Multiple sequence alignment - TraesCS7D01G071800

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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 TraesCS7D01G071800 chr7D 100.000 3652 0 0 1 3652 42212199 42215850 0.000000e+00 6745
1 TraesCS7D01G071800 chr7D 96.345 3092 99 9 1 3089 41917434 41914354 0.000000e+00 5072
2 TraesCS7D01G071800 chr7D 93.372 3244 188 19 1 3233 42084824 42081597 0.000000e+00 4774
3 TraesCS7D01G071800 chr7D 94.056 572 27 4 3087 3652 41875289 41874719 0.000000e+00 861
4 TraesCS7D01G071800 chr7D 85.496 393 25 6 3225 3609 42435549 42435917 7.400000e-102 381
5 TraesCS7D01G071800 chr7B 91.740 3620 240 24 1 3609 2564604 2561033 0.000000e+00 4974
6 TraesCS7D01G071800 chr4A 91.499 3623 250 33 1 3609 649144376 649147954 0.000000e+00 4931
7 TraesCS7D01G071800 chr4A 91.233 3616 254 31 1 3606 657366544 657370106 0.000000e+00 4863
8 TraesCS7D01G071800 chr4A 91.150 3616 259 28 1 3606 657306849 657310413 0.000000e+00 4848
9 TraesCS7D01G071800 chr4A 90.535 3064 206 40 538 3574 649007116 649010122 0.000000e+00 3975
10 TraesCS7D01G071800 chr4A 89.980 3064 231 39 538 3574 649056792 649059806 0.000000e+00 3888
11 TraesCS7D01G071800 chr4A 92.015 2755 193 18 474 3208 649184120 649186867 0.000000e+00 3843
12 TraesCS7D01G071800 chr4A 92.925 2092 128 10 1 2084 649173850 649175929 0.000000e+00 3025
13 TraesCS7D01G071800 chr4A 91.959 485 38 1 2847 3331 649157020 649157503 0.000000e+00 678
14 TraesCS7D01G071800 chr4A 84.733 393 29 9 3225 3609 649195951 649196320 7.450000e-97 364
15 TraesCS7D01G071800 chr7A 90.935 3563 269 29 33 3566 41618775 41622312 0.000000e+00 4741
16 TraesCS7D01G071800 chr7A 83.221 447 31 13 3225 3652 41791230 41791651 1.600000e-98 370
17 TraesCS7D01G071800 chr2B 91.669 3145 237 15 1 3128 783889647 783886511 0.000000e+00 4333
18 TraesCS7D01G071800 chr2B 88.912 965 100 6 1 963 784346516 784347475 0.000000e+00 1182
19 TraesCS7D01G071800 chrUn 92.509 2750 179 11 474 3208 250935696 250932959 0.000000e+00 3912
20 TraesCS7D01G071800 chrUn 89.530 1299 89 16 2315 3606 361890052 361891310 0.000000e+00 1602
21 TraesCS7D01G071800 chrUn 87.879 198 21 2 3416 3613 250930290 250930096 2.840000e-56 230
22 TraesCS7D01G071800 chrUn 87.879 198 21 2 3416 3613 283093503 283093697 2.840000e-56 230


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 TraesCS7D01G071800 chr7D 42212199 42215850 3651 False 6745 6745 100.000 1 3652 1 chr7D.!!$F1 3651
1 TraesCS7D01G071800 chr7D 41914354 41917434 3080 True 5072 5072 96.345 1 3089 1 chr7D.!!$R2 3088
2 TraesCS7D01G071800 chr7D 42081597 42084824 3227 True 4774 4774 93.372 1 3233 1 chr7D.!!$R3 3232
3 TraesCS7D01G071800 chr7D 41874719 41875289 570 True 861 861 94.056 3087 3652 1 chr7D.!!$R1 565
4 TraesCS7D01G071800 chr7B 2561033 2564604 3571 True 4974 4974 91.740 1 3609 1 chr7B.!!$R1 3608
5 TraesCS7D01G071800 chr4A 649144376 649147954 3578 False 4931 4931 91.499 1 3609 1 chr4A.!!$F3 3608
6 TraesCS7D01G071800 chr4A 657366544 657370106 3562 False 4863 4863 91.233 1 3606 1 chr4A.!!$F9 3605
7 TraesCS7D01G071800 chr4A 657306849 657310413 3564 False 4848 4848 91.150 1 3606 1 chr4A.!!$F8 3605
8 TraesCS7D01G071800 chr4A 649007116 649010122 3006 False 3975 3975 90.535 538 3574 1 chr4A.!!$F1 3036
9 TraesCS7D01G071800 chr4A 649056792 649059806 3014 False 3888 3888 89.980 538 3574 1 chr4A.!!$F2 3036
10 TraesCS7D01G071800 chr4A 649184120 649186867 2747 False 3843 3843 92.015 474 3208 1 chr4A.!!$F6 2734
11 TraesCS7D01G071800 chr4A 649173850 649175929 2079 False 3025 3025 92.925 1 2084 1 chr4A.!!$F5 2083
12 TraesCS7D01G071800 chr7A 41618775 41622312 3537 False 4741 4741 90.935 33 3566 1 chr7A.!!$F1 3533
13 TraesCS7D01G071800 chr2B 783886511 783889647 3136 True 4333 4333 91.669 1 3128 1 chr2B.!!$R1 3127
14 TraesCS7D01G071800 chr2B 784346516 784347475 959 False 1182 1182 88.912 1 963 1 chr2B.!!$F1 962
15 TraesCS7D01G071800 chrUn 250930096 250935696 5600 True 2071 3912 90.194 474 3613 2 chrUn.!!$R1 3139
16 TraesCS7D01G071800 chrUn 361890052 361891310 1258 False 1602 1602 89.530 2315 3606 1 chrUn.!!$F2 1291

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
296 298 0.886490 GTAAGGCCATCCATGCTCGG 60.886 60.0 5.01 0.0 33.74 4.63 F
1214 1252 0.034574 TACCCACAAGATGCGCCAAT 60.035 50.0 4.18 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1680 1.279271 CCCCTAGTGTTTCCAGGTCAG 59.721 57.143 0.0 0.0 0.0 3.51 R
2690 2756 0.105964 AGGAGCCTAGCGATGGAAGA 60.106 55.000 0.0 0.0 0.0 2.87 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
296 298 0.886490 GTAAGGCCATCCATGCTCGG 60.886 60.000 5.01 0.00 33.74 4.63
823 855 5.769484 AGATGGAATACTAGTACACACCG 57.231 43.478 4.31 0.00 0.00 4.94
1202 1240 1.612991 GCCACACATGTCATACCCACA 60.613 52.381 0.00 0.00 0.00 4.17
1214 1252 0.034574 TACCCACAAGATGCGCCAAT 60.035 50.000 4.18 0.00 0.00 3.16
1399 1437 4.675146 GCTTCACAGCAAAGTTTCTTGTCA 60.675 41.667 0.00 0.00 46.49 3.58
1620 1658 5.278169 CGTTATACGAAGCCTGGTATGTACT 60.278 44.000 0.61 0.00 46.05 2.73
1909 1971 1.195674 GACGCAGGCTTCAAAAGAGAC 59.804 52.381 0.00 0.00 0.00 3.36
1996 2059 1.936547 GCTCGCCATCTTCCACTAAAG 59.063 52.381 0.00 0.00 0.00 1.85
2029 2092 2.331893 CCTTGTGATGGCGGCGAAA 61.332 57.895 12.98 0.00 0.00 3.46
2257 2320 8.964533 ATTCTATTCATCTCCTACAGGTACAT 57.035 34.615 0.00 0.00 36.34 2.29
2276 2339 4.887748 ACATGGGAGCATTAGTAAGATCG 58.112 43.478 0.00 0.00 0.00 3.69
2590 2655 2.173569 GGAGAGGATTGGCTGGTATTGT 59.826 50.000 0.00 0.00 0.00 2.71
2644 2709 5.010617 TCAAATCAGTGATAGGCGCTATGTA 59.989 40.000 7.64 0.00 35.06 2.29
2690 2756 0.318360 TGTCTTCGACAACGCGATGT 60.318 50.000 22.64 22.64 39.78 3.06
2881 5413 2.475864 TCAATGCAATGAAACGCAAAGC 59.524 40.909 0.85 0.00 42.37 3.51
2940 5560 3.781808 TGTAGTTTACCAGGGCTAGTGA 58.218 45.455 0.00 0.00 0.00 3.41
3090 5742 5.692115 TCAAGGGCTTTATACTCACATGA 57.308 39.130 0.00 0.00 0.00 3.07
3165 5820 6.017400 ACTTGAATTTACACATGCAGAAGG 57.983 37.500 0.00 0.00 0.00 3.46
3272 5927 9.450807 AAAAGATAATCAAGTCAAAGTTGTTCG 57.549 29.630 0.00 0.00 30.75 3.95
3446 6130 9.524106 AACATTTGCTTGATATGTACATGATTG 57.476 29.630 18.81 6.06 32.51 2.67
3449 6133 8.510243 TTTGCTTGATATGTACATGATTGAGT 57.490 30.769 18.81 0.00 0.00 3.41
3569 6264 4.091509 CGTAATTTCCTTCTCAGAACCACG 59.908 45.833 0.00 0.00 0.00 4.94
3575 6270 2.802816 CCTTCTCAGAACCACGTTCAAG 59.197 50.000 7.24 4.47 44.11 3.02
3585 6280 2.213499 CCACGTTCAAGAGTTGCTTCT 58.787 47.619 0.00 0.00 33.60 2.85
3609 6304 6.756221 TCCACTTCCTTTAGAGTTTAGACAC 58.244 40.000 0.00 0.00 0.00 3.67
3613 6308 5.740290 TCCTTTAGAGTTTAGACACCCTG 57.260 43.478 0.00 0.00 0.00 4.45
3626 6321 1.552337 ACACCCTGTCTGTAGATGCAG 59.448 52.381 0.00 0.00 37.81 4.41
3647 6342 2.838202 GGGAGAATGGAGTGTACCTCAA 59.162 50.000 11.82 3.09 42.40 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 5.112220 TGTTCTTTTGTCTGCTGCTATTG 57.888 39.130 0.00 0.00 0.00 1.90
432 436 6.381133 AGAAAGATTGTTGGTGTTTCTTTCCT 59.619 34.615 16.08 5.49 46.89 3.36
823 855 6.635030 AAAGATTTATTGACGCCTTATCCC 57.365 37.500 0.00 0.00 0.00 3.85
909 944 6.675002 GCTCGATGAATCTTTGGATGCATATC 60.675 42.308 0.00 0.00 45.56 1.63
1141 1179 3.832619 CAAGATGCAGCTTGAGGCGATT 61.833 50.000 35.31 0.00 46.31 3.34
1202 1240 4.905429 TGGTATGTATATTGGCGCATCTT 58.095 39.130 10.83 0.00 0.00 2.40
1214 1252 9.132923 TCACAAACAAGGTTTTTGGTATGTATA 57.867 29.630 7.80 0.00 38.12 1.47
1317 1355 6.458206 CGATGGACCAACATTTATCGTCATTT 60.458 38.462 0.00 0.00 34.43 2.32
1353 1391 4.081406 TGACTATTGTGCTCTTTGCCATT 58.919 39.130 0.00 0.00 42.00 3.16
1399 1437 3.614092 CACTATTCTCACCACTTGCCAT 58.386 45.455 0.00 0.00 0.00 4.40
1639 1680 1.279271 CCCCTAGTGTTTCCAGGTCAG 59.721 57.143 0.00 0.00 0.00 3.51
1687 1736 4.440112 GCCTTGTGCCCACTGAAAATATAC 60.440 45.833 0.00 0.00 0.00 1.47
1772 1826 7.139896 ACAGTCTATCGCTCTATACAATGAG 57.860 40.000 0.00 0.00 0.00 2.90
1909 1971 3.054166 CTGCAACCACAAACATGTCATG 58.946 45.455 11.41 11.41 0.00 3.07
2257 2320 3.069586 CCACGATCTTACTAATGCTCCCA 59.930 47.826 0.00 0.00 0.00 4.37
2276 2339 5.527582 ACTGAAATTCAACTATATCGCCCAC 59.472 40.000 0.00 0.00 0.00 4.61
2508 2573 7.496529 TCCAATGATTCGGATATTCTTTGAC 57.503 36.000 10.57 0.00 30.14 3.18
2590 2655 3.329386 GCGATATTCTTGGCATCTGCTA 58.671 45.455 1.70 0.00 41.70 3.49
2644 2709 6.882610 TCGCTGATTTGATAATTTAGCCAT 57.117 33.333 0.00 0.00 33.90 4.40
2690 2756 0.105964 AGGAGCCTAGCGATGGAAGA 60.106 55.000 0.00 0.00 0.00 2.87
2736 2802 3.018901 CCCCTGCCTTAGCCCAAT 58.981 61.111 0.00 0.00 38.69 3.16
2839 2905 5.650283 TGAAAGGATGGGGAAAAGTTACAT 58.350 37.500 0.00 0.00 0.00 2.29
2940 5560 4.220821 TCTCAAAGAATCAACCGTCTAGCT 59.779 41.667 0.00 0.00 0.00 3.32
3090 5742 8.553696 CAACAAAAATTAGAAAGCTCTTTGCAT 58.446 29.630 0.00 0.00 45.94 3.96
3165 5820 3.141002 ACATCATGTTCAAGCGAATGC 57.859 42.857 0.00 0.00 43.24 3.56
3169 5824 5.681337 TGTTAAACATCATGTTCAAGCGA 57.319 34.783 2.74 0.00 40.14 4.93
3227 5882 5.879223 TCTTTTGCACCATTTGTTGTTGATT 59.121 32.000 0.00 0.00 0.00 2.57
3409 6093 5.976458 TCAAGCAAATGTTTGGAGAACTTT 58.024 33.333 9.62 0.00 38.57 2.66
3446 6130 3.274288 CCTGGCTTGAAGATTGGTACTC 58.726 50.000 0.00 0.00 0.00 2.59
3449 6133 1.340991 GGCCTGGCTTGAAGATTGGTA 60.341 52.381 19.68 0.00 0.00 3.25
3569 6264 3.471680 AGTGGAGAAGCAACTCTTGAAC 58.528 45.455 9.39 4.78 37.13 3.18
3575 6270 2.849294 AGGAAGTGGAGAAGCAACTC 57.151 50.000 2.23 2.23 36.31 3.01
3585 6280 6.239515 GGTGTCTAAACTCTAAAGGAAGTGGA 60.240 42.308 0.00 0.00 0.00 4.02
3613 6308 3.494048 CCATTCTCCCTGCATCTACAGAC 60.494 52.174 0.00 0.00 40.25 3.51
3626 6321 2.467880 TGAGGTACACTCCATTCTCCC 58.532 52.381 8.36 0.00 46.01 4.30


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

AutoCloner maintained by Alex Coulton.