Multiple sequence alignment - TraesCS7D01G379500

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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 TraesCS7D01G379500 chr7D 100.000 3797 0 0 1 3797 491801330 491797534 0.000000e+00 7012.0
1 TraesCS7D01G379500 chr7D 93.196 3248 183 22 262 3494 491791017 491787793 0.000000e+00 4739.0
2 TraesCS7D01G379500 chr7D 87.932 2718 285 28 273 2972 491864565 491861873 0.000000e+00 3162.0
3 TraesCS7D01G379500 chr7D 85.768 267 17 3 3534 3797 306456234 306456482 2.910000e-66 263.0
4 TraesCS7D01G379500 chr7D 80.464 302 46 8 2971 3259 491861999 491861698 6.390000e-53 219.0
5 TraesCS7D01G379500 chr7D 94.017 117 7 0 147 263 491792290 491792174 1.080000e-40 178.0
6 TraesCS7D01G379500 chr7D 82.979 141 16 5 2962 3095 491798499 491798360 1.850000e-23 121.0
7 TraesCS7D01G379500 chr7D 95.238 42 1 1 3491 3532 1801063 1801023 8.800000e-07 65.8
8 TraesCS7D01G379500 chr7D 97.297 37 0 1 3493 3529 517989604 517989639 1.140000e-05 62.1
9 TraesCS7D01G379500 chr7D 97.222 36 0 1 3494 3529 517949637 517949671 4.100000e-05 60.2
10 TraesCS7D01G379500 chr7B 94.688 3426 157 7 147 3548 521133925 521130501 0.000000e+00 5295.0
11 TraesCS7D01G379500 chr7B 92.133 2771 178 21 262 3020 521123812 521121070 0.000000e+00 3873.0
12 TraesCS7D01G379500 chr7B 88.038 2441 250 22 273 2696 521142914 521140499 0.000000e+00 2852.0
13 TraesCS7D01G379500 chr7B 91.304 483 32 7 3018 3494 521120874 521120396 0.000000e+00 651.0
14 TraesCS7D01G379500 chr7B 92.593 216 13 2 50 262 521125120 521124905 1.320000e-79 307.0
15 TraesCS7D01G379500 chr7B 83.688 141 15 5 2832 2971 521131087 521130954 3.980000e-25 126.0
16 TraesCS7D01G379500 chr7A 92.947 3247 188 18 262 3494 558082614 558079395 0.000000e+00 4689.0
17 TraesCS7D01G379500 chr7A 95.877 2401 90 4 716 3108 558093050 558090651 0.000000e+00 3877.0
18 TraesCS7D01G379500 chr7A 87.358 2737 284 40 271 2972 558102228 558099519 0.000000e+00 3081.0
19 TraesCS7D01G379500 chr7A 95.000 780 32 5 1 773 558093798 558093019 0.000000e+00 1218.0
20 TraesCS7D01G379500 chr7A 94.159 428 20 5 3107 3532 558090365 558089941 0.000000e+00 647.0
21 TraesCS7D01G379500 chr7A 78.188 298 48 10 2974 3259 558099636 558099344 1.400000e-39 174.0
22 TraesCS7D01G379500 chr7A 92.437 119 7 1 147 263 558083843 558083725 6.520000e-38 169.0
23 TraesCS7D01G379500 chr7A 83.688 141 15 5 2832 2971 558079924 558079791 3.980000e-25 126.0
24 TraesCS7D01G379500 chr7A 82.443 131 16 4 2971 3095 558090917 558090788 1.440000e-19 108.0
25 TraesCS7D01G379500 chr7A 82.645 121 10 7 2975 3095 558080024 558079915 3.120000e-16 97.1
26 TraesCS7D01G379500 chr2D 75.499 1702 344 48 1148 2790 599927236 599928923 0.000000e+00 765.0
27 TraesCS7D01G379500 chr3B 88.129 278 13 6 3521 3797 39464850 39465108 2.850000e-81 313.0
28 TraesCS7D01G379500 chr4D 94.554 202 9 2 3530 3729 439770762 439770561 1.020000e-80 311.0
29 TraesCS7D01G379500 chr4B 94.444 198 10 1 3533 3729 187737206 187737009 1.710000e-78 303.0
30 TraesCS7D01G379500 chr3D 94.416 197 10 1 3534 3729 255424678 255424482 6.160000e-78 302.0
31 TraesCS7D01G379500 chr3D 97.297 37 0 1 3493 3529 309669544 309669509 1.140000e-05 62.1
32 TraesCS7D01G379500 chr1A 92.823 209 13 2 3523 3729 478205618 478205826 6.160000e-78 302.0
33 TraesCS7D01G379500 chr1A 92.344 209 14 2 3523 3729 478208699 478208907 2.870000e-76 296.0
34 TraesCS7D01G379500 chr5D 93.970 199 11 1 3532 3729 132472631 132472829 2.220000e-77 300.0
35 TraesCS7D01G379500 chr5D 93.909 197 11 1 3534 3729 451067143 451067339 2.870000e-76 296.0
36 TraesCS7D01G379500 chr5D 83.408 223 17 8 3576 3797 84800711 84800508 5.010000e-44 189.0
37 TraesCS7D01G379500 chr6A 93.909 197 11 1 3534 3729 465626641 465626445 2.870000e-76 296.0
38 TraesCS7D01G379500 chr3A 86.792 265 12 5 3534 3797 742045917 742046159 1.340000e-69 274.0
39 TraesCS7D01G379500 chr2A 83.922 255 22 2 3544 3797 41477739 41477503 3.820000e-55 226.0
40 TraesCS7D01G379500 chr2A 91.667 48 4 0 456 503 611302949 611302996 2.450000e-07 67.6
41 TraesCS7D01G379500 chr2A 97.143 35 0 1 3495 3529 32274574 32274607 1.470000e-04 58.4
42 TraesCS7D01G379500 chr4A 82.331 266 22 6 3534 3797 592494190 592493948 1.380000e-49 207.0
43 TraesCS7D01G379500 chr4A 82.331 266 22 6 3534 3797 592772988 592772746 1.380000e-49 207.0
44 TraesCS7D01G379500 chr4A 82.331 266 22 6 3534 3797 593061066 593060824 1.380000e-49 207.0
45 TraesCS7D01G379500 chr4A 81.579 266 24 6 3534 3797 591549039 591549281 2.990000e-46 196.0
46 TraesCS7D01G379500 chr4A 92.683 41 2 1 3492 3532 375312803 375312764 1.470000e-04 58.4
47 TraesCS7D01G379500 chr1D 82.400 125 3 2 3674 3797 391296528 391296422 1.450000e-14 91.6
48 TraesCS7D01G379500 chr5A 93.750 48 3 0 458 505 565499016 565498969 5.260000e-09 73.1
49 TraesCS7D01G379500 chr2B 95.000 40 1 1 3493 3532 40822470 40822432 1.140000e-05 62.1
50 TraesCS7D01G379500 chr2B 97.297 37 0 1 3493 3529 153852457 153852492 1.140000e-05 62.1


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 TraesCS7D01G379500 chr7D 491797534 491801330 3796 True 3566.500000 7012 91.48950 1 3797 2 chr7D.!!$R3 3796
1 TraesCS7D01G379500 chr7D 491787793 491792290 4497 True 2458.500000 4739 93.60650 147 3494 2 chr7D.!!$R2 3347
2 TraesCS7D01G379500 chr7D 491861698 491864565 2867 True 1690.500000 3162 84.19800 273 3259 2 chr7D.!!$R4 2986
3 TraesCS7D01G379500 chr7B 521140499 521142914 2415 True 2852.000000 2852 88.03800 273 2696 1 chr7B.!!$R1 2423
4 TraesCS7D01G379500 chr7B 521130501 521133925 3424 True 2710.500000 5295 89.18800 147 3548 2 chr7B.!!$R3 3401
5 TraesCS7D01G379500 chr7B 521120396 521125120 4724 True 1610.333333 3873 92.01000 50 3494 3 chr7B.!!$R2 3444
6 TraesCS7D01G379500 chr7A 558099344 558102228 2884 True 1627.500000 3081 82.77300 271 3259 2 chr7A.!!$R3 2988
7 TraesCS7D01G379500 chr7A 558089941 558093798 3857 True 1462.500000 3877 91.86975 1 3532 4 chr7A.!!$R2 3531
8 TraesCS7D01G379500 chr7A 558079395 558083843 4448 True 1270.275000 4689 87.92925 147 3494 4 chr7A.!!$R1 3347
9 TraesCS7D01G379500 chr2D 599927236 599928923 1687 False 765.000000 765 75.49900 1148 2790 1 chr2D.!!$F1 1642
10 TraesCS7D01G379500 chr1A 478205618 478208907 3289 False 299.000000 302 92.58350 3523 3729 2 chr1A.!!$F1 206

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
809 2186 0.178992 CTCTTGGGCAGTGGAAACCA 60.179 55.0 0.0 0.0 0.00 3.67 F
1332 2718 0.034896 GTGGACCGTTCACCATCTGT 59.965 55.0 0.0 0.0 38.48 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2687 4132 0.251916 TGGCCGGTCCAACTCATTAG 59.748 55.000 14.27 0.0 43.21 1.73 R
3004 4457 3.259064 GAGCTATTACACGCTCCAAACA 58.741 45.455 0.00 0.0 45.21 2.83 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
140 144 4.466828 CAAGTCGGCACTATTTGTCAAAG 58.533 43.478 4.03 0.00 30.14 2.77
220 226 2.565394 GCGTCGTCGTCGCCTATTG 61.565 63.158 23.17 0.00 46.61 1.90
223 229 0.457337 GTCGTCGTCGCCTATTGGTT 60.457 55.000 0.00 0.00 36.96 3.67
269 1585 6.126038 TGTCTTCAACCTATCTCCTCCTCTAT 60.126 42.308 0.00 0.00 0.00 1.98
323 1639 2.707849 GGCAGGGCAAGCAGACATG 61.708 63.158 2.86 0.00 40.91 3.21
357 1673 0.839946 ATGGCTACCCTCCACATGTC 59.160 55.000 0.00 0.00 36.26 3.06
593 1930 2.767972 AGATCCATGTCATCACTCCCA 58.232 47.619 5.04 0.00 0.00 4.37
636 1973 2.088763 CAATCGCCGGATCCGATCG 61.089 63.158 35.42 32.15 43.90 3.69
685 2022 1.464997 GATGGCAACCTTGTCGTCTTC 59.535 52.381 4.85 0.00 43.58 2.87
697 2034 0.460459 TCGTCTTCAACAACGCCACA 60.460 50.000 0.00 0.00 38.72 4.17
809 2186 0.178992 CTCTTGGGCAGTGGAAACCA 60.179 55.000 0.00 0.00 0.00 3.67
855 2232 1.260538 TGCTGTGGGAGAGCTTCGAT 61.261 55.000 0.00 0.00 37.35 3.59
881 2258 1.299648 CCGACATCCTGCTCCCAAA 59.700 57.895 0.00 0.00 0.00 3.28
891 2268 0.539438 TGCTCCCAAACGCCAAGATT 60.539 50.000 0.00 0.00 0.00 2.40
909 2286 0.257328 TTGGCTGGAACAAGGTCACA 59.743 50.000 0.00 0.00 38.70 3.58
925 2302 2.425592 CAGGCCTGAACCGTGTCA 59.574 61.111 29.88 0.00 33.69 3.58
927 2304 2.140792 AGGCCTGAACCGTGTCAGT 61.141 57.895 3.11 0.00 43.02 3.41
1207 2593 5.425577 TGAGATATCTTCGTTCCTCTTCG 57.574 43.478 6.70 0.00 0.00 3.79
1327 2713 0.533978 CACATGTGGACCGTTCACCA 60.534 55.000 18.51 0.00 34.46 4.17
1332 2718 0.034896 GTGGACCGTTCACCATCTGT 59.965 55.000 0.00 0.00 38.48 3.41
1387 2773 1.587933 GAGCTTCTCCAGGACGTCGT 61.588 60.000 9.92 7.31 0.00 4.34
1390 2776 0.882474 CTTCTCCAGGACGTCGTCTT 59.118 55.000 23.69 14.84 32.47 3.01
1439 2825 0.108585 GGGTGCTCCAGAAACACTCA 59.891 55.000 7.20 0.00 34.83 3.41
1488 2892 0.955428 CAGACGTGTTCCACCCCATG 60.955 60.000 0.00 0.00 0.00 3.66
1605 3015 3.386402 GCTCTGCTTACTCCTACCAAGAT 59.614 47.826 0.00 0.00 0.00 2.40
1765 3181 3.009723 GCAGCTGGAGTTGTTATTGCTA 58.990 45.455 17.12 0.00 0.00 3.49
1781 3197 4.921470 TTGCTACAAGCGTTATCAGTTC 57.079 40.909 0.00 0.00 46.26 3.01
1930 3349 5.149977 GCTGTGCTACAAAGAATTTCTCAC 58.850 41.667 0.00 3.43 35.03 3.51
2001 3423 3.082548 TGACCTGACTAGTGTAGCAGTC 58.917 50.000 0.00 3.56 41.31 3.51
2242 3678 1.067821 CCATCGGAGTTGCTAGAGGAC 59.932 57.143 0.00 0.00 0.00 3.85
2439 3875 2.660064 CCCAGAGTGGCTTAGCGGT 61.660 63.158 0.00 0.00 35.79 5.68
2552 3997 0.819259 AGCAGCAACAACCATGTCGT 60.819 50.000 0.00 0.00 39.40 4.34
2664 4109 2.167487 TGAGGTTGAAAGGGTTTGCAAC 59.833 45.455 0.00 3.09 39.76 4.17
3095 4746 6.368791 TGCGTCTTATAGTGCATTTGATATCC 59.631 38.462 0.00 0.00 31.31 2.59
3195 5147 9.816354 AAGTACACCAATTAAATGATAAATGCC 57.184 29.630 0.00 0.00 0.00 4.40
3598 5556 6.963242 TCTAGTACGTTAGCTTGTGATTTACG 59.037 38.462 0.00 0.00 0.00 3.18
3601 5559 4.053295 ACGTTAGCTTGTGATTTACGTGT 58.947 39.130 0.00 0.00 39.03 4.49
3712 5671 3.884037 AGTGGAATTGGTTCAGAAGGT 57.116 42.857 0.00 0.00 36.01 3.50
3765 7246 9.830975 TTACGGGATTGATTATCATATACATGG 57.169 33.333 0.00 0.00 34.77 3.66
3776 7257 4.956085 TCATATACATGGAAGGTTGGACG 58.044 43.478 0.00 0.00 32.61 4.79
3782 7263 0.765135 TGGAAGGTTGGACGAAGGGA 60.765 55.000 0.00 0.00 0.00 4.20
3785 7266 1.278127 GAAGGTTGGACGAAGGGATGA 59.722 52.381 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 144 4.762251 AGGACAAATAGTGCAGACCTTTTC 59.238 41.667 0.00 0.00 41.69 2.29
220 226 2.489722 GAGAGGGAAGACAATGCAAACC 59.510 50.000 0.00 0.00 0.00 3.27
223 229 1.347707 ACGAGAGGGAAGACAATGCAA 59.652 47.619 0.00 0.00 0.00 4.08
269 1585 0.335361 ACGAAGGAGGCTTAGGAGGA 59.665 55.000 0.00 0.00 0.00 3.71
629 1966 1.248101 TGTGTTGCTCTCCGATCGGA 61.248 55.000 33.55 33.55 42.90 4.55
636 1973 4.574599 ATTTGAAGTTGTGTTGCTCTCC 57.425 40.909 0.00 0.00 0.00 3.71
649 1986 6.218746 GTTGCCATCTTCTGAAATTTGAAGT 58.781 36.000 14.55 4.06 40.20 3.01
685 2022 0.660005 CGGATTGTGTGGCGTTGTTG 60.660 55.000 0.00 0.00 0.00 3.33
697 2034 2.264794 GACCAGACGGCGGATTGT 59.735 61.111 13.24 2.55 34.57 2.71
809 2186 3.006967 ACTTGACAGGCTTTCTATGACGT 59.993 43.478 1.90 0.00 0.00 4.34
855 2232 0.035820 GCAGGATGTCGGTTGGGTTA 60.036 55.000 0.00 0.00 39.31 2.85
891 2268 0.179020 CTGTGACCTTGTTCCAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
909 2286 0.830444 TACTGACACGGTTCAGGCCT 60.830 55.000 17.08 0.00 46.38 5.19
925 2302 1.025812 CGGCTCTTCCACGAGATACT 58.974 55.000 0.00 0.00 32.74 2.12
927 2304 0.106868 TCCGGCTCTTCCACGAGATA 60.107 55.000 0.00 0.00 32.74 1.98
1207 2593 0.850856 GTCTGACCAAACACGTCGAC 59.149 55.000 5.18 5.18 32.68 4.20
1298 2684 1.223211 CCACATGTGGCGTATGGGA 59.777 57.895 31.13 0.00 44.73 4.37
1327 2713 0.973632 TGTGAGTTGCCGGTACAGAT 59.026 50.000 1.90 0.00 0.00 2.90
1332 2718 2.745037 GGGTGTGAGTTGCCGGTA 59.255 61.111 1.90 0.00 0.00 4.02
1387 2773 1.626356 CCGAGCTCCCAATCCCAAGA 61.626 60.000 8.47 0.00 0.00 3.02
1390 2776 2.285368 ACCGAGCTCCCAATCCCA 60.285 61.111 8.47 0.00 0.00 4.37
1439 2825 4.445832 TGCCATTGCAATCCAGCT 57.554 50.000 20.39 0.00 46.66 4.24
1488 2892 0.881118 ATGGCAATGTCACACGAACC 59.119 50.000 0.00 0.00 0.00 3.62
1490 2894 2.682352 CCATATGGCAATGTCACACGAA 59.318 45.455 9.29 0.00 0.00 3.85
1585 2995 4.585162 GCTATCTTGGTAGGAGTAAGCAGA 59.415 45.833 0.00 0.00 0.00 4.26
1765 3181 2.038557 ACCCAGAACTGATAACGCTTGT 59.961 45.455 3.19 0.00 0.00 3.16
1781 3197 4.728409 TGAGCATCAGCAACCCAG 57.272 55.556 0.00 0.00 42.56 4.45
1909 3328 6.054941 TCAGTGAGAAATTCTTTGTAGCACA 58.945 36.000 11.20 0.00 0.00 4.57
1930 3349 0.752054 CCTCCTGCTCCTAGCTTCAG 59.248 60.000 0.00 0.00 42.97 3.02
2028 3450 1.352017 TCTGCCCTGAATTGCTTCTCA 59.648 47.619 0.00 0.00 32.29 3.27
2242 3678 2.106566 ACTCTGATGCAGGTAGGACAG 58.893 52.381 0.00 0.00 31.51 3.51
2439 3875 7.537715 CATCCACTTTTGATGTAATAGCAACA 58.462 34.615 0.00 0.00 33.79 3.33
2664 4109 2.899976 TGGATACACCAACATGCTACG 58.100 47.619 0.00 0.00 46.75 3.51
2687 4132 0.251916 TGGCCGGTCCAACTCATTAG 59.748 55.000 14.27 0.00 43.21 1.73
3004 4457 3.259064 GAGCTATTACACGCTCCAAACA 58.741 45.455 0.00 0.00 45.21 2.83
3073 4724 9.077674 CGTAGGATATCAAATGCACTATAAGAC 57.922 37.037 4.83 0.00 0.00 3.01
3095 4746 9.256477 TCATTAAGTGATTTAGTATTGCCGTAG 57.744 33.333 0.00 0.00 0.00 3.51
3195 5147 8.994429 ATATTTATGAGTTCAGATAGCCTTCG 57.006 34.615 0.00 0.00 0.00 3.79
3232 5184 3.868077 GGTGCACAGATTGATGACTAGTC 59.132 47.826 20.43 16.32 0.00 2.59
3290 5242 7.660617 TCGACTGTAATATAGACACTCCCTAAG 59.339 40.741 0.00 0.00 0.00 2.18
3476 5433 6.070481 TCCTAACAATTACACTGTCATGGCTA 60.070 38.462 0.00 0.00 0.00 3.93
3478 5435 4.941263 TCCTAACAATTACACTGTCATGGC 59.059 41.667 0.00 0.00 0.00 4.40
3479 5437 7.630242 ATTCCTAACAATTACACTGTCATGG 57.370 36.000 0.00 0.00 0.00 3.66
3712 5671 9.027202 GGTTCCCATTTCACCTTAATTTACTTA 57.973 33.333 0.00 0.00 0.00 2.24
3742 5755 8.962884 TTCCATGTATATGATAATCAATCCCG 57.037 34.615 0.25 0.00 36.36 5.14
3744 5757 9.911788 ACCTTCCATGTATATGATAATCAATCC 57.088 33.333 0.25 0.00 36.36 3.01
3765 7246 1.278127 TCATCCCTTCGTCCAACCTTC 59.722 52.381 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.