Multiple sequence alignment - TraesCS3D01G395500

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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 TraesCS3D01G395500 chr3D 100.000 1941 0 0 1 1941 511257187 511255247 0.000000e+00 3585.0
1 TraesCS3D01G395500 chr3D 91.885 382 22 6 1561 1941 188365131 188364758 2.080000e-145 525.0
2 TraesCS3D01G395500 chr3D 100.000 124 0 0 2234 2357 511254954 511254831 1.820000e-56 230.0
3 TraesCS3D01G395500 chr3D 83.824 204 14 13 1104 1307 580427872 580427688 2.410000e-40 176.0
4 TraesCS3D01G395500 chr3D 98.000 50 1 0 616 665 89281278 89281327 1.160000e-13 87.9
5 TraesCS3D01G395500 chr3D 100.000 34 0 0 320 353 347609189 347609222 1.960000e-06 63.9
6 TraesCS3D01G395500 chr4A 97.623 673 12 3 1 671 552250210 552249540 0.000000e+00 1151.0
7 TraesCS3D01G395500 chr4A 89.597 769 27 9 796 1557 552248729 552248007 0.000000e+00 928.0
8 TraesCS3D01G395500 chr4A 87.562 402 24 8 1174 1557 556468196 556467803 2.150000e-120 442.0
9 TraesCS3D01G395500 chr4A 97.740 177 1 3 682 857 552248892 552248718 3.810000e-78 302.0
10 TraesCS3D01G395500 chr4A 82.713 376 17 12 704 1066 556468551 556468211 8.240000e-75 291.0
11 TraesCS3D01G395500 chr4A 92.562 121 5 1 2241 2357 92722776 92722656 1.120000e-38 171.0
12 TraesCS3D01G395500 chr4A 100.000 33 0 0 658 690 552249531 552249499 7.030000e-06 62.1
13 TraesCS3D01G395500 chr5B 96.928 586 14 3 88 671 103635467 103636050 0.000000e+00 979.0
14 TraesCS3D01G395500 chr5B 80.378 423 38 24 914 1318 626044278 626043883 1.780000e-71 279.0
15 TraesCS3D01G395500 chr5B 100.000 83 0 0 595 677 93673720 93673802 1.130000e-33 154.0
16 TraesCS3D01G395500 chr5B 90.179 112 7 2 704 815 626044817 626044710 2.440000e-30 143.0
17 TraesCS3D01G395500 chr5B 89.189 111 8 2 1198 1305 117892637 117892528 4.090000e-28 135.0
18 TraesCS3D01G395500 chr5B 100.000 37 0 0 654 690 103636055 103636091 4.200000e-08 69.4
19 TraesCS3D01G395500 chr1A 96.386 581 18 2 21 599 210660039 210659460 0.000000e+00 953.0
20 TraesCS3D01G395500 chr1A 97.064 545 12 3 58 600 178262328 178262870 0.000000e+00 915.0
21 TraesCS3D01G395500 chr1A 96.875 544 14 2 58 599 210843844 210843302 0.000000e+00 907.0
22 TraesCS3D01G395500 chr1A 96.691 544 14 3 58 599 210880243 210879702 0.000000e+00 902.0
23 TraesCS3D01G395500 chr1A 96.685 543 15 2 58 598 27783134 27783675 0.000000e+00 900.0
24 TraesCS3D01G395500 chr1A 95.963 545 18 3 58 600 416213895 416214437 0.000000e+00 881.0
25 TraesCS3D01G395500 chr1A 98.148 54 1 0 21 74 27783070 27783123 6.930000e-16 95.3
26 TraesCS3D01G395500 chr1A 98.148 54 1 0 21 74 210843909 210843856 6.930000e-16 95.3
27 TraesCS3D01G395500 chr1A 98.039 51 1 0 21 71 178262263 178262313 3.230000e-14 89.8
28 TraesCS3D01G395500 chr1A 96.226 53 2 0 534 586 540657764 540657816 1.160000e-13 87.9
29 TraesCS3D01G395500 chr1A 97.778 45 1 0 313 357 540661365 540661409 6.980000e-11 78.7
30 TraesCS3D01G395500 chr5A 97.292 554 11 3 58 608 575303488 575302936 0.000000e+00 937.0
31 TraesCS3D01G395500 chr5A 97.248 545 12 2 58 600 524280846 524281389 0.000000e+00 920.0
32 TraesCS3D01G395500 chr5A 91.667 384 25 5 1560 1941 677171890 677172268 2.080000e-145 525.0
33 TraesCS3D01G395500 chr5A 90.625 128 8 1 2234 2357 646848650 646848777 1.450000e-37 167.0
34 TraesCS3D01G395500 chr5A 96.296 54 2 0 21 74 493305788 493305735 3.230000e-14 89.8
35 TraesCS3D01G395500 chr5A 96.296 54 2 0 21 74 524280781 524280834 3.230000e-14 89.8
36 TraesCS3D01G395500 chr5A 96.296 54 2 0 21 74 575303553 575303500 3.230000e-14 89.8
37 TraesCS3D01G395500 chr1B 95.563 586 22 3 88 671 79197864 79198447 0.000000e+00 935.0
38 TraesCS3D01G395500 chr1B 94.578 166 8 1 682 846 79199097 79199262 3.010000e-64 255.0
39 TraesCS3D01G395500 chr1B 86.957 92 1 2 837 924 520093695 520093611 2.490000e-15 93.5
40 TraesCS3D01G395500 chr1B 88.732 71 4 3 379 445 431253960 431254030 1.500000e-12 84.2
41 TraesCS3D01G395500 chr1B 100.000 33 0 0 658 690 79198456 79198488 7.030000e-06 62.1
42 TraesCS3D01G395500 chr3A 97.615 545 10 2 58 600 78937120 78937663 0.000000e+00 931.0
43 TraesCS3D01G395500 chr3A 92.000 125 6 1 2236 2356 24438830 24438954 3.110000e-39 172.0
44 TraesCS3D01G395500 chr3A 96.296 54 2 0 21 74 325585237 325585184 3.230000e-14 89.8
45 TraesCS3D01G395500 chr2A 97.431 545 11 2 58 600 665850410 665850953 0.000000e+00 926.0
46 TraesCS3D01G395500 chr2A 86.492 533 38 14 1046 1555 373454009 373453488 2.650000e-154 555.0
47 TraesCS3D01G395500 chr2A 91.948 385 24 6 1560 1941 5130897 5130517 1.240000e-147 532.0
48 TraesCS3D01G395500 chr2A 90.625 128 8 1 2234 2357 384674414 384674287 1.450000e-37 167.0
49 TraesCS3D01G395500 chr2A 98.148 54 1 0 21 74 665850345 665850398 6.930000e-16 95.3
50 TraesCS3D01G395500 chr7A 97.064 545 13 2 58 600 284051793 284051250 0.000000e+00 915.0
51 TraesCS3D01G395500 chr7A 96.881 545 14 2 58 600 539964097 539963554 0.000000e+00 909.0
52 TraesCS3D01G395500 chr7A 97.826 46 1 0 21 66 539964158 539964113 1.940000e-11 80.5
53 TraesCS3D01G395500 chr6A 96.514 545 16 2 58 600 599381459 599382002 0.000000e+00 898.0
54 TraesCS3D01G395500 chr6A 91.948 385 17 8 1560 1941 535373334 535373707 5.770000e-146 527.0
55 TraesCS3D01G395500 chr6A 97.101 138 3 1 463 600 167143931 167143795 5.070000e-57 231.0
56 TraesCS3D01G395500 chr6D 91.486 646 38 9 914 1557 414471712 414472342 0.000000e+00 872.0
57 TraesCS3D01G395500 chr6D 93.211 383 15 7 1560 1941 423799542 423799914 9.520000e-154 553.0
58 TraesCS3D01G395500 chr6D 86.051 552 33 11 1040 1557 448377635 448377094 9.520000e-154 553.0
59 TraesCS3D01G395500 chr6D 91.927 384 23 6 1560 1941 464065379 464065756 4.460000e-147 531.0
60 TraesCS3D01G395500 chr6D 91.358 81 7 0 121 201 323972468 323972388 6.890000e-21 111.0
61 TraesCS3D01G395500 chr7D 88.104 538 31 10 1040 1554 481607907 481608434 2.000000e-170 608.0
62 TraesCS3D01G395500 chr7D 88.806 402 19 5 1175 1557 227555188 227555582 9.860000e-129 470.0
63 TraesCS3D01G395500 chr7D 84.816 461 25 21 706 1153 261518627 261519055 2.800000e-114 422.0
64 TraesCS3D01G395500 chr7D 85.612 417 20 4 706 1109 227554460 227554849 3.650000e-108 401.0
65 TraesCS3D01G395500 chr7D 92.069 290 15 4 1269 1557 261526634 261526916 3.650000e-108 401.0
66 TraesCS3D01G395500 chr7D 92.188 128 6 2 2234 2357 630694494 630694367 6.690000e-41 178.0
67 TraesCS3D01G395500 chr7D 100.000 30 0 0 597 626 55216300 55216329 3.270000e-04 56.5
68 TraesCS3D01G395500 chr2D 93.717 382 16 6 1563 1941 157143690 157143314 1.220000e-157 566.0
69 TraesCS3D01G395500 chr2D 93.211 383 20 5 1560 1941 121768049 121768426 2.050000e-155 558.0
70 TraesCS3D01G395500 chr2D 93.316 374 13 6 1560 1932 527543139 527542777 2.060000e-150 542.0
71 TraesCS3D01G395500 chr2D 90.625 128 8 1 2234 2357 157143297 157143170 1.450000e-37 167.0
72 TraesCS3D01G395500 chr3B 82.482 411 30 14 922 1307 826615473 826615080 2.920000e-84 322.0
73 TraesCS3D01G395500 chr5D 92.969 128 5 1 2234 2357 312381857 312381730 1.440000e-42 183.0
74 TraesCS3D01G395500 chr1D 93.388 121 4 4 2241 2357 457137591 457137471 2.410000e-40 176.0
75 TraesCS3D01G395500 chr1D 91.406 128 7 2 2234 2357 411379030 411379157 3.110000e-39 172.0
76 TraesCS3D01G395500 chr1D 87.500 104 9 3 1207 1307 470826588 470826690 1.480000e-22 117.0
77 TraesCS3D01G395500 chr7B 98.485 66 1 0 231 296 194787861 194787926 1.480000e-22 117.0
78 TraesCS3D01G395500 chr4B 97.500 40 1 0 546 585 654111092 654111053 4.200000e-08 69.4


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 TraesCS3D01G395500 chr3D 511254831 511257187 2356 True 1907.500000 3585 100.000000 1 2357 2 chr3D.!!$R3 2356
1 TraesCS3D01G395500 chr4A 552248007 552250210 2203 True 610.775000 1151 96.240000 1 1557 4 chr4A.!!$R2 1556
2 TraesCS3D01G395500 chr4A 556467803 556468551 748 True 366.500000 442 85.137500 704 1557 2 chr4A.!!$R3 853
3 TraesCS3D01G395500 chr5B 103635467 103636091 624 False 524.200000 979 98.464000 88 690 2 chr5B.!!$F2 602
4 TraesCS3D01G395500 chr5B 626043883 626044817 934 True 211.000000 279 85.278500 704 1318 2 chr5B.!!$R2 614
5 TraesCS3D01G395500 chr1A 210659460 210660039 579 True 953.000000 953 96.386000 21 599 1 chr1A.!!$R1 578
6 TraesCS3D01G395500 chr1A 210879702 210880243 541 True 902.000000 902 96.691000 58 599 1 chr1A.!!$R2 541
7 TraesCS3D01G395500 chr1A 416213895 416214437 542 False 881.000000 881 95.963000 58 600 1 chr1A.!!$F1 542
8 TraesCS3D01G395500 chr1A 178262263 178262870 607 False 502.400000 915 97.551500 21 600 2 chr1A.!!$F3 579
9 TraesCS3D01G395500 chr1A 210843302 210843909 607 True 501.150000 907 97.511500 21 599 2 chr1A.!!$R3 578
10 TraesCS3D01G395500 chr1A 27783070 27783675 605 False 497.650000 900 97.416500 21 598 2 chr1A.!!$F2 577
11 TraesCS3D01G395500 chr5A 575302936 575303553 617 True 513.400000 937 96.794000 21 608 2 chr5A.!!$R2 587
12 TraesCS3D01G395500 chr5A 524280781 524281389 608 False 504.900000 920 96.772000 21 600 2 chr5A.!!$F3 579
13 TraesCS3D01G395500 chr1B 79197864 79199262 1398 False 417.366667 935 96.713667 88 846 3 chr1B.!!$F2 758
14 TraesCS3D01G395500 chr3A 78937120 78937663 543 False 931.000000 931 97.615000 58 600 1 chr3A.!!$F2 542
15 TraesCS3D01G395500 chr2A 373453488 373454009 521 True 555.000000 555 86.492000 1046 1555 1 chr2A.!!$R2 509
16 TraesCS3D01G395500 chr2A 665850345 665850953 608 False 510.650000 926 97.789500 21 600 2 chr2A.!!$F1 579
17 TraesCS3D01G395500 chr7A 284051250 284051793 543 True 915.000000 915 97.064000 58 600 1 chr7A.!!$R1 542
18 TraesCS3D01G395500 chr7A 539963554 539964158 604 True 494.750000 909 97.353500 21 600 2 chr7A.!!$R2 579
19 TraesCS3D01G395500 chr6A 599381459 599382002 543 False 898.000000 898 96.514000 58 600 1 chr6A.!!$F2 542
20 TraesCS3D01G395500 chr6D 414471712 414472342 630 False 872.000000 872 91.486000 914 1557 1 chr6D.!!$F1 643
21 TraesCS3D01G395500 chr6D 448377094 448377635 541 True 553.000000 553 86.051000 1040 1557 1 chr6D.!!$R2 517
22 TraesCS3D01G395500 chr7D 481607907 481608434 527 False 608.000000 608 88.104000 1040 1554 1 chr7D.!!$F4 514
23 TraesCS3D01G395500 chr7D 227554460 227555582 1122 False 435.500000 470 87.209000 706 1557 2 chr7D.!!$F5 851
24 TraesCS3D01G395500 chr2D 157143170 157143690 520 True 366.500000 566 92.171000 1563 2357 2 chr2D.!!$R2 794

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
52 53 2.099756 GCAATGCACTACTCCAAATCCC 59.900 50.000 0.0 0.0 0.00 3.85 F
1171 2599 4.154347 CTGCTCCCGCCTCTGGAC 62.154 72.222 0.0 0.0 34.43 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 2611 1.379044 GGACGAGGACGAGGGGTAA 60.379 63.158 0.00 0.00 42.66 2.85 R
2323 3836 1.589196 GCGTACCTCGAGATGTGGC 60.589 63.158 15.71 8.71 42.86 5.01 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
52 53 2.099756 GCAATGCACTACTCCAAATCCC 59.900 50.000 0.00 0.00 0.00 3.85
139 168 7.706607 TCCAGTATGTCAGATTTGATTTAGTCG 59.293 37.037 0.00 0.00 35.39 4.18
1171 2599 4.154347 CTGCTCCCGCCTCTGGAC 62.154 72.222 0.00 0.00 34.43 4.02
1205 2633 3.203412 CCTCGTCCTCGTCCTCCG 61.203 72.222 0.00 0.00 38.33 4.63
1493 2998 0.916358 AGCAGTGGGGGCTGATTAGT 60.916 55.000 0.00 0.00 40.80 2.24
1494 2999 0.837272 GCAGTGGGGGCTGATTAGTA 59.163 55.000 0.00 0.00 38.70 1.82
1495 3000 1.202698 GCAGTGGGGGCTGATTAGTAG 60.203 57.143 0.00 0.00 38.70 2.57
1517 3023 6.954487 AGTAACAGTTTAAAAGGTGGAAGG 57.046 37.500 0.00 0.00 0.00 3.46
1518 3024 5.831525 AGTAACAGTTTAAAAGGTGGAAGGG 59.168 40.000 0.00 0.00 0.00 3.95
1519 3025 4.259933 ACAGTTTAAAAGGTGGAAGGGT 57.740 40.909 0.00 0.00 0.00 4.34
1557 3063 1.539827 ACAAATGAACTAAGGTGCGGC 59.460 47.619 0.00 0.00 0.00 6.53
1558 3064 1.135402 CAAATGAACTAAGGTGCGGCC 60.135 52.381 0.00 0.00 37.58 6.13
1559 3065 1.024579 AATGAACTAAGGTGCGGCCG 61.025 55.000 24.05 24.05 43.70 6.13
1560 3066 2.047560 GAACTAAGGTGCGGCCGT 60.048 61.111 28.70 9.01 43.70 5.68
1561 3067 2.047560 AACTAAGGTGCGGCCGTC 60.048 61.111 28.70 19.46 43.70 4.79
1562 3068 3.600898 AACTAAGGTGCGGCCGTCC 62.601 63.158 28.70 27.18 43.70 4.79
1608 3114 3.825611 CCCGCTTCCGCATTTGGG 61.826 66.667 0.00 0.00 35.30 4.12
1646 3152 2.096248 CGCTGGCCTAAACCCATTTTA 58.904 47.619 3.32 0.00 0.00 1.52
1652 3158 2.231721 GCCTAAACCCATTTTAACGGCA 59.768 45.455 0.00 0.00 39.34 5.69
1653 3159 3.118920 GCCTAAACCCATTTTAACGGCAT 60.119 43.478 0.00 0.00 39.34 4.40
1759 3265 1.135831 CACGCGTCCACATTTGCATTA 60.136 47.619 9.86 0.00 0.00 1.90
1830 3339 4.808238 GGCGTCGTCGTCGTCCTC 62.808 72.222 13.09 0.00 39.49 3.71
2290 3803 0.464735 AGCATCTCCTCGTACTCGCT 60.465 55.000 0.00 0.00 36.96 4.93
2297 3810 3.079941 CTCGTACTCGCTGCGACGA 62.080 63.158 27.46 27.46 40.36 4.20
2351 3864 3.775654 AGGTACGCCTGCTCCTGC 61.776 66.667 0.00 0.00 45.05 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.479837 TCAACAGCAACTACTTGACCG 58.520 47.619 0.00 0.00 0.00 4.79
139 168 3.307242 CACTACACGCAGCTCTAAATTCC 59.693 47.826 0.00 0.00 0.00 3.01
386 415 4.881019 ATCTACTCTGAACAGTGCTTGT 57.119 40.909 1.73 0.00 43.45 3.16
593 625 9.113838 AGTCTCCAATAGCAACACAAAATATAG 57.886 33.333 0.00 0.00 0.00 1.31
1168 2596 4.424566 TAAGTGACGGCCGCGTCC 62.425 66.667 28.58 12.87 38.04 4.79
1169 2597 3.177249 GTAAGTGACGGCCGCGTC 61.177 66.667 28.58 17.65 39.16 5.19
1170 2598 4.729856 GGTAAGTGACGGCCGCGT 62.730 66.667 28.58 6.48 0.00 6.01
1173 2601 3.366739 GAGGGGTAAGTGACGGCCG 62.367 68.421 26.86 26.86 0.00 6.13
1174 2602 2.582978 GAGGGGTAAGTGACGGCC 59.417 66.667 0.00 0.00 0.00 6.13
1175 2603 2.183555 CGAGGGGTAAGTGACGGC 59.816 66.667 0.00 0.00 0.00 5.68
1176 2604 1.509923 GACGAGGGGTAAGTGACGG 59.490 63.158 0.00 0.00 0.00 4.79
1183 2611 1.379044 GGACGAGGACGAGGGGTAA 60.379 63.158 0.00 0.00 42.66 2.85
1493 2998 6.999871 CCCTTCCACCTTTTAAACTGTTACTA 59.000 38.462 0.00 0.00 0.00 1.82
1494 2999 5.831525 CCCTTCCACCTTTTAAACTGTTACT 59.168 40.000 0.00 0.00 0.00 2.24
1495 3000 5.595542 ACCCTTCCACCTTTTAAACTGTTAC 59.404 40.000 0.00 0.00 0.00 2.50
1562 3068 3.047877 GTCTGGCCGACCCAAACG 61.048 66.667 14.46 0.00 44.81 3.60
1563 3069 3.047877 CGTCTGGCCGACCCAAAC 61.048 66.667 18.07 0.34 44.81 2.93
1564 3070 4.323477 CCGTCTGGCCGACCCAAA 62.323 66.667 18.07 0.00 44.81 3.28
1568 3074 4.736896 GTGTCCGTCTGGCCGACC 62.737 72.222 18.07 8.23 39.56 4.79
1694 3200 6.759356 GGCCGGCTTTAATGTTTAATTAATGT 59.241 34.615 28.56 0.00 0.00 2.71
1741 3247 2.254918 TTAATGCAAATGTGGACGCG 57.745 45.000 3.53 3.53 0.00 6.01
2297 3810 3.141488 CGGCTGGTAGAGGAGCGT 61.141 66.667 0.00 0.00 35.95 5.07
2323 3836 1.589196 GCGTACCTCGAGATGTGGC 60.589 63.158 15.71 8.71 42.86 5.01


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

AutoCloner maintained by Alex Coulton.