Multiple sequence alignment - TraesCS3B01G195300

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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 TraesCS3B01G195300 chr3B 100.000 3155 0 0 1 3155 221911452 221914606 0.000000e+00 5827.0
1 TraesCS3B01G195300 chr3B 97.852 2793 33 7 378 3155 221979309 221982089 0.000000e+00 4800.0
2 TraesCS3B01G195300 chr3B 93.473 1961 75 23 378 2309 215571457 215573393 0.000000e+00 2863.0
3 TraesCS3B01G195300 chr3B 96.956 1708 41 5 792 2493 215384958 215386660 0.000000e+00 2856.0
4 TraesCS3B01G195300 chr3B 95.023 1306 52 8 826 2128 215310364 215311659 0.000000e+00 2039.0
5 TraesCS3B01G195300 chr3B 91.500 1200 78 10 737 1918 215104490 215105683 0.000000e+00 1629.0
6 TraesCS3B01G195300 chr3B 92.602 1122 47 11 843 1964 221457693 221458778 0.000000e+00 1580.0
7 TraesCS3B01G195300 chr3B 93.632 691 42 2 2465 3155 215386663 215387351 0.000000e+00 1031.0
8 TraesCS3B01G195300 chr3B 91.602 643 42 4 2506 3148 221467241 221467871 0.000000e+00 878.0
9 TraesCS3B01G195300 chr3B 98.316 475 8 0 1954 2428 221466768 221467242 0.000000e+00 833.0
10 TraesCS3B01G195300 chr3B 94.456 469 16 7 378 838 215308890 215309356 0.000000e+00 713.0
11 TraesCS3B01G195300 chr3B 94.118 459 18 5 378 829 221457067 221457523 0.000000e+00 689.0
12 TraesCS3B01G195300 chr3B 95.561 428 13 3 378 801 221748641 221749066 0.000000e+00 680.0
13 TraesCS3B01G195300 chr3B 95.262 401 13 5 378 774 215384366 215384764 5.740000e-177 630.0
14 TraesCS3B01G195300 chr3B 92.670 382 23 5 1 377 221747336 221747717 2.140000e-151 545.0
15 TraesCS3B01G195300 chr3B 92.651 381 22 6 1 377 221978419 221978797 7.700000e-151 544.0
16 TraesCS3B01G195300 chr3B 92.368 380 25 4 1 377 221456173 221456551 3.580000e-149 538.0
17 TraesCS3B01G195300 chr3B 92.126 381 25 5 1 377 215383473 215383852 1.670000e-147 532.0
18 TraesCS3B01G195300 chr3B 91.864 381 27 3 1 377 215307999 215308379 2.160000e-146 529.0
19 TraesCS3B01G195300 chr3B 93.839 211 11 2 2946 3155 221753057 221753266 1.830000e-82 316.0
20 TraesCS3B01G195300 chr3B 90.000 210 16 1 2946 3155 215115615 215115819 1.870000e-67 267.0
21 TraesCS3B01G195300 chr3B 95.918 147 6 0 2125 2271 215314370 215314516 4.070000e-59 239.0
22 TraesCS3B01G195300 chr3B 92.262 168 10 2 1995 2160 221750207 221750373 5.260000e-58 235.0
23 TraesCS3B01G195300 chr3B 90.854 164 11 3 1999 2160 215114890 215115051 1.910000e-52 217.0
24 TraesCS3B01G195300 chr3B 84.426 122 11 4 2307 2421 203346827 203346947 2.570000e-21 113.0
25 TraesCS3B01G195300 chr3B 84.426 122 11 4 2307 2421 203553951 203554071 2.570000e-21 113.0
26 TraesCS3B01G195300 chr3B 95.312 64 2 1 2839 2902 203554326 203554388 2.000000e-17 100.0
27 TraesCS3B01G195300 chr3A 90.521 1287 72 24 907 2160 166923328 166924597 0.000000e+00 1655.0
28 TraesCS3B01G195300 chr3A 91.559 1007 67 9 1002 1999 159831982 159832979 0.000000e+00 1373.0
29 TraesCS3B01G195300 chr3A 88.142 565 39 14 2592 3155 166924834 166925371 0.000000e+00 647.0
30 TraesCS3B01G195300 chr3A 79.331 508 61 21 435 909 166922769 166923265 1.830000e-82 316.0
31 TraesCS3B01G195300 chr3A 87.597 129 15 1 2051 2179 177889141 177889268 7.050000e-32 148.0
32 TraesCS3B01G195300 chr3A 89.744 117 9 3 2307 2421 159833074 159833189 2.540000e-31 147.0
33 TraesCS3B01G195300 chr3A 95.588 68 3 0 3088 3155 181107338 181107405 3.330000e-20 110.0
34 TraesCS3B01G195300 chr3A 91.892 74 6 0 2839 2912 159433624 159433697 1.550000e-18 104.0
35 TraesCS3B01G195300 chr3A 98.039 51 1 0 1995 2045 159833004 159833054 4.330000e-14 89.8
36 TraesCS3B01G195300 chr3A 93.478 46 2 1 2745 2790 159433569 159433613 2.030000e-07 67.6
37 TraesCS3B01G195300 chr3D 92.528 1084 63 9 907 1975 149204949 149206029 0.000000e+00 1537.0
38 TraesCS3B01G195300 chr3D 92.364 1087 63 9 907 1975 149544110 149545194 0.000000e+00 1530.0
39 TraesCS3B01G195300 chr3D 93.744 1023 51 4 907 1916 147336153 147335131 0.000000e+00 1522.0
40 TraesCS3B01G195300 chr3D 88.685 1034 70 16 1003 1999 149769974 149768951 0.000000e+00 1218.0
41 TraesCS3B01G195300 chr3D 86.607 560 36 19 2592 3150 149545624 149546145 1.630000e-162 582.0
42 TraesCS3B01G195300 chr3D 82.821 390 49 15 1 373 149542770 149543158 1.810000e-87 333.0
43 TraesCS3B01G195300 chr3D 86.306 314 30 9 1999 2303 149206090 149206399 2.350000e-86 329.0
44 TraesCS3B01G195300 chr3D 82.609 391 48 17 1 373 149203616 149204004 8.440000e-86 327.0
45 TraesCS3B01G195300 chr3D 85.670 321 32 11 1999 2309 147334720 147334404 3.030000e-85 326.0
46 TraesCS3B01G195300 chr3D 90.795 239 14 4 378 610 149543664 149543900 2.360000e-81 313.0
47 TraesCS3B01G195300 chr3D 89.958 239 16 4 378 610 149204507 149204743 5.110000e-78 302.0
48 TraesCS3B01G195300 chr3D 92.073 164 11 1 1999 2160 149545261 149545424 2.450000e-56 230.0
49 TraesCS3B01G195300 chr3D 88.485 165 8 7 453 610 147336523 147336363 4.150000e-44 189.0
50 TraesCS3B01G195300 chr3D 98.913 92 1 0 726 817 149204737 149204828 7.000000e-37 165.0
51 TraesCS3B01G195300 chr3D 97.849 93 2 0 726 818 149543894 149543986 9.060000e-36 161.0
52 TraesCS3B01G195300 chr3D 86.164 159 4 7 726 880 147336369 147336225 4.210000e-34 156.0
53 TraesCS3B01G195300 chr3D 92.473 93 7 0 378 470 147336638 147336546 1.970000e-27 134.0
54 TraesCS3B01G195300 chr3D 94.737 76 4 0 2839 2914 141412094 141412169 5.530000e-23 119.0
55 TraesCS3B01G195300 chr3D 95.455 66 3 0 3088 3153 149207004 149207069 4.300000e-19 106.0
56 TraesCS3B01G195300 chr3D 94.118 68 4 0 3088 3155 149222680 149222747 1.550000e-18 104.0
57 TraesCS3B01G195300 chr3D 88.889 81 9 0 2342 2422 147334643 147334563 2.000000e-17 100.0
58 TraesCS3B01G195300 chr3D 88.889 81 9 0 2342 2422 149206167 149206247 2.000000e-17 100.0
59 TraesCS3B01G195300 chr3D 98.039 51 1 0 1995 2045 141411677 141411727 4.330000e-14 89.8
60 TraesCS3B01G195300 chr6A 87.805 123 12 3 2310 2430 146440536 146440415 1.180000e-29 141.0
61 TraesCS3B01G195300 chr6A 96.721 61 2 0 2839 2899 146438854 146438794 5.570000e-18 102.0
62 TraesCS3B01G195300 chr1B 77.586 174 27 10 572 738 416831648 416831480 9.320000e-16 95.3
63 TraesCS3B01G195300 chr1B 89.130 46 2 2 2463 2508 508087129 508087171 2.000000e-03 54.7
64 TraesCS3B01G195300 chrUn 85.227 88 5 3 2426 2507 39265908 39265823 2.020000e-12 84.2
65 TraesCS3B01G195300 chr2A 85.227 88 4 4 2423 2504 755365805 755365889 7.250000e-12 82.4
66 TraesCS3B01G195300 chr2A 85.915 71 6 2 2444 2512 56880708 56880776 4.370000e-09 73.1
67 TraesCS3B01G195300 chr2A 87.500 64 6 1 2449 2512 56886429 56886368 4.370000e-09 73.1
68 TraesCS3B01G195300 chr1D 87.931 58 4 3 29 84 204005018 204004962 7.300000e-07 65.8
69 TraesCS3B01G195300 chr2B 82.500 80 6 4 2421 2493 508247473 508247395 2.630000e-06 63.9


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 TraesCS3B01G195300 chr3B 221911452 221914606 3154 False 5827.000000 5827 100.000000 1 3155 1 chr3B.!!$F4 3154
1 TraesCS3B01G195300 chr3B 215571457 215573393 1936 False 2863.000000 2863 93.473000 378 2309 1 chr3B.!!$F3 1931
2 TraesCS3B01G195300 chr3B 221978419 221982089 3670 False 2672.000000 4800 95.251500 1 3155 2 chr3B.!!$F12 3154
3 TraesCS3B01G195300 chr3B 215104490 215105683 1193 False 1629.000000 1629 91.500000 737 1918 1 chr3B.!!$F2 1181
4 TraesCS3B01G195300 chr3B 215383473 215387351 3878 False 1262.250000 2856 94.494000 1 3155 4 chr3B.!!$F8 3154
5 TraesCS3B01G195300 chr3B 221456173 221458778 2605 False 935.666667 1580 93.029333 1 1964 3 chr3B.!!$F9 1963
6 TraesCS3B01G195300 chr3B 215307999 215314516 6517 False 880.000000 2039 94.315250 1 2271 4 chr3B.!!$F7 2270
7 TraesCS3B01G195300 chr3B 221466768 221467871 1103 False 855.500000 878 94.959000 1954 3148 2 chr3B.!!$F10 1194
8 TraesCS3B01G195300 chr3B 221747336 221753266 5930 False 444.000000 680 93.583000 1 3155 4 chr3B.!!$F11 3154
9 TraesCS3B01G195300 chr3B 215114890 215115819 929 False 242.000000 267 90.427000 1999 3155 2 chr3B.!!$F6 1156
10 TraesCS3B01G195300 chr3A 166922769 166925371 2602 False 872.666667 1655 85.998000 435 3155 3 chr3A.!!$F5 2720
11 TraesCS3B01G195300 chr3A 159831982 159833189 1207 False 536.600000 1373 93.114000 1002 2421 3 chr3A.!!$F4 1419
12 TraesCS3B01G195300 chr3D 149768951 149769974 1023 True 1218.000000 1218 88.685000 1003 1999 1 chr3D.!!$R1 996
13 TraesCS3B01G195300 chr3D 149542770 149546145 3375 False 524.833333 1530 90.418167 1 3150 6 chr3D.!!$F4 3149
14 TraesCS3B01G195300 chr3D 149203616 149207069 3453 False 409.428571 1537 90.665429 1 3153 7 chr3D.!!$F3 3152
15 TraesCS3B01G195300 chr3D 147334404 147336638 2234 True 404.500000 1522 89.237500 378 2422 6 chr3D.!!$R2 2044

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
905 3394 4.03769 CGAAAAGCATCGGATTGGATTTC 58.962 43.478 0.0 0.0 39.12 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2777 8844 1.967319 ACATTGTCTTGTTCGGTGCT 58.033 45.0 0.0 0.0 0.0 4.4 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
127 130 4.412207 GGTTAGCCGATTCAACAAATGTC 58.588 43.478 0.00 0.0 0.00 3.06
373 395 7.936584 TCAAAAACATAATCTCGGTTTGAAGT 58.063 30.769 0.00 0.0 35.14 3.01
905 3394 4.037690 CGAAAAGCATCGGATTGGATTTC 58.962 43.478 0.00 0.0 39.12 2.17
2068 5022 8.645814 TCTGTCTAGTCTAGGTGTAAATTTGA 57.354 34.615 7.05 0.0 0.00 2.69
2438 8142 6.441604 TCCTTTTAAATACTACTCCCTCCGTT 59.558 38.462 0.00 0.0 0.00 4.44
2460 8178 6.632834 CGTTCCATTAAGACTTTTTGACACTG 59.367 38.462 0.00 0.0 0.00 3.66
2504 8253 7.424172 TCTTATATTATATGGGACGGAGGGAA 58.576 38.462 0.00 0.0 0.00 3.97
2625 8688 4.209538 TGATGAAGGCTACAATCCCAATG 58.790 43.478 0.00 0.0 0.00 2.82
2638 8701 1.133513 TCCCAATGGACAGTGCAAACT 60.134 47.619 0.00 0.0 35.03 2.66
2777 8844 1.071542 TCTCCAAGGCACATTCGTCAA 59.928 47.619 0.00 0.0 0.00 3.18
2927 11059 1.850377 TTTGCTCCAACACAAATGCG 58.150 45.000 0.00 0.0 31.09 4.73
2949 11223 2.480845 ACGGTTGTCAAGCTCTTACAC 58.519 47.619 12.65 0.0 0.00 2.90
2978 11252 5.982516 GCCATACATTTTCAGTCACAAAACA 59.017 36.000 0.00 0.0 0.00 2.83
2979 11253 6.144402 GCCATACATTTTCAGTCACAAAACAG 59.856 38.462 0.00 0.0 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.604626 TTTGAAATTTGTGAACATTGTTGAAAC 57.395 25.926 6.80 3.53 0.00 2.78
127 130 7.897575 TCGGGAACAATTTTTAAATTCATGG 57.102 32.000 0.00 0.00 36.52 3.66
362 384 7.876068 ACAAGAATAGTGATTACTTCAAACCGA 59.124 33.333 0.00 0.00 38.36 4.69
373 395 6.071616 GGCCCAAAACACAAGAATAGTGATTA 60.072 38.462 0.00 0.00 40.16 1.75
905 3394 2.928116 GTGAGTCGTCCCCTTTAAATCG 59.072 50.000 0.00 0.00 0.00 3.34
2068 5022 6.573664 TTGGTCAAGTTCGATTTCAATGAT 57.426 33.333 0.00 0.00 0.00 2.45
2438 8142 6.039270 CACCAGTGTCAAAAAGTCTTAATGGA 59.961 38.462 4.67 0.00 0.00 3.41
2460 8178 5.438761 AAGATGCTTTTTGACACTACACC 57.561 39.130 0.00 0.00 0.00 4.16
2625 8688 2.287608 GGCTTACAAGTTTGCACTGTCC 60.288 50.000 0.00 0.00 31.60 4.02
2638 8701 2.176045 TCATCTGAGGACGGCTTACAA 58.824 47.619 0.00 0.00 0.00 2.41
2777 8844 1.967319 ACATTGTCTTGTTCGGTGCT 58.033 45.000 0.00 0.00 0.00 4.40
2927 11059 3.059800 GTGTAAGAGCTTGACAACCGTTC 60.060 47.826 0.00 0.00 0.00 3.95
2949 11223 4.616802 GTGACTGAAAATGTATGGCGTTTG 59.383 41.667 0.00 0.00 36.51 2.93


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

AutoCloner maintained by Alex Coulton.