Multiple sequence alignment - TraesCS1B01G033400

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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 TraesCS1B01G033400 chr1B 100.000 5099 0 0 1 5099 16227502 16232600 0.000000e+00 9417.0
1 TraesCS1B01G033400 chr1B 92.247 2038 111 19 3065 5099 619259205 619257212 0.000000e+00 2844.0
2 TraesCS1B01G033400 chr1B 97.260 73 2 0 2980 3052 16228962 16229034 1.930000e-24 124.0
3 TraesCS1B01G033400 chr6B 97.369 4371 86 14 253 4618 59412755 59417101 0.000000e+00 7408.0
4 TraesCS1B01G033400 chr6B 98.367 490 4 1 4614 5099 59417259 59417748 0.000000e+00 857.0
5 TraesCS1B01G033400 chr6B 98.630 73 1 0 2980 3052 59413944 59414016 4.140000e-26 130.0
6 TraesCS1B01G033400 chr2B 97.340 2406 55 6 2403 4805 523773858 523771459 0.000000e+00 4080.0
7 TraesCS1B01G033400 chr2B 96.649 2417 73 5 1 2411 523788912 523786498 0.000000e+00 4008.0
8 TraesCS1B01G033400 chr2B 97.721 1141 24 2 3666 4805 523771455 523770316 0.000000e+00 1962.0
9 TraesCS1B01G033400 chr2B 97.721 1141 22 4 3666 4805 523770312 523769175 0.000000e+00 1960.0
10 TraesCS1B01G033400 chr2B 94.107 577 29 2 1763 2339 31073589 31073018 0.000000e+00 872.0
11 TraesCS1B01G033400 chr2B 92.447 331 15 5 353 673 28235522 28235852 1.000000e-126 464.0
12 TraesCS1B01G033400 chr2B 96.685 181 5 1 1 180 28235066 28235246 2.980000e-77 300.0
13 TraesCS1B01G033400 chr2B 96.685 181 5 1 1 180 246074034 246073854 2.980000e-77 300.0
14 TraesCS1B01G033400 chr2B 93.277 119 7 1 715 833 28236483 28236600 1.890000e-39 174.0
15 TraesCS1B01G033400 chr2B 76.613 124 25 3 4937 5056 480923901 480923778 1.190000e-06 65.8
16 TraesCS1B01G033400 chr7A 94.928 2425 73 15 2148 4568 254259796 254257418 0.000000e+00 3751.0
17 TraesCS1B01G033400 chr7A 94.026 1289 72 3 830 2114 254261083 254259796 0.000000e+00 1949.0
18 TraesCS1B01G033400 chr7B 91.161 2059 127 27 3063 5099 725192742 725190717 0.000000e+00 2743.0
19 TraesCS1B01G033400 chr7B 92.097 1202 91 4 1140 2339 623124044 623125243 0.000000e+00 1690.0
20 TraesCS1B01G033400 chr7B 91.996 912 70 3 830 1739 623111373 623112283 0.000000e+00 1277.0
21 TraesCS1B01G033400 chr2D 95.332 1521 60 4 830 2339 79515963 79514443 0.000000e+00 2405.0
22 TraesCS1B01G033400 chr2D 93.277 119 8 0 715 833 461677897 461677779 5.250000e-40 176.0
23 TraesCS1B01G033400 chr2D 98.701 77 0 1 2977 3052 79515334 79515258 8.910000e-28 135.0
24 TraesCS1B01G033400 chr2D 97.778 45 1 0 673 717 461730194 461730150 1.520000e-10 78.7
25 TraesCS1B01G033400 chr4D 91.954 1566 90 18 3065 4614 359683108 359681563 0.000000e+00 2161.0
26 TraesCS1B01G033400 chr4D 92.464 491 32 3 4614 5099 359681483 359680993 0.000000e+00 697.0
27 TraesCS1B01G033400 chr6D 92.580 1523 79 11 830 2339 443352688 443354189 0.000000e+00 2156.0
28 TraesCS1B01G033400 chr6D 91.064 996 58 10 830 1812 443453797 443454774 0.000000e+00 1317.0
29 TraesCS1B01G033400 chr6D 91.472 727 22 7 1 717 382557413 382558109 0.000000e+00 963.0
30 TraesCS1B01G033400 chr6D 95.361 582 16 3 1 581 5882571 5883142 0.000000e+00 915.0
31 TraesCS1B01G033400 chr6D 94.819 579 29 1 1763 2341 39511936 39512513 0.000000e+00 902.0
32 TraesCS1B01G033400 chr6D 95.217 230 10 1 3065 3294 47795835 47796063 3.750000e-96 363.0
33 TraesCS1B01G033400 chr6D 97.479 119 3 0 715 833 382558555 382558673 2.410000e-48 204.0
34 TraesCS1B01G033400 chr6D 98.630 73 1 0 2980 3052 443454419 443454491 4.140000e-26 130.0
35 TraesCS1B01G033400 chr6D 97.260 73 2 0 2980 3052 443353311 443353383 1.930000e-24 124.0
36 TraesCS1B01G033400 chr6A 94.644 1363 61 6 830 2185 612595092 612596449 0.000000e+00 2102.0
37 TraesCS1B01G033400 chr6A 96.923 1235 38 0 3865 5099 612596447 612597681 0.000000e+00 2071.0
38 TraesCS1B01G033400 chr6A 94.932 296 13 2 353 646 580324524 580324819 3.600000e-126 462.0
39 TraesCS1B01G033400 chr6A 96.685 181 5 1 1 180 410566769 410566589 2.980000e-77 300.0
40 TraesCS1B01G033400 chr6A 98.425 127 2 0 917 1043 518393489 518393363 1.850000e-54 224.0
41 TraesCS1B01G033400 chr6A 97.260 73 2 0 2980 3052 612595723 612595795 1.930000e-24 124.0
42 TraesCS1B01G033400 chr6A 97.619 42 1 0 274 315 410566454 410566413 7.080000e-09 73.1
43 TraesCS1B01G033400 chrUn 97.338 1127 28 2 3666 4791 413673022 413674147 0.000000e+00 1914.0
44 TraesCS1B01G033400 chrUn 92.424 330 15 5 353 672 348694189 348693860 3.600000e-126 462.0
45 TraesCS1B01G033400 chrUn 97.619 42 1 0 274 315 348694330 348694289 7.080000e-09 73.1
46 TraesCS1B01G033400 chr5B 92.149 726 20 6 1 717 382949181 382949878 0.000000e+00 990.0
47 TraesCS1B01G033400 chr5B 94.306 562 24 5 3065 3626 100030264 100029711 0.000000e+00 854.0
48 TraesCS1B01G033400 chr5B 93.534 232 15 0 4868 5099 100016061 100015830 3.780000e-91 346.0
49 TraesCS1B01G033400 chr5B 95.868 121 5 0 713 833 382950326 382950446 4.030000e-46 196.0
50 TraesCS1B01G033400 chr5A 93.788 660 33 6 2326 2982 606331522 606332176 0.000000e+00 985.0
51 TraesCS1B01G033400 chr5A 92.447 331 15 5 353 673 478999061 478998731 1.000000e-126 464.0
52 TraesCS1B01G033400 chr5A 93.277 119 7 1 715 833 478998100 478997983 1.890000e-39 174.0
53 TraesCS1B01G033400 chr5A 97.778 45 1 0 673 717 520440502 520440458 1.520000e-10 78.7
54 TraesCS1B01G033400 chr5D 94.136 648 31 5 2337 2982 498269985 498270627 0.000000e+00 979.0
55 TraesCS1B01G033400 chr3D 94.136 648 31 5 2337 2982 365839839 365839197 0.000000e+00 979.0
56 TraesCS1B01G033400 chr3D 93.981 648 32 5 2337 2982 134597130 134596488 0.000000e+00 974.0
57 TraesCS1B01G033400 chr3D 93.981 648 32 5 2337 2982 535657126 535657768 0.000000e+00 974.0
58 TraesCS1B01G033400 chr3D 90.406 542 31 6 3065 3596 75117499 75116969 0.000000e+00 693.0
59 TraesCS1B01G033400 chr3D 89.372 414 30 7 4691 5099 75116965 75116561 4.550000e-140 508.0
60 TraesCS1B01G033400 chr3D 94.850 233 10 2 3065 3296 535657760 535657991 3.750000e-96 363.0
61 TraesCS1B01G033400 chr2A 94.109 645 32 4 2340 2982 659057470 659056830 0.000000e+00 976.0
62 TraesCS1B01G033400 chr7D 94.502 582 15 3 1 581 235470356 235469791 0.000000e+00 881.0
63 TraesCS1B01G033400 chr7D 96.639 119 4 0 715 833 235464529 235464411 1.120000e-46 198.0
64 TraesCS1B01G033400 chr7D 91.729 133 3 1 593 717 235465110 235464978 1.460000e-40 178.0
65 TraesCS1B01G033400 chr1D 90.925 584 18 5 1 581 192429059 192428508 0.000000e+00 752.0
66 TraesCS1B01G033400 chr1D 96.639 119 4 0 715 833 192423244 192423126 1.120000e-46 198.0
67 TraesCS1B01G033400 chr1D 91.729 133 3 1 593 717 192423825 192423693 1.460000e-40 178.0
68 TraesCS1B01G033400 chr4A 92.447 331 15 5 353 673 740825268 740824938 1.000000e-126 464.0
69 TraesCS1B01G033400 chr4A 84.536 194 19 8 3321 3514 715599531 715599713 1.130000e-41 182.0


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 TraesCS1B01G033400 chr1B 16227502 16232600 5098 False 4770.500000 9417 98.630000 1 5099 2 chr1B.!!$F1 5098
1 TraesCS1B01G033400 chr1B 619257212 619259205 1993 True 2844.000000 2844 92.247000 3065 5099 1 chr1B.!!$R1 2034
2 TraesCS1B01G033400 chr6B 59412755 59417748 4993 False 2798.333333 7408 98.122000 253 5099 3 chr6B.!!$F1 4846
3 TraesCS1B01G033400 chr2B 523786498 523788912 2414 True 4008.000000 4008 96.649000 1 2411 1 chr2B.!!$R4 2410
4 TraesCS1B01G033400 chr2B 523769175 523773858 4683 True 2667.333333 4080 97.594000 2403 4805 3 chr2B.!!$R5 2402
5 TraesCS1B01G033400 chr2B 31073018 31073589 571 True 872.000000 872 94.107000 1763 2339 1 chr2B.!!$R1 576
6 TraesCS1B01G033400 chr2B 28235066 28236600 1534 False 312.666667 464 94.136333 1 833 3 chr2B.!!$F1 832
7 TraesCS1B01G033400 chr7A 254257418 254261083 3665 True 2850.000000 3751 94.477000 830 4568 2 chr7A.!!$R1 3738
8 TraesCS1B01G033400 chr7B 725190717 725192742 2025 True 2743.000000 2743 91.161000 3063 5099 1 chr7B.!!$R1 2036
9 TraesCS1B01G033400 chr7B 623124044 623125243 1199 False 1690.000000 1690 92.097000 1140 2339 1 chr7B.!!$F2 1199
10 TraesCS1B01G033400 chr7B 623111373 623112283 910 False 1277.000000 1277 91.996000 830 1739 1 chr7B.!!$F1 909
11 TraesCS1B01G033400 chr2D 79514443 79515963 1520 True 1270.000000 2405 97.016500 830 3052 2 chr2D.!!$R3 2222
12 TraesCS1B01G033400 chr4D 359680993 359683108 2115 True 1429.000000 2161 92.209000 3065 5099 2 chr4D.!!$R1 2034
13 TraesCS1B01G033400 chr6D 443352688 443354189 1501 False 1140.000000 2156 94.920000 830 3052 2 chr6D.!!$F5 2222
14 TraesCS1B01G033400 chr6D 5882571 5883142 571 False 915.000000 915 95.361000 1 581 1 chr6D.!!$F1 580
15 TraesCS1B01G033400 chr6D 39511936 39512513 577 False 902.000000 902 94.819000 1763 2341 1 chr6D.!!$F2 578
16 TraesCS1B01G033400 chr6D 443453797 443454774 977 False 723.500000 1317 94.847000 830 3052 2 chr6D.!!$F6 2222
17 TraesCS1B01G033400 chr6D 382557413 382558673 1260 False 583.500000 963 94.475500 1 833 2 chr6D.!!$F4 832
18 TraesCS1B01G033400 chr6A 612595092 612597681 2589 False 1432.333333 2102 96.275667 830 5099 3 chr6A.!!$F2 4269
19 TraesCS1B01G033400 chrUn 413673022 413674147 1125 False 1914.000000 1914 97.338000 3666 4791 1 chrUn.!!$F1 1125
20 TraesCS1B01G033400 chr5B 100029711 100030264 553 True 854.000000 854 94.306000 3065 3626 1 chr5B.!!$R2 561
21 TraesCS1B01G033400 chr5B 382949181 382950446 1265 False 593.000000 990 94.008500 1 833 2 chr5B.!!$F1 832
22 TraesCS1B01G033400 chr5A 606331522 606332176 654 False 985.000000 985 93.788000 2326 2982 1 chr5A.!!$F1 656
23 TraesCS1B01G033400 chr5A 478997983 478999061 1078 True 319.000000 464 92.862000 353 833 2 chr5A.!!$R2 480
24 TraesCS1B01G033400 chr5D 498269985 498270627 642 False 979.000000 979 94.136000 2337 2982 1 chr5D.!!$F1 645
25 TraesCS1B01G033400 chr3D 365839197 365839839 642 True 979.000000 979 94.136000 2337 2982 1 chr3D.!!$R2 645
26 TraesCS1B01G033400 chr3D 134596488 134597130 642 True 974.000000 974 93.981000 2337 2982 1 chr3D.!!$R1 645
27 TraesCS1B01G033400 chr3D 535657126 535657991 865 False 668.500000 974 94.415500 2337 3296 2 chr3D.!!$F1 959
28 TraesCS1B01G033400 chr3D 75116561 75117499 938 True 600.500000 693 89.889000 3065 5099 2 chr3D.!!$R3 2034
29 TraesCS1B01G033400 chr2A 659056830 659057470 640 True 976.000000 976 94.109000 2340 2982 1 chr2A.!!$R1 642
30 TraesCS1B01G033400 chr7D 235469791 235470356 565 True 881.000000 881 94.502000 1 581 1 chr7D.!!$R1 580
31 TraesCS1B01G033400 chr1D 192428508 192429059 551 True 752.000000 752 90.925000 1 581 1 chr1D.!!$R1 580

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
631 845 1.860641 TGCTAAGGATGGAGGAACGA 58.139 50.0 0.00 0.0 0.00 3.85 F
2096 3430 0.250513 GGACGGAGCAACCTTCTGAT 59.749 55.0 6.45 0.0 37.15 2.90 F
2663 3998 0.868406 GCCCACAACTCTTGAGTTCG 59.132 55.0 12.51 10.8 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 3939 0.179040 TCGTCACCCCCAAAGTCAAC 60.179 55.000 0.0 0.0 0.0 3.18 R
3602 4960 2.690840 TCTCCATAGCTTTCTACCCCC 58.309 52.381 0.0 0.0 0.0 5.40 R
4547 7060 1.199789 CCGCAGCTAATGAAAGCACAA 59.800 47.619 0.0 0.0 45.3 3.33 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
241 245 6.103997 GTCGTTTAAGAGAGAGAGAGAGAGA 58.896 44.000 0.00 0.00 0.00 3.10
243 247 6.153851 TCGTTTAAGAGAGAGAGAGAGAGAGA 59.846 42.308 0.00 0.00 0.00 3.10
245 249 7.556844 GTTTAAGAGAGAGAGAGAGAGAGAGA 58.443 42.308 0.00 0.00 0.00 3.10
473 685 6.293955 GCTTCTTGTGCACCTTGATTTAGTTA 60.294 38.462 15.69 0.00 0.00 2.24
482 694 8.081633 TGCACCTTGATTTAGTTATGTTCTTTG 58.918 33.333 0.00 0.00 0.00 2.77
631 845 1.860641 TGCTAAGGATGGAGGAACGA 58.139 50.000 0.00 0.00 0.00 3.85
745 2052 2.723719 GCGTCGCTGTCCGGTTTAC 61.724 63.158 10.68 0.00 37.59 2.01
1326 2645 1.374125 CTGATGGTGGTCGCGAACA 60.374 57.895 25.58 25.58 0.00 3.18
1337 2656 2.506217 GCGAACATCGGCGACTCA 60.506 61.111 13.76 0.00 40.84 3.41
1512 2831 3.653835 TCTGAATCGGAGAGGAGAAGA 57.346 47.619 0.00 0.00 43.63 2.87
1907 3235 6.537301 TCAGTTTGAACTTGTAAGGTGTACTG 59.463 38.462 0.00 0.00 37.08 2.74
2096 3430 0.250513 GGACGGAGCAACCTTCTGAT 59.749 55.000 6.45 0.00 37.15 2.90
2372 3707 6.807720 GTCATGTGATTTATGAATGTGCAACA 59.192 34.615 0.00 0.00 39.47 3.33
2663 3998 0.868406 GCCCACAACTCTTGAGTTCG 59.132 55.000 12.51 10.80 0.00 3.95
2738 4073 4.811908 TCTTGCATGTGATCAATGGTTTG 58.188 39.130 15.25 3.10 0.00 2.93
3250 4590 4.034048 TCTGAAAGTTTTTCTCTGTGTCGC 59.966 41.667 3.53 0.00 33.76 5.19
3310 4650 5.412594 TGTATCTCTGAATTGTTGTTGGCTC 59.587 40.000 0.00 0.00 0.00 4.70
3319 4659 2.198969 TTGTTGGCTCCATGCGCAA 61.199 52.632 17.11 0.00 44.05 4.85
3596 4954 9.068008 TGAAAACGTCTTCTGAATGTTAAAAAC 57.932 29.630 2.87 0.00 0.00 2.43
3602 4960 7.114811 CGTCTTCTGAATGTTAAAAACCCAATG 59.885 37.037 0.00 0.00 0.00 2.82
3887 6394 4.886579 AGACCATTTTCTGATGTTTTGGC 58.113 39.130 0.00 0.00 0.00 4.52
3932 6439 3.141398 GTGTGTGACCAACTGATCATGT 58.859 45.455 0.00 0.00 0.00 3.21
3936 6443 4.389992 GTGTGACCAACTGATCATGTAGTG 59.610 45.833 0.00 0.00 0.00 2.74
4485 6997 9.371136 AGAGTAAAAGAAAGAAAAAGCAAAAGG 57.629 29.630 0.00 0.00 0.00 3.11
4689 8531 4.905429 TCTGCCAAGTAAATAGAAGTGCA 58.095 39.130 0.00 0.00 0.00 4.57
4717 8559 4.652421 TCCTGACGGGCATTAGTATACTTT 59.348 41.667 11.40 0.00 34.39 2.66
4865 8714 0.036306 CCGGTTGAGGTTTAGTGGCT 59.964 55.000 0.00 0.00 0.00 4.75
5074 8925 6.995091 GGGAGTAGTTGCTTGAGATTATTCAT 59.005 38.462 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 213 6.745116 TCTCTCTCTTAAACGACATGTTGAA 58.255 36.000 20.26 2.95 40.84 2.69
225 229 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
241 245 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
243 247 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
245 249 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
473 685 3.902881 TTGGCACCAAACAAAGAACAT 57.097 38.095 0.00 0.00 32.44 2.71
482 694 3.057526 GTCCTAAGACATTGGCACCAAAC 60.058 47.826 6.14 1.81 42.99 2.93
631 845 3.067106 CTGCATACTGGAACTTGACGTT 58.933 45.455 0.00 0.00 38.91 3.99
745 2052 0.179189 GGCGATCCGAACAGCAAAAG 60.179 55.000 0.00 0.00 0.00 2.27
2086 3420 3.698289 TCTACGGAGTGATCAGAAGGTT 58.302 45.455 0.00 0.00 45.73 3.50
2096 3430 6.447162 CATGCAACTATAATCTACGGAGTGA 58.553 40.000 0.00 0.00 45.73 3.41
2372 3707 7.119553 GCATGGTCAAACAATTTAAATCCACAT 59.880 33.333 0.10 0.00 0.00 3.21
2373 3708 6.426328 GCATGGTCAAACAATTTAAATCCACA 59.574 34.615 0.10 0.00 0.00 4.17
2604 3939 0.179040 TCGTCACCCCCAAAGTCAAC 60.179 55.000 0.00 0.00 0.00 3.18
3250 4590 3.679824 AAGAACCAGAAAGTAGGACGG 57.320 47.619 0.00 0.00 0.00 4.79
3602 4960 2.690840 TCTCCATAGCTTTCTACCCCC 58.309 52.381 0.00 0.00 0.00 5.40
3789 6292 7.939782 TCTGCAACAAACTCTGAAATTGATTA 58.060 30.769 8.55 0.00 0.00 1.75
3887 6394 5.464722 CCTCAAGAATCAATACATCAGGTCG 59.535 44.000 0.00 0.00 0.00 4.79
4485 6997 4.775236 AGCACACATTTCTTATCCTCTCC 58.225 43.478 0.00 0.00 0.00 3.71
4547 7060 1.199789 CCGCAGCTAATGAAAGCACAA 59.800 47.619 0.00 0.00 45.30 3.33
4689 8531 2.039879 ACTAATGCCCGTCAGGAAAAGT 59.960 45.455 0.00 0.00 41.02 2.66
5074 8925 7.849804 GACATTCTAAGAATGCCACTTTCTA 57.150 36.000 0.00 0.00 33.17 2.10


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

AutoCloner maintained by Alex Coulton.