Multiple sequence alignment - TraesCS6D01G182400

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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 TraesCS6D01G182400 chr6D 100.000 3576 0 0 1 3576 212805577 212802002 0.000000e+00 6604
1 TraesCS6D01G182400 chr6D 100.000 118 0 0 3998 4115 212801580 212801463 6.930000e-53 219
2 TraesCS6D01G182400 chr6B 97.283 3312 76 9 267 3576 315650640 315653939 0.000000e+00 5605
3 TraesCS6D01G182400 chr6B 97.710 262 2 2 1 262 315650348 315650605 8.110000e-122 448
4 TraesCS6D01G182400 chr6B 93.162 117 7 1 3998 4113 315654006 315654122 1.970000e-38 171
5 TraesCS6D01G182400 chr6B 94.030 67 4 0 3510 3576 10584013 10583947 7.280000e-18 102
6 TraesCS6D01G182400 chrUn 98.498 2796 32 2 263 3058 72997523 72994738 0.000000e+00 4922
7 TraesCS6D01G182400 chrUn 97.130 453 12 1 3060 3511 421865345 421864893 0.000000e+00 763
8 TraesCS6D01G182400 chrUn 98.092 262 2 1 1 262 72997812 72997554 1.740000e-123 453
9 TraesCS6D01G182400 chrUn 94.286 70 4 0 3507 3576 29808578 29808509 1.560000e-19 108
10 TraesCS6D01G182400 chrUn 96.774 62 2 0 4052 4113 474476577 474476638 2.020000e-18 104
11 TraesCS6D01G182400 chrUn 100.000 53 0 0 3998 4050 475578940 475578992 9.410000e-17 99
12 TraesCS6D01G182400 chr7A 95.714 70 3 0 3507 3576 32807190 32807259 3.360000e-21 113
13 TraesCS6D01G182400 chr3B 95.588 68 3 0 3507 3574 2480867 2480800 4.350000e-20 110
14 TraesCS6D01G182400 chr3D 94.286 70 4 0 3507 3576 346196200 346196131 1.560000e-19 108
15 TraesCS6D01G182400 chr3D 95.522 67 3 0 3510 3576 593205428 593205362 1.560000e-19 108
16 TraesCS6D01G182400 chr2B 95.522 67 3 0 3507 3573 653973410 653973344 1.560000e-19 108
17 TraesCS6D01G182400 chr1D 94.286 70 4 0 3507 3576 35867358 35867289 1.560000e-19 108


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 TraesCS6D01G182400 chr6D 212801463 212805577 4114 True 3411.500000 6604 100.000000 1 4115 2 chr6D.!!$R1 4114
1 TraesCS6D01G182400 chr6B 315650348 315654122 3774 False 2074.666667 5605 96.051667 1 4113 3 chr6B.!!$F1 4112
2 TraesCS6D01G182400 chrUn 72994738 72997812 3074 True 2687.500000 4922 98.295000 1 3058 2 chrUn.!!$R3 3057

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
455 486 3.270877 GAATTCAGTGGGCGAACTATGT 58.729 45.455 0.00 0.00 0.00 2.29 F
1063 1094 2.600470 AACAACAACTTGTGGCCATG 57.400 45.000 9.72 4.94 39.88 3.66 F
1401 1432 4.379813 GGAGTGCCTACAAAACATCATGTG 60.380 45.833 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1860 7.104290 AGTTACTGGAATACTAAAACAGGAGC 58.896 38.462 0.00 0.00 33.63 4.70 R
2787 2818 0.320247 CAGCAGTGTGACCAGGAGAC 60.320 60.000 0.00 0.00 0.00 3.36 R
3374 3407 0.731514 ACTCGGTGTTGCATCGTACG 60.732 55.000 9.53 9.53 39.21 3.67 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
395 426 9.703892 CTCGGAGAACATTATAGATGATTCTTT 57.296 33.333 0.00 0.00 34.09 2.52
455 486 3.270877 GAATTCAGTGGGCGAACTATGT 58.729 45.455 0.00 0.00 0.00 2.29
1011 1042 8.891671 ACAAAGAATACAAAATGAAGTGCAAT 57.108 26.923 0.00 0.00 0.00 3.56
1063 1094 2.600470 AACAACAACTTGTGGCCATG 57.400 45.000 9.72 4.94 39.88 3.66
1401 1432 4.379813 GGAGTGCCTACAAAACATCATGTG 60.380 45.833 0.00 0.00 0.00 3.21
1829 1860 7.901029 TCTATGGAATCTAGTGCCTGATTAAG 58.099 38.462 0.00 0.00 33.60 1.85
2567 2598 5.047092 CACTCATCCCAATACTTTGCCTTTT 60.047 40.000 0.00 0.00 0.00 2.27
3021 3052 2.294512 GGAAGCTATTATGCAACTGGCC 59.705 50.000 0.00 0.00 43.89 5.36
3128 3159 3.385111 AGGTTATAGAGTTGGAAGAGCCG 59.615 47.826 0.00 0.00 40.66 5.52
3187 3218 7.284074 TGTCATGGAAGTAAGGAAAACTGTTA 58.716 34.615 0.00 0.00 0.00 2.41
3191 3222 9.280174 CATGGAAGTAAGGAAAACTGTTAAGTA 57.720 33.333 0.00 0.00 34.77 2.24
3203 3234 9.724839 GAAAACTGTTAAGTACAAATGCTGTAA 57.275 29.630 0.00 0.00 42.23 2.41
3214 3245 6.369059 ACAAATGCTGTAAGATCAGTATGC 57.631 37.500 0.00 0.00 39.81 3.14
3263 3295 7.362056 CCATCGTTCCATCTAGAAATTGTTGTT 60.362 37.037 0.00 0.00 0.00 2.83
3265 3297 6.485313 TCGTTCCATCTAGAAATTGTTGTTGT 59.515 34.615 0.00 0.00 0.00 3.32
3366 3399 1.931172 CACAGACGACGTTTCCTTGTT 59.069 47.619 0.13 0.00 0.00 2.83
3374 3407 3.120649 CGACGTTTCCTTGTTCAATCCTC 60.121 47.826 0.00 0.00 0.00 3.71
3390 3423 1.410737 CCTCGTACGATGCAACACCG 61.411 60.000 19.87 3.33 0.00 4.94
3409 3442 1.672737 CGAGTGGTCTGCTGCACATTA 60.673 52.381 0.00 0.00 0.00 1.90
3447 3480 1.068127 GGGATGCTGCACATTGAATCC 59.932 52.381 3.57 6.03 39.84 3.01
3452 3485 1.133790 GCTGCACATTGAATCCACCTC 59.866 52.381 0.00 0.00 0.00 3.85
3453 3486 2.439409 CTGCACATTGAATCCACCTCA 58.561 47.619 0.00 0.00 0.00 3.86
3455 3488 1.474077 GCACATTGAATCCACCTCACC 59.526 52.381 0.00 0.00 0.00 4.02
3501 3534 6.573680 CGGACATGGATTATACGGGAAGTATT 60.574 42.308 0.00 0.00 43.12 1.89
3521 3554 6.874134 AGTATTGTACATGTTCTTGTCAGACC 59.126 38.462 2.30 0.00 0.00 3.85
3527 3560 4.949856 ACATGTTCTTGTCAGACCTTTGTT 59.050 37.500 0.00 0.00 0.00 2.83
4048 4081 1.221566 CCGGATGCATGTCCTGTGA 59.778 57.895 2.46 0.00 36.07 3.58
4057 4090 3.754850 TGCATGTCCTGTGATTCTGAAAG 59.245 43.478 0.00 0.00 0.00 2.62
4075 4108 6.750501 TCTGAAAGAACATCCGAGTAATTACG 59.249 38.462 9.91 0.00 42.31 3.18
4102 4136 2.045926 GGGTGATCAGCGGCACTT 60.046 61.111 18.14 0.00 35.43 3.16
4113 4147 4.513442 TCAGCGGCACTTTGTTATCTTAT 58.487 39.130 1.45 0.00 0.00 1.73
4114 4148 4.941263 TCAGCGGCACTTTGTTATCTTATT 59.059 37.500 1.45 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 208 2.156917 CCGTGTCACTGACAGGTAGTA 58.843 52.381 23.68 0.00 43.57 1.82
208 209 0.959553 CCGTGTCACTGACAGGTAGT 59.040 55.000 23.68 0.00 43.57 2.73
209 210 0.243907 CCCGTGTCACTGACAGGTAG 59.756 60.000 23.68 14.50 43.57 3.18
455 486 6.012508 ACAATGAAATAGGAAACCTGAGGAGA 60.013 38.462 4.99 0.00 34.61 3.71
1011 1042 4.269523 AACTCCCGCCAGCAAGCA 62.270 61.111 0.00 0.00 0.00 3.91
1063 1094 6.799512 AGAAGATTGCAGGCATACATAAAAC 58.200 36.000 0.00 0.00 0.00 2.43
1829 1860 7.104290 AGTTACTGGAATACTAAAACAGGAGC 58.896 38.462 0.00 0.00 33.63 4.70
2787 2818 0.320247 CAGCAGTGTGACCAGGAGAC 60.320 60.000 0.00 0.00 0.00 3.36
3021 3052 2.029728 CGCTGAAACAATTAGCTCTCGG 59.970 50.000 0.00 0.00 35.36 4.63
3128 3159 3.608316 ACAGAAGCAGAACATCTCCTC 57.392 47.619 0.00 0.00 0.00 3.71
3187 3218 9.102757 CATACTGATCTTACAGCATTTGTACTT 57.897 33.333 0.00 0.00 41.86 2.24
3191 3222 5.882000 TGCATACTGATCTTACAGCATTTGT 59.118 36.000 0.00 0.00 43.96 2.83
3203 3234 2.636893 GGGGAGACATGCATACTGATCT 59.363 50.000 0.00 0.00 0.00 2.75
3318 3351 6.464222 CAGACCACTGGAAGAAGTACATTTA 58.536 40.000 0.71 0.00 40.14 1.40
3330 3363 1.227943 GTGCAGCAGACCACTGGAA 60.228 57.895 0.71 0.00 43.62 3.53
3331 3364 2.427320 GTGCAGCAGACCACTGGA 59.573 61.111 0.71 0.00 43.62 3.86
3332 3365 2.111669 TGTGCAGCAGACCACTGG 59.888 61.111 0.00 0.00 43.62 4.00
3366 3399 2.094442 TGTTGCATCGTACGAGGATTGA 60.094 45.455 31.79 11.74 0.00 2.57
3374 3407 0.731514 ACTCGGTGTTGCATCGTACG 60.732 55.000 9.53 9.53 39.21 3.67
3390 3423 2.099141 TAATGTGCAGCAGACCACTC 57.901 50.000 0.00 0.00 33.26 3.51
3396 3429 5.010922 ACAAAAGGATTTAATGTGCAGCAGA 59.989 36.000 0.00 0.00 37.28 4.26
3397 3430 5.232463 ACAAAAGGATTTAATGTGCAGCAG 58.768 37.500 0.00 0.00 37.28 4.24
3409 3442 2.436173 TCCCCGCAAAACAAAAGGATTT 59.564 40.909 0.00 0.00 42.41 2.17
3447 3480 2.507110 ATCGAACTGCCGGTGAGGTG 62.507 60.000 1.90 0.00 43.70 4.00
3452 3485 0.179100 ATCAGATCGAACTGCCGGTG 60.179 55.000 17.19 0.00 37.75 4.94
3453 3486 0.179100 CATCAGATCGAACTGCCGGT 60.179 55.000 17.19 1.56 37.75 5.28
3455 3488 0.926155 CACATCAGATCGAACTGCCG 59.074 55.000 17.19 12.50 37.75 5.69
3501 3534 4.955811 AGGTCTGACAAGAACATGTACA 57.044 40.909 10.38 0.00 43.18 2.90
3556 3589 1.026584 CCGGCATCTGCATCAATCAA 58.973 50.000 4.33 0.00 44.36 2.57
3557 3590 2.710440 CCGGCATCTGCATCAATCA 58.290 52.632 4.33 0.00 44.36 2.57
4009 4042 4.023193 CGGAAACTTTGGTTGCTCAAGTAT 60.023 41.667 0.00 0.00 35.63 2.12
4011 4044 2.099098 CGGAAACTTTGGTTGCTCAAGT 59.901 45.455 0.00 0.00 35.63 3.16
4012 4045 2.543653 CCGGAAACTTTGGTTGCTCAAG 60.544 50.000 0.00 0.00 35.63 3.02
4048 4081 9.099454 GTAATTACTCGGATGTTCTTTCAGAAT 57.901 33.333 8.41 0.00 36.50 2.40
4057 4090 5.338365 ACAGTCGTAATTACTCGGATGTTC 58.662 41.667 13.56 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.