Multiple sequence alignment - TraesCS7B01G480100

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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 TraesCS7B01G480100 chr7B 100.000 2546 0 0 1 2546 734144708 734147253 0.000000e+00 4702
1 TraesCS7B01G480100 chr7B 95.030 1992 71 12 575 2543 720989198 720987212 0.000000e+00 3105
2 TraesCS7B01G480100 chr7B 95.199 1958 68 11 608 2543 708943230 708941277 0.000000e+00 3072
3 TraesCS7B01G480100 chr1B 95.477 1990 61 14 580 2543 581717566 581715580 0.000000e+00 3149
4 TraesCS7B01G480100 chr1B 95.181 1992 68 12 574 2543 561526119 561528104 0.000000e+00 3121
5 TraesCS7B01G480100 chr1B 95.161 1984 68 15 582 2543 671392208 671394185 0.000000e+00 3107
6 TraesCS7B01G480100 chr1B 95.058 1983 67 15 584 2543 520844119 520842145 0.000000e+00 3090
7 TraesCS7B01G480100 chr1B 89.751 361 31 3 583 942 645321436 645321791 8.300000e-125 457
8 TraesCS7B01G480100 chr4A 95.276 1990 66 12 577 2543 705529260 705527276 0.000000e+00 3129
9 TraesCS7B01G480100 chr3B 95.164 1985 68 14 583 2543 108092313 108090333 0.000000e+00 3109
10 TraesCS7B01G480100 chr2B 95.028 1991 71 14 575 2543 692955889 692957873 0.000000e+00 3103
11 TraesCS7B01G480100 chr7D 90.028 1755 131 18 1 1719 574727713 574725967 0.000000e+00 2231
12 TraesCS7B01G480100 chr7D 94.511 583 31 1 1 583 520694538 520693957 0.000000e+00 898
13 TraesCS7B01G480100 chr2D 91.004 1145 65 19 581 1719 435209596 435210708 0.000000e+00 1509
14 TraesCS7B01G480100 chr2D 94.701 585 28 2 1 583 336748752 336749335 0.000000e+00 905
15 TraesCS7B01G480100 chr2D 94.340 583 32 1 1 583 108741658 108741077 0.000000e+00 893
16 TraesCS7B01G480100 chr2D 94.168 583 33 1 1 583 483278337 483278918 0.000000e+00 887
17 TraesCS7B01G480100 chr2D 92.479 359 22 2 584 942 16065486 16065839 2.260000e-140 508
18 TraesCS7B01G480100 chr3D 94.854 583 29 1 1 583 23004586 23004005 0.000000e+00 909
19 TraesCS7B01G480100 chr6D 94.168 583 33 1 1 583 139613136 139612555 0.000000e+00 887
20 TraesCS7B01G480100 chr4D 94.168 583 33 1 1 583 33248411 33247830 0.000000e+00 887
21 TraesCS7B01G480100 chr4D 94.148 581 33 1 3 583 385437676 385438255 0.000000e+00 883
22 TraesCS7B01G480100 chrUn 85.714 693 86 12 1 683 87150534 87149845 0.000000e+00 719
23 TraesCS7B01G480100 chr5D 90.164 366 29 4 584 942 357075968 357075603 1.070000e-128 470
24 TraesCS7B01G480100 chr5A 89.362 376 30 7 572 944 689409592 689409224 4.960000e-127 464
25 TraesCS7B01G480100 chr5A 88.827 358 35 3 582 935 28960261 28959905 3.890000e-118 435
26 TraesCS7B01G480100 chr4B 90.169 356 25 7 586 934 251255863 251256215 2.990000e-124 455
27 TraesCS7B01G480100 chr4B 88.556 367 36 5 579 942 648647871 648648234 8.360000e-120 440


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 TraesCS7B01G480100 chr7B 734144708 734147253 2545 False 4702 4702 100.000 1 2546 1 chr7B.!!$F1 2545
1 TraesCS7B01G480100 chr7B 720987212 720989198 1986 True 3105 3105 95.030 575 2543 1 chr7B.!!$R2 1968
2 TraesCS7B01G480100 chr7B 708941277 708943230 1953 True 3072 3072 95.199 608 2543 1 chr7B.!!$R1 1935
3 TraesCS7B01G480100 chr1B 581715580 581717566 1986 True 3149 3149 95.477 580 2543 1 chr1B.!!$R2 1963
4 TraesCS7B01G480100 chr1B 561526119 561528104 1985 False 3121 3121 95.181 574 2543 1 chr1B.!!$F1 1969
5 TraesCS7B01G480100 chr1B 671392208 671394185 1977 False 3107 3107 95.161 582 2543 1 chr1B.!!$F3 1961
6 TraesCS7B01G480100 chr1B 520842145 520844119 1974 True 3090 3090 95.058 584 2543 1 chr1B.!!$R1 1959
7 TraesCS7B01G480100 chr4A 705527276 705529260 1984 True 3129 3129 95.276 577 2543 1 chr4A.!!$R1 1966
8 TraesCS7B01G480100 chr3B 108090333 108092313 1980 True 3109 3109 95.164 583 2543 1 chr3B.!!$R1 1960
9 TraesCS7B01G480100 chr2B 692955889 692957873 1984 False 3103 3103 95.028 575 2543 1 chr2B.!!$F1 1968
10 TraesCS7B01G480100 chr7D 574725967 574727713 1746 True 2231 2231 90.028 1 1719 1 chr7D.!!$R2 1718
11 TraesCS7B01G480100 chr7D 520693957 520694538 581 True 898 898 94.511 1 583 1 chr7D.!!$R1 582
12 TraesCS7B01G480100 chr2D 435209596 435210708 1112 False 1509 1509 91.004 581 1719 1 chr2D.!!$F3 1138
13 TraesCS7B01G480100 chr2D 336748752 336749335 583 False 905 905 94.701 1 583 1 chr2D.!!$F2 582
14 TraesCS7B01G480100 chr2D 108741077 108741658 581 True 893 893 94.340 1 583 1 chr2D.!!$R1 582
15 TraesCS7B01G480100 chr2D 483278337 483278918 581 False 887 887 94.168 1 583 1 chr2D.!!$F4 582
16 TraesCS7B01G480100 chr3D 23004005 23004586 581 True 909 909 94.854 1 583 1 chr3D.!!$R1 582
17 TraesCS7B01G480100 chr6D 139612555 139613136 581 True 887 887 94.168 1 583 1 chr6D.!!$R1 582
18 TraesCS7B01G480100 chr4D 33247830 33248411 581 True 887 887 94.168 1 583 1 chr4D.!!$R1 582
19 TraesCS7B01G480100 chr4D 385437676 385438255 579 False 883 883 94.148 3 583 1 chr4D.!!$F1 580
20 TraesCS7B01G480100 chrUn 87149845 87150534 689 True 719 719 85.714 1 683 1 chrUn.!!$R1 682

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
65 66 0.526662 ACCTCGCGACTAACTCCTTG 59.473 55.0 3.71 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2089 1.483827 CTCTTGCCATCTGTCCTAGCA 59.516 52.381 0.0 0.0 0.0 3.49 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
34 35 4.280174 ACTGGCAAGTCTCTTTACTCGTTA 59.720 41.667 0.00 0.00 26.77 3.18
65 66 0.526662 ACCTCGCGACTAACTCCTTG 59.473 55.000 3.71 0.00 0.00 3.61
71 73 2.541556 GCGACTAACTCCTTGGTCATC 58.458 52.381 0.00 0.00 37.66 2.92
119 125 0.834261 GAGAGGGCCCAGAGATACCC 60.834 65.000 27.56 0.76 43.17 3.69
261 267 4.408921 CACAAGGTATTCCTCTGGTATCCA 59.591 45.833 0.00 0.00 44.35 3.41
380 388 5.826737 GGATCTTGTCCATCACATCATTCTT 59.173 40.000 0.00 0.00 46.96 2.52
398 407 5.869649 TTCTTCTAATGATGTGATCCCGA 57.130 39.130 0.00 0.00 0.00 5.14
412 422 6.118852 TGTGATCCCGATATCAAATGACAAA 58.881 36.000 3.12 0.00 37.61 2.83
504 515 9.403583 AGGGACACGATATTTGTTTATGTATTT 57.596 29.630 0.00 0.00 0.00 1.40
845 883 2.074547 GCTATATTAGCGGGCGACAA 57.925 50.000 0.00 0.00 42.62 3.18
873 911 2.182791 CACGGCGACAGAGAGCAT 59.817 61.111 16.62 0.00 34.54 3.79
1257 1296 2.095364 GCAGGTGACATGCTTCTTTCTG 60.095 50.000 15.63 0.00 40.59 3.02
1527 1569 3.818210 TCGCACTGGTTGTAATGTTGAAT 59.182 39.130 0.00 0.00 0.00 2.57
1607 1649 9.191995 GAAATTCACCTAGTTTAAATGTTGGTG 57.808 33.333 19.31 19.31 43.22 4.17
1629 1674 9.273016 TGGTGAAAGTTGTTTAAATGTTGAAAA 57.727 25.926 0.00 0.00 0.00 2.29
1735 1783 8.418597 AATGCAGCTAATGAATTATTCCAGAT 57.581 30.769 2.22 0.00 35.17 2.90
1838 1887 8.987890 CCGTGATTTAAATCAAAGACCAAAATT 58.012 29.630 28.02 0.00 46.13 1.82
1852 1901 8.750515 AAGACCAAAATTTCATGGAAAATGTT 57.249 26.923 14.54 0.00 39.12 2.71
1970 2021 4.436113 AGGGTGGAAAATGCACAAAAAT 57.564 36.364 4.42 0.00 40.73 1.82
1981 2032 0.585838 CACAAAAATTTGGTGCGGCC 59.414 50.000 10.38 0.00 42.34 6.13
2003 2054 1.664306 GACTCGAACCCAAGACCGT 59.336 57.895 0.00 0.00 0.00 4.83
2038 2089 1.550130 TTAGGGCTGCGCTGGTAACT 61.550 55.000 27.01 3.65 37.61 2.24
2322 2380 0.099613 AATGTTTGCACACGCGTGAA 59.900 45.000 42.94 25.39 46.80 3.18
2332 2390 1.200484 ACACGCGTGAAAGTGGTTTTT 59.800 42.857 42.94 15.44 42.25 1.94
2540 2600 3.230134 CCCCCTCTTTTGAATGACAACA 58.770 45.455 0.00 0.00 38.29 3.33
2541 2601 3.005791 CCCCCTCTTTTGAATGACAACAC 59.994 47.826 0.00 0.00 38.29 3.32
2542 2602 3.636300 CCCCTCTTTTGAATGACAACACA 59.364 43.478 0.00 0.00 38.29 3.72
2543 2603 4.281688 CCCCTCTTTTGAATGACAACACAT 59.718 41.667 0.00 0.00 38.29 3.21
2544 2604 5.476599 CCCCTCTTTTGAATGACAACACATA 59.523 40.000 0.00 0.00 38.29 2.29
2545 2605 6.015519 CCCCTCTTTTGAATGACAACACATAA 60.016 38.462 0.00 0.00 38.29 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.899120 AGTCGCGAGGTGATATATTACAT 57.101 39.130 10.24 2.27 0.00 2.29
42 43 1.945394 GGAGTTAGTCGCGAGGTGATA 59.055 52.381 10.24 0.00 0.00 2.15
261 267 7.468141 TCGACTATGATATTATGCAACTCCT 57.532 36.000 0.00 0.00 0.00 3.69
380 388 7.480760 TTGATATCGGGATCACATCATTAGA 57.519 36.000 0.00 0.00 35.56 2.10
504 515 8.047911 TGATCGGAAACCCTAAATAAATGTGTA 58.952 33.333 0.00 0.00 0.00 2.90
511 522 9.635404 ATTGTATTGATCGGAAACCCTAAATAA 57.365 29.630 0.00 0.00 0.00 1.40
518 529 6.293462 GCTAGAATTGTATTGATCGGAAACCC 60.293 42.308 0.00 0.00 0.00 4.11
652 672 0.769247 ACGGACTAGGGGCAAAACTT 59.231 50.000 0.00 0.00 0.00 2.66
1257 1296 2.512515 GCCAGAGCATCGACCCAC 60.513 66.667 0.00 0.00 42.67 4.61
1527 1569 8.169393 TCCATAATTCATGCCTTTCCATACATA 58.831 33.333 0.00 0.00 32.84 2.29
1629 1674 7.410120 AAATGTTGGTCACTTCTTCTTCTTT 57.590 32.000 0.00 0.00 0.00 2.52
1852 1901 2.836636 ACATCTACCAGAGCTGAGGA 57.163 50.000 7.99 0.00 0.00 3.71
1940 1990 4.820716 TGCATTTTCCACCCTTCATTTTTG 59.179 37.500 0.00 0.00 0.00 2.44
1981 2032 2.264794 CTTGGGTTCGAGTCCCCG 59.735 66.667 20.23 10.81 44.44 5.73
2003 2054 2.379972 CCTAAACACCACAAACCCACA 58.620 47.619 0.00 0.00 0.00 4.17
2038 2089 1.483827 CTCTTGCCATCTGTCCTAGCA 59.516 52.381 0.00 0.00 0.00 3.49
2179 2236 1.410882 GCAGCCCTAAACACCACAAAA 59.589 47.619 0.00 0.00 0.00 2.44
2219 2276 3.245229 ACCCATGTCAAACTCTTGCCATA 60.245 43.478 0.00 0.00 29.52 2.74
2322 2380 5.762711 AGTGCAAAACAAAGAAAAACCACTT 59.237 32.000 0.00 0.00 0.00 3.16
2332 2390 6.652481 TCCAAAATTTCAGTGCAAAACAAAGA 59.348 30.769 0.00 0.00 0.00 2.52
2496 2556 3.008594 TGAGAAGCCCTCCGTTTTATTCA 59.991 43.478 1.79 0.00 41.25 2.57


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

AutoCloner maintained by Alex Coulton.