GCCGCATTCCCAATACGTATAA 58.931 45.455 8.83 0.00 0.00 0.98
2028 2149 2.306341 AATCTCACTCATGGACTGCG 57.694 50.000 0.00 0.00 0.00 5.18
2031 2152 1.472878 TCTCACTCATGGACTGCGTAC 59.527 52.381 0.00 0.00 0.00 3.67
2051 2176 5.333875 CGTACGTATGCTGCAGACTCTATTA 60.334 44.000 23.09 5.84 0.00 0.98
2114 2242 1.227853 GCCGGCGGGAAAGTCATAT 60.228 57.895 29.48 0.00 34.06 1.78
2984 3183 9.549078 TTTGCGTTACATATATAAACCATGAGA 57.451 29.630 0.00 0.00 0.00 3.27
2985 3184 8.757164 TGCGTTACATATATAAACCATGAGAG 57.243 34.615 0.00 0.00 0.00 3.20
2986 3185 7.330946 TGCGTTACATATATAAACCATGAGAGC 59.669 37.037 0.00 2.77 0.00 4.09
2987 3186 7.201530 GCGTTACATATATAAACCATGAGAGCC 60.202 40.741 0.00 0.00 0.00 4.70
2988 3187 8.035394 CGTTACATATATAAACCATGAGAGCCT 58.965 37.037 0.00 0.00 0.00 4.58
2989 3188 9.372369 GTTACATATATAAACCATGAGAGCCTC 57.628 37.037 0.00 0.00 0.00 4.70
2990 3189 6.951971 ACATATATAAACCATGAGAGCCTCC 58.048 40.000 0.00 0.00 0.00 4.30
2991 3190 6.732862 ACATATATAAACCATGAGAGCCTCCT 59.267 38.462 0.00 0.00 0.00 3.69
2992 3191 3.853355 ATAAACCATGAGAGCCTCCTG 57.147 47.619 0.00 1.36 0.00 3.86
2993 3192 0.622665 AAACCATGAGAGCCTCCTGG 59.377 55.000 18.40 18.40 46.74 4.45
2994 3193 0.252881 AACCATGAGAGCCTCCTGGA 60.253 55.000 23.52 0.00 45.09 3.86
2995 3194 0.690411 ACCATGAGAGCCTCCTGGAG 60.690 60.000 23.52 17.02 45.09 3.86
3005 3204 2.426842 CCTCCTGGAGGGATTGTTTC 57.573 55.000 31.49 0.00 45.43 2.78
3006 3205 1.635487 CCTCCTGGAGGGATTGTTTCA 59.365 52.381 31.49 0.00 45.43 2.69
3007 3206 2.243221 CCTCCTGGAGGGATTGTTTCAT 59.757 50.000 31.49 0.00 45.43 2.57
3008 3207 3.285484 CTCCTGGAGGGATTGTTTCATG 58.715 50.000 16.19 0.00 44.15 3.07
3009 3208 2.918934 TCCTGGAGGGATTGTTTCATGA 59.081 45.455 0.00 0.00 39.58 3.07
3010 3209 3.528905 TCCTGGAGGGATTGTTTCATGAT 59.471 43.478 0.00 0.00 39.58 2.45
3011 3210 3.887716 CCTGGAGGGATTGTTTCATGATC 59.112 47.826 0.00 0.00 37.23 2.92
3012 3211 3.544684 TGGAGGGATTGTTTCATGATCG 58.455 45.455 0.00 0.00 0.00 3.69
3013 3212 3.199727 TGGAGGGATTGTTTCATGATCGA 59.800 43.478 0.00 0.00 0.00 3.59
3014 3213 3.812053 GGAGGGATTGTTTCATGATCGAG 59.188 47.826 0.00 0.00 0.00 4.04
3015 3214 4.443457 GGAGGGATTGTTTCATGATCGAGA 60.443 45.833 0.00 0.00 0.00 4.04
3016 3215 5.102953 AGGGATTGTTTCATGATCGAGAA 57.897 39.130 0.00 0.00 0.00 2.87
3017 3216 5.500234 AGGGATTGTTTCATGATCGAGAAA 58.500 37.500 0.00 7.95 0.00 2.52
3018 3217 5.587844 AGGGATTGTTTCATGATCGAGAAAG 59.412 40.000 11.34 0.00 34.69 2.62
3019 3218 5.586243 GGGATTGTTTCATGATCGAGAAAGA 59.414 40.000 11.34 8.48 34.69 2.52
3020 3219 6.238320 GGGATTGTTTCATGATCGAGAAAGAG 60.238 42.308 11.34 0.00 34.69 2.85
3021 3220 5.536554 TTGTTTCATGATCGAGAAAGAGC 57.463 39.130 11.34 3.40 34.69 4.09
3022 3221 4.568956 TGTTTCATGATCGAGAAAGAGCA 58.431 39.130 11.34 5.44 41.01 4.26
3023 3222 4.628766 TGTTTCATGATCGAGAAAGAGCAG 59.371 41.667 11.34 0.00 40.05 4.24
3024 3223 2.819115 TCATGATCGAGAAAGAGCAGC 58.181 47.619 0.00 0.00 40.05 5.25
3025 3224 2.429971 TCATGATCGAGAAAGAGCAGCT 59.570 45.455 0.00 0.00 40.05 4.24
3316 3515 2.275089 CAATCCCCATGGTGCCGA 59.725 61.111 11.73 0.59 0.00 5.54
3386 3591 4.660938 GCAACCACGGCCCCTCTT 62.661 66.667 0.00 0.00 0.00 2.85
3616 3824 2.267006 CATGTCGCAGGGAGCACT 59.733 61.111 0.00 0.00 46.13 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.635663 GGGCAAGTCATCGAACACGG 61.636 60.000 0.00 0.00 0.00 4.94
146 147 4.161333 GCGTGATTTCTGGATTTGAAGTG 58.839 43.478 0.00 0.00 0.00 3.16
197 198 3.805108 GCCATCCGATCAGATAACAAGCT 60.805 47.826 0.00 0.00 0.00 3.74
612 613 3.197766 TCATGATTTGCTAGTTCCCTCGT 59.802 43.478 0.00 0.00 0.00 4.18
749 752 7.957992 AATAGTATAGTATGACCCCACTAGC 57.042 40.000 0.70 0.00 31.10 3.42
750 753 9.629878 CCTAATAGTATAGTATGACCCCACTAG 57.370 40.741 0.70 0.00 31.10 2.57
751 754 9.355378 TCCTAATAGTATAGTATGACCCCACTA 57.645 37.037 0.70 0.00 0.00 2.74
752 755 8.240881 TCCTAATAGTATAGTATGACCCCACT 57.759 38.462 0.70 0.00 0.00 4.00
961 984 1.134699 CACGAGGCTAGGCTCAAATGA 60.135 52.381 36.72 0.00 0.00 2.57
973 996 1.608283 GGAGTTTGCTAACACGAGGCT 60.608 52.381 13.46 0.00 36.70 4.58
1457 1527 2.791004 ACGTTGAACTTGCGTGTAGTAC 59.209 45.455 0.00 0.00 37.47 2.73
1511 1602 0.985490 GGAGAAGATGGAGCCCCTGT 60.985 60.000 0.00 0.00 0.00 4.00
1560 1651 3.387947 CCGTCGTACTTGGGCCCT 61.388 66.667 25.70 5.02 0.00 5.19
1601 1692 2.994995 TGTCACCGAGGTGCCGAT 60.995 61.111 16.95 0.00 45.04 4.18
1614 1705 2.425592 CCGTCCAGCTTGGTGTCA 59.574 61.111 0.00 0.00 39.03 3.58
1753 1853 8.556194 CACACAAGCTTAGTCAATTACTTAACA 58.444 33.333 0.00 0.00 39.80 2.41
2003 2121 5.587844 GCAGTCCATGAGTGAGATTATTGTT 59.412 40.000 0.00 0.00 35.20 2.83
2028 2149 2.853731 AGAGTCTGCAGCATACGTAC 57.146 50.000 9.47 0.00 0.00 3.67
2031 2152 3.917380 GCTAATAGAGTCTGCAGCATACG 59.083 47.826 9.47 0.00 0.00 3.06
2051 2176 2.045926 GCCACCTGGTTCATCGCT 60.046 61.111 0.00 0.00 37.57 4.93
2105 2233 8.690884 CCGATGGAGATGACTATATATGACTTT 58.309 37.037 0.00 0.00 0.00 2.66
2114 2242 3.507622 CACAGCCGATGGAGATGACTATA 59.492 47.826 0.00 0.00 0.00 1.31
2989 3188 3.370840 TCATGAAACAATCCCTCCAGG 57.629 47.619 0.00 0.00 0.00 4.45
2990 3189 3.562973 CGATCATGAAACAATCCCTCCAG 59.437 47.826 0.00 0.00 0.00 3.86
2991 3190 3.199727 TCGATCATGAAACAATCCCTCCA 59.800 43.478 0.00 0.00 0.00 3.86
2992 3191 3.808728 TCGATCATGAAACAATCCCTCC 58.191 45.455 0.00 0.00 0.00 4.30
2993 3192 4.697514 TCTCGATCATGAAACAATCCCTC 58.302 43.478 0.00 0.00 0.00 4.30
2994 3193 4.760530 TCTCGATCATGAAACAATCCCT 57.239 40.909 0.00 0.00 0.00 4.20
2995 3194 5.586243 TCTTTCTCGATCATGAAACAATCCC 59.414 40.000 0.00 0.00 0.00 3.85
2996 3195 6.668541 TCTTTCTCGATCATGAAACAATCC 57.331 37.500 0.00 0.00 0.00 3.01
2997 3196 6.183360 TGCTCTTTCTCGATCATGAAACAATC 60.183 38.462 0.00 0.00 0.00 2.67
2998 3197 5.645067 TGCTCTTTCTCGATCATGAAACAAT 59.355 36.000 0.00 0.00 0.00 2.71
2999 3198 4.996758 TGCTCTTTCTCGATCATGAAACAA 59.003 37.500 0.00 0.00 0.00 2.83
3000 3199 4.568956 TGCTCTTTCTCGATCATGAAACA 58.431 39.130 0.00 2.28 0.00 2.83
3001 3200 4.493872 GCTGCTCTTTCTCGATCATGAAAC 60.494 45.833 0.00 0.00 0.00 2.78
3002 3201 3.620374 GCTGCTCTTTCTCGATCATGAAA 59.380 43.478 0.00 9.01 0.00 2.69
3003 3202 3.118847 AGCTGCTCTTTCTCGATCATGAA 60.119 43.478 0.00 0.00 0.00 2.57
3004 3203 2.429971 AGCTGCTCTTTCTCGATCATGA 59.570 45.455 0.00 0.00 0.00 3.07
3005 3204 2.540516 CAGCTGCTCTTTCTCGATCATG 59.459 50.000 0.00 0.00 0.00 3.07
3006 3205 2.483363 CCAGCTGCTCTTTCTCGATCAT 60.483 50.000 8.66 0.00 0.00 2.45
3007 3206 1.134877 CCAGCTGCTCTTTCTCGATCA 60.135 52.381 8.66 0.00 0.00 2.92
3008 3207 1.135915 TCCAGCTGCTCTTTCTCGATC 59.864 52.381 8.66 0.00 0.00 3.69
3009 3208 1.189752 TCCAGCTGCTCTTTCTCGAT 58.810 50.000 8.66 0.00 0.00 3.59
3010 3209 0.969149 TTCCAGCTGCTCTTTCTCGA 59.031 50.000 8.66 0.00 0.00 4.04
3011 3210 1.800805 TTTCCAGCTGCTCTTTCTCG 58.199 50.000 8.66 0.00 0.00 4.04
3259 3458 4.400961 GGAAGGAGCTGCTGCCGT 62.401 66.667 17.78 11.33 40.80 5.68
3316 3515 1.679944 CGCCTTGTTCAGACCATCCAT 60.680 52.381 0.00 0.00 0.00 3.41
3403 3608 0.685097 TGCAGCTCCCTAAACTCGTT 59.315 50.000 0.00 0.00 0.00 3.85
3616 3824 3.261897 CCCTTTCTTCTCCAGCAGTCTTA 59.738 47.826 0.00 0.00 0.00 2.10


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.