Multiple sequence alignment - TraesCS2B01G091100

Loading Multiple Alignment...

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 TraesCS2B01G091100 chr2B 100.000 4442 0 0 1 4442 52513522 52509081 0.000000e+00 8203
1 TraesCS2B01G091100 chr2B 94.545 4051 158 12 1 4030 52222179 52226187 0.000000e+00 6198
2 TraesCS2B01G091100 chr2B 89.320 721 72 5 3723 4440 298486671 298487389 0.000000e+00 900
3 TraesCS2B01G091100 chr2B 87.852 568 58 4 3884 4440 23774722 23774155 0.000000e+00 656
4 TraesCS2B01G091100 chr2D 93.902 2132 93 13 1602 3724 31896803 31898906 0.000000e+00 3182
5 TraesCS2B01G091100 chr2D 92.073 1375 88 5 249 1604 31895385 31896757 0.000000e+00 1916
6 TraesCS2B01G091100 chr2D 91.250 720 60 3 3724 4440 225072246 225072965 0.000000e+00 977
7 TraesCS2B01G091100 chr2D 90.028 722 65 7 3724 4440 100524348 100525067 0.000000e+00 928
8 TraesCS2B01G091100 chr2D 89.365 724 63 12 3727 4440 438109861 438109142 0.000000e+00 898
9 TraesCS2B01G091100 chr2D 91.453 351 29 1 217 566 561897736 561897386 8.640000e-132 481
10 TraesCS2B01G091100 chr2A 92.210 2131 119 24 1602 3722 33952700 33954793 0.000000e+00 2972
11 TraesCS2B01G091100 chr2A 91.418 1375 98 4 249 1604 33785500 33786873 0.000000e+00 1868
12 TraesCS2B01G091100 chr2A 91.055 1375 102 12 249 1604 33951282 33952654 0.000000e+00 1838
13 TraesCS2B01G091100 chr2A 91.395 1290 65 10 2445 3722 33790456 33791711 0.000000e+00 1725
14 TraesCS2B01G091100 chr2A 93.662 852 49 4 1602 2451 33786919 33787767 0.000000e+00 1269
15 TraesCS2B01G091100 chr5D 87.738 1941 205 23 1620 3539 227545148 227547076 0.000000e+00 2235
16 TraesCS2B01G091100 chr5D 86.174 933 102 15 685 1596 227544151 227545077 0.000000e+00 983
17 TraesCS2B01G091100 chr5D 89.444 720 66 10 3727 4440 110584521 110583806 0.000000e+00 900
18 TraesCS2B01G091100 chr5B 85.521 2141 261 40 1602 3721 250952496 250954608 0.000000e+00 2191
19 TraesCS2B01G091100 chr5B 84.863 1024 112 21 596 1596 250951439 250952442 0.000000e+00 992
20 TraesCS2B01G091100 chr5B 85.417 144 15 6 57 198 602847225 602847364 1.290000e-30 145
21 TraesCS2B01G091100 chr5A 87.047 1876 209 25 1602 3460 305279058 305280916 0.000000e+00 2087
22 TraesCS2B01G091100 chr5A 86.301 1022 111 14 596 1596 305277991 305279004 0.000000e+00 1085
23 TraesCS2B01G091100 chr5A 81.091 275 24 18 3450 3721 305280968 305281217 1.260000e-45 195
24 TraesCS2B01G091100 chr6D 82.771 1927 288 30 1646 3534 441713476 441711556 0.000000e+00 1679
25 TraesCS2B01G091100 chr6A 82.065 1985 302 35 1594 3534 590895558 590893584 0.000000e+00 1644
26 TraesCS2B01G091100 chr6B 82.326 1935 285 33 1646 3534 667247656 667245733 0.000000e+00 1626
27 TraesCS2B01G091100 chr3D 93.655 725 38 2 3723 4440 526361323 526362046 0.000000e+00 1077
28 TraesCS2B01G091100 chr3D 92.329 717 52 3 3727 4440 469502980 469502264 0.000000e+00 1016
29 TraesCS2B01G091100 chr3D 90.390 718 64 5 3727 4440 166877596 166876880 0.000000e+00 939
30 TraesCS2B01G091100 chr3D 91.453 351 30 0 216 566 374077694 374077344 2.400000e-132 483
31 TraesCS2B01G091100 chr1D 90.833 720 63 2 3724 4440 191956395 191957114 0.000000e+00 961
32 TraesCS2B01G091100 chr3B 91.379 348 30 0 219 566 631007245 631007592 1.120000e-130 477
33 TraesCS2B01G091100 chr3A 91.404 349 28 2 219 566 496644531 496644184 1.120000e-130 477
34 TraesCS2B01G091100 chr3A 91.143 350 29 1 219 566 466817424 466817075 1.450000e-129 473
35 TraesCS2B01G091100 chr4D 82.192 146 18 8 57 198 46473127 46472986 7.810000e-23 119
36 TraesCS2B01G091100 chr4B 80.000 145 20 9 57 198 67877289 67877151 1.020000e-16 99


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 TraesCS2B01G091100 chr2B 52509081 52513522 4441 True 8203.000000 8203 100.000000 1 4442 1 chr2B.!!$R2 4441
1 TraesCS2B01G091100 chr2B 52222179 52226187 4008 False 6198.000000 6198 94.545000 1 4030 1 chr2B.!!$F1 4029
2 TraesCS2B01G091100 chr2B 298486671 298487389 718 False 900.000000 900 89.320000 3723 4440 1 chr2B.!!$F2 717
3 TraesCS2B01G091100 chr2B 23774155 23774722 567 True 656.000000 656 87.852000 3884 4440 1 chr2B.!!$R1 556
4 TraesCS2B01G091100 chr2D 31895385 31898906 3521 False 2549.000000 3182 92.987500 249 3724 2 chr2D.!!$F3 3475
5 TraesCS2B01G091100 chr2D 225072246 225072965 719 False 977.000000 977 91.250000 3724 4440 1 chr2D.!!$F2 716
6 TraesCS2B01G091100 chr2D 100524348 100525067 719 False 928.000000 928 90.028000 3724 4440 1 chr2D.!!$F1 716
7 TraesCS2B01G091100 chr2D 438109142 438109861 719 True 898.000000 898 89.365000 3727 4440 1 chr2D.!!$R1 713
8 TraesCS2B01G091100 chr2A 33951282 33954793 3511 False 2405.000000 2972 91.632500 249 3722 2 chr2A.!!$F2 3473
9 TraesCS2B01G091100 chr2A 33785500 33791711 6211 False 1620.666667 1868 92.158333 249 3722 3 chr2A.!!$F1 3473
10 TraesCS2B01G091100 chr5D 227544151 227547076 2925 False 1609.000000 2235 86.956000 685 3539 2 chr5D.!!$F1 2854
11 TraesCS2B01G091100 chr5D 110583806 110584521 715 True 900.000000 900 89.444000 3727 4440 1 chr5D.!!$R1 713
12 TraesCS2B01G091100 chr5B 250951439 250954608 3169 False 1591.500000 2191 85.192000 596 3721 2 chr5B.!!$F2 3125
13 TraesCS2B01G091100 chr5A 305277991 305281217 3226 False 1122.333333 2087 84.813000 596 3721 3 chr5A.!!$F1 3125
14 TraesCS2B01G091100 chr6D 441711556 441713476 1920 True 1679.000000 1679 82.771000 1646 3534 1 chr6D.!!$R1 1888
15 TraesCS2B01G091100 chr6A 590893584 590895558 1974 True 1644.000000 1644 82.065000 1594 3534 1 chr6A.!!$R1 1940
16 TraesCS2B01G091100 chr6B 667245733 667247656 1923 True 1626.000000 1626 82.326000 1646 3534 1 chr6B.!!$R1 1888
17 TraesCS2B01G091100 chr3D 526361323 526362046 723 False 1077.000000 1077 93.655000 3723 4440 1 chr3D.!!$F1 717
18 TraesCS2B01G091100 chr3D 469502264 469502980 716 True 1016.000000 1016 92.329000 3727 4440 1 chr3D.!!$R3 713
19 TraesCS2B01G091100 chr3D 166876880 166877596 716 True 939.000000 939 90.390000 3727 4440 1 chr3D.!!$R1 713
20 TraesCS2B01G091100 chr1D 191956395 191957114 719 False 961.000000 961 90.833000 3724 4440 1 chr1D.!!$F1 716

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
406 407 5.429109 TCTTAGACTTGCCTCTAGGACTAGA 59.571 44.000 8.63 8.63 39.67 2.43 F
759 760 7.506114 TCAACTAGGGTCAACATTATCCATAC 58.494 38.462 0.00 0.00 0.00 2.39 F
2184 2283 3.346315 TGCACCATTAAGTGATGTCCAG 58.654 45.455 0.00 0.00 40.34 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1799 0.706433 ATTGGGCTTGTGGGATGACT 59.294 50.000 0.0 0.0 0.00 3.41 R
2470 5271 4.243007 AGCAACATGAAACCTAGCAAAC 57.757 40.909 0.0 0.0 0.00 2.93 R
3954 6854 0.603707 CGCACACACCTTCATCTGGT 60.604 55.000 0.0 0.0 38.53 4.00 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
123 124 8.512956 CAATTCCAAATATTCCAAAACATTGCA 58.487 29.630 0.00 0.00 0.00 4.08
206 207 6.367969 CCAAAGCAATCTTCAATCTTCCAAAG 59.632 38.462 0.00 0.00 0.00 2.77
366 367 6.317391 TCATATGCACGTGTGGAATGATAAAA 59.683 34.615 18.38 0.00 33.77 1.52
406 407 5.429109 TCTTAGACTTGCCTCTAGGACTAGA 59.571 44.000 8.63 8.63 39.67 2.43
759 760 7.506114 TCAACTAGGGTCAACATTATCCATAC 58.494 38.462 0.00 0.00 0.00 2.39
1424 1446 7.759489 ATTTGAAGTAAACAGTGGCAGATTA 57.241 32.000 0.00 0.00 0.00 1.75
1989 2074 8.846211 TGTCAAAGCAATAATTACCTAATAGCC 58.154 33.333 0.00 0.00 0.00 3.93
2184 2283 3.346315 TGCACCATTAAGTGATGTCCAG 58.654 45.455 0.00 0.00 40.34 3.86
2220 2321 7.182361 TGCGATATGATGTCAATCTTTCTTC 57.818 36.000 0.00 0.00 33.61 2.87
2462 5263 5.968676 TTGGGTATATCCAAGCTACAGTT 57.031 39.130 13.73 0.00 41.44 3.16
2470 5271 3.466836 TCCAAGCTACAGTTGTGACAAG 58.533 45.455 0.00 0.00 0.00 3.16
2592 5398 7.441890 TTGACGTTGGAACACATTTATGTAT 57.558 32.000 0.00 0.00 39.29 2.29
2634 5446 1.133699 GCCCTGATCATGATTGTGGGA 60.134 52.381 29.84 6.91 35.40 4.37
2664 5476 3.813166 GCAAGTTAGCTCAAGTGTTGGTA 59.187 43.478 0.00 0.00 0.00 3.25
2674 5486 5.570844 GCTCAAGTGTTGGTATAGGAGGAAA 60.571 44.000 0.00 0.00 0.00 3.13
2999 5820 1.021202 CTTCACCTCGCCACAAACAA 58.979 50.000 0.00 0.00 0.00 2.83
3686 6584 5.713792 TGCCGAATAAGAATAGGAGAGAG 57.286 43.478 0.00 0.00 0.00 3.20
3869 6769 1.735018 CGGATGCATCAAACACGGTTA 59.265 47.619 27.25 0.00 0.00 2.85
3903 6803 0.541392 TGTGCGATGAAGGGCATACT 59.459 50.000 0.00 0.00 41.83 2.12
3930 6830 5.493133 AGTTCAATTAACTGTTTGCGACA 57.507 34.783 0.00 0.00 46.90 4.35
3954 6854 2.100087 GAGGAACAAAAGAAACGGGCAA 59.900 45.455 0.00 0.00 0.00 4.52
3988 6890 4.501559 GTGTGTGCGATATACAACATACGT 59.498 41.667 0.00 0.00 31.85 3.57
4034 6936 4.966965 TTAGGCAACACAAAAGAAACGA 57.033 36.364 0.00 0.00 41.41 3.85
4084 6986 2.304092 AGCATACGGTTCACTCGGATA 58.696 47.619 0.00 0.00 28.99 2.59
4125 7027 0.666374 ACAAAAGAAACGGGAAGCCG 59.334 50.000 0.00 0.00 39.31 5.52
4288 7191 2.280524 TCTGTGGCAACCGTTCGG 60.281 61.111 9.81 9.81 0.00 4.30
4344 7259 0.667993 CACCGCTTCTTTGCCTTTCA 59.332 50.000 0.00 0.00 0.00 2.69
4345 7260 1.270550 CACCGCTTCTTTGCCTTTCAT 59.729 47.619 0.00 0.00 0.00 2.57
4348 7263 2.599659 CGCTTCTTTGCCTTTCATTCC 58.400 47.619 0.00 0.00 0.00 3.01
4349 7264 2.030007 CGCTTCTTTGCCTTTCATTCCA 60.030 45.455 0.00 0.00 0.00 3.53
4350 7265 3.367703 CGCTTCTTTGCCTTTCATTCCAT 60.368 43.478 0.00 0.00 0.00 3.41
4351 7266 4.179298 GCTTCTTTGCCTTTCATTCCATC 58.821 43.478 0.00 0.00 0.00 3.51
4353 7268 5.648572 CTTCTTTGCCTTTCATTCCATCTC 58.351 41.667 0.00 0.00 0.00 2.75
4424 7342 5.022282 TCTGCCATTGTTCGATCATCTTA 57.978 39.130 0.00 0.00 0.00 2.10
4440 7358 4.726317 TCATCTTATCCATGGAGGGAACAA 59.274 41.667 21.33 6.12 41.12 2.83
4441 7359 4.778213 TCTTATCCATGGAGGGAACAAG 57.222 45.455 21.33 14.54 41.12 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.468746 TGTATAATGGCTTGGTCTATTTCGC 59.531 40.000 0.00 0.00 0.00 4.70
16 17 7.490962 TTGTATAATGGCTTGGTCTATTTCG 57.509 36.000 0.00 0.00 0.00 3.46
96 97 8.513774 GCAATGTTTTGGAATATTTGGAATTGT 58.486 29.630 0.00 0.00 33.22 2.71
109 110 1.202627 GGTGGCTGCAATGTTTTGGAA 60.203 47.619 0.50 0.00 32.35 3.53
123 124 0.253160 TAGTCCTGATTGGGGTGGCT 60.253 55.000 0.00 0.00 36.20 4.75
158 159 5.590663 GGGAGATGGATCAAAACCTTTAGAC 59.409 44.000 0.00 0.00 0.00 2.59
206 207 7.704899 GGCATATTTCCAACACTTAAATGTACC 59.295 37.037 0.00 0.00 30.75 3.34
378 379 3.576550 CCTAGAGGCAAGTCTAAGATCCC 59.423 52.174 0.00 0.00 0.00 3.85
381 382 5.137412 AGTCCTAGAGGCAAGTCTAAGAT 57.863 43.478 0.00 0.00 34.44 2.40
388 389 6.322712 CACTTTATCTAGTCCTAGAGGCAAGT 59.677 42.308 9.69 12.38 44.47 3.16
406 407 4.819630 ACGTGATCACCAACAACACTTTAT 59.180 37.500 20.03 0.00 0.00 1.40
518 519 7.721842 TCAATTCATAACAGACAAGTTTGGGTA 59.278 33.333 0.00 0.00 33.07 3.69
552 553 7.482654 TTGATTGCTCTTTGATTATAGACGG 57.517 36.000 0.00 0.00 0.00 4.79
759 760 9.495754 GGAAAGATCTTCAAAATTATTGTCTCG 57.504 33.333 8.78 0.00 0.00 4.04
1022 1043 7.129457 AGATATGCTAAGAGAATGGTCACAA 57.871 36.000 0.00 0.00 0.00 3.33
1190 1212 4.681781 CGGCATCTCCTCAACTTCATAGTT 60.682 45.833 0.00 0.00 45.40 2.24
1570 1593 4.261489 GCCTTGCTTGATGATCATACCAAG 60.261 45.833 23.41 23.41 39.06 3.61
1720 1799 0.706433 ATTGGGCTTGTGGGATGACT 59.294 50.000 0.00 0.00 0.00 3.41
1917 1999 6.343716 TGTTGTGCATTTAACATCTCCAAT 57.656 33.333 9.25 0.00 32.30 3.16
2184 2283 6.764094 ACATCATATCGCAACAAAATTTTGC 58.236 32.000 26.94 15.57 44.94 3.68
2462 5263 4.265893 TGAAACCTAGCAAACTTGTCACA 58.734 39.130 0.00 0.00 0.00 3.58
2470 5271 4.243007 AGCAACATGAAACCTAGCAAAC 57.757 40.909 0.00 0.00 0.00 2.93
2556 5360 7.691050 GTGTTCCAACGTCAATAAAAGCTATAC 59.309 37.037 0.00 0.00 0.00 1.47
2592 5398 4.700213 GCAAGTCTTTAAGCCATCAACCTA 59.300 41.667 0.00 0.00 0.00 3.08
2964 5785 6.456795 AGGTGAAGCTATCCTTTTAATTGC 57.543 37.500 0.00 0.00 32.78 3.56
3372 6197 6.099701 AGTGGCTATGTCCATCAACATAACTA 59.900 38.462 0.00 0.00 40.60 2.24
3373 6198 5.104360 AGTGGCTATGTCCATCAACATAACT 60.104 40.000 0.00 0.00 40.60 2.24
3686 6584 8.841444 CACACATAGTGCAATTAATAGGTTTC 57.159 34.615 0.00 0.00 42.15 2.78
3869 6769 1.268335 CGCACACGCAACTAAAACCTT 60.268 47.619 0.00 0.00 38.40 3.50
3930 6830 2.956333 CCCGTTTCTTTTGTTCCTCCTT 59.044 45.455 0.00 0.00 0.00 3.36
3954 6854 0.603707 CGCACACACCTTCATCTGGT 60.604 55.000 0.00 0.00 38.53 4.00
3988 6890 4.035091 CACAAACAGTTCATCCGAGTGAAA 59.965 41.667 4.37 0.00 39.61 2.69
4084 6986 5.105554 TGTGTTGCCTAATCACAAACAGTTT 60.106 36.000 0.00 0.00 38.80 2.66
4125 7027 2.380084 TATCGCACACACCTTCTTCC 57.620 50.000 0.00 0.00 0.00 3.46
4288 7191 4.475135 GAAGAGCCGCCTGGGGAC 62.475 72.222 12.98 0.00 35.78 4.46
4299 7210 0.391130 TGCCACGGTACATGAAGAGC 60.391 55.000 0.00 0.00 0.00 4.09
4331 7242 5.078949 TGAGATGGAATGAAAGGCAAAGAA 58.921 37.500 0.00 0.00 0.00 2.52
4344 7259 2.625737 CGACAGCAGTTGAGATGGAAT 58.374 47.619 0.00 0.00 0.00 3.01
4345 7260 1.941209 GCGACAGCAGTTGAGATGGAA 60.941 52.381 0.00 0.00 44.35 3.53


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

AutoCloner maintained by Alex Coulton.