Multiple sequence alignment - TraesCS4D01G190000

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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 TraesCS4D01G190000 chr4D 100.000 3231 0 0 1 3231 332128795 332132025 0.000000e+00 5967.0
1 TraesCS4D01G190000 chr4D 88.798 366 18 4 2192 2536 487243881 487244244 8.280000e-116 427.0
2 TraesCS4D01G190000 chr4D 100.000 38 0 0 2195 2232 295217857 295217820 1.610000e-08 71.3
3 TraesCS4D01G190000 chr7D 95.652 3243 109 12 1 3231 594650008 594653230 0.000000e+00 5179.0
4 TraesCS4D01G190000 chr6D 95.326 3252 120 8 1 3231 73255330 73252090 0.000000e+00 5134.0
5 TraesCS4D01G190000 chr6D 95.858 169 7 0 3063 3231 172926543 172926375 1.140000e-69 274.0
6 TraesCS4D01G190000 chr6D 96.341 164 6 0 3067 3230 440890271 440890108 1.480000e-68 270.0
7 TraesCS4D01G190000 chr6D 78.082 146 13 9 2339 2480 1937321 1937191 1.240000e-09 75.0
8 TraesCS4D01G190000 chr5D 96.091 2584 72 13 653 3231 339382186 339384745 0.000000e+00 4185.0
9 TraesCS4D01G190000 chr5D 95.685 1993 67 7 671 2658 29628242 29630220 0.000000e+00 3186.0
10 TraesCS4D01G190000 chr5D 96.313 651 20 3 1 651 29627295 29627941 0.000000e+00 1066.0
11 TraesCS4D01G190000 chr5D 88.140 371 17 4 2192 2537 438275684 438275316 1.790000e-112 416.0
12 TraesCS4D01G190000 chr5D 95.858 169 7 0 3063 3231 56853841 56854009 1.140000e-69 274.0
13 TraesCS4D01G190000 chr5D 93.939 165 9 1 3067 3231 426993414 426993251 6.920000e-62 248.0
14 TraesCS4D01G190000 chr5D 82.379 227 27 4 1927 2142 559731551 559731775 5.500000e-43 185.0
15 TraesCS4D01G190000 chr5D 89.051 137 14 1 2927 3063 521674411 521674276 5.540000e-38 169.0
16 TraesCS4D01G190000 chr5D 81.152 191 22 11 1686 1867 559731365 559731550 1.210000e-29 141.0
17 TraesCS4D01G190000 chr2D 96.597 2527 79 3 710 3231 147701329 147703853 0.000000e+00 4183.0
18 TraesCS4D01G190000 chr2D 90.071 1259 83 14 756 1982 233888319 233889567 0.000000e+00 1594.0
19 TraesCS4D01G190000 chr2D 94.553 716 25 12 1 706 92456481 92457192 0.000000e+00 1094.0
20 TraesCS4D01G190000 chr2D 95.626 663 25 4 1 661 147700265 147700925 0.000000e+00 1061.0
21 TraesCS4D01G190000 chr2D 89.779 362 18 8 2192 2536 574799847 574799488 2.290000e-121 446.0
22 TraesCS4D01G190000 chr2D 88.556 367 18 5 2192 2537 233889729 233890092 1.070000e-114 424.0
23 TraesCS4D01G190000 chr3D 95.803 1930 71 6 1 1925 231534696 231532772 0.000000e+00 3107.0
24 TraesCS4D01G190000 chr3D 97.082 1268 31 3 1968 3231 231532772 231531507 0.000000e+00 2132.0
25 TraesCS4D01G190000 chr3D 90.634 363 15 3 2192 2537 419549759 419549399 6.310000e-127 464.0
26 TraesCS4D01G190000 chr3D 93.590 234 10 2 2308 2537 18637267 18637035 8.580000e-91 344.0
27 TraesCS4D01G190000 chr3D 97.006 167 5 0 3063 3229 480723463 480723629 6.820000e-72 281.0
28 TraesCS4D01G190000 chr3D 95.858 169 7 0 3063 3231 415926318 415926486 1.140000e-69 274.0
29 TraesCS4D01G190000 chr3D 95.385 130 6 0 2934 3063 458628660 458628531 1.170000e-49 207.0
30 TraesCS4D01G190000 chr1B 91.819 1149 63 13 815 1938 151150013 151148871 0.000000e+00 1572.0
31 TraesCS4D01G190000 chr1B 95.671 231 9 1 1940 2170 151148744 151148515 1.420000e-98 370.0
32 TraesCS4D01G190000 chr1B 94.857 175 9 0 2889 3063 518540348 518540174 1.140000e-69 274.0
33 TraesCS4D01G190000 chr1B 94.079 152 8 1 2192 2343 151148443 151148293 2.510000e-56 230.0
34 TraesCS4D01G190000 chr4A 89.655 1102 81 12 756 1828 322881875 322882972 0.000000e+00 1373.0
35 TraesCS4D01G190000 chr4A 94.591 684 35 2 2192 2874 322883206 322883888 0.000000e+00 1057.0
36 TraesCS4D01G190000 chr4A 95.918 343 14 0 2889 3231 322884532 322884874 1.010000e-154 556.0
37 TraesCS4D01G190000 chr4A 96.471 170 5 1 3063 3231 712891206 712891037 2.450000e-71 279.0
38 TraesCS4D01G190000 chr1A 91.806 720 53 5 1 717 522944406 522945122 0.000000e+00 998.0
39 TraesCS4D01G190000 chr1A 91.401 721 55 6 1 717 522936338 522937055 0.000000e+00 981.0
40 TraesCS4D01G190000 chr1A 89.373 367 13 5 2192 2537 174398625 174398264 3.830000e-119 438.0
41 TraesCS4D01G190000 chr1A 82.941 340 38 13 2535 2874 486054149 486053830 4.080000e-74 289.0
42 TraesCS4D01G190000 chr1A 94.083 169 10 0 3063 3231 14979543 14979711 1.150000e-64 257.0
43 TraesCS4D01G190000 chr1A 93.143 175 12 0 2889 3063 486053051 486052877 1.150000e-64 257.0
44 TraesCS4D01G190000 chr5B 91.185 726 51 6 1 717 415392444 415393165 0.000000e+00 974.0
45 TraesCS4D01G190000 chr5B 89.600 500 38 8 1685 2175 25484517 25485011 9.840000e-175 623.0
46 TraesCS4D01G190000 chr5B 87.528 441 33 10 1713 2142 693996100 693996529 1.040000e-134 490.0
47 TraesCS4D01G190000 chr5B 89.646 367 15 4 2192 2537 17697988 17698352 2.290000e-121 446.0
48 TraesCS4D01G190000 chr5B 96.471 170 5 1 3063 3231 665599608 665599439 2.450000e-71 279.0
49 TraesCS4D01G190000 chr5B 93.956 182 10 1 2192 2373 25485073 25485253 1.140000e-69 274.0
50 TraesCS4D01G190000 chr2B 93.538 619 38 2 2256 2874 306848658 306848042 0.000000e+00 920.0
51 TraesCS4D01G190000 chr2B 95.349 344 14 2 2888 3231 306847740 306847399 2.190000e-151 545.0
52 TraesCS4D01G190000 chr3A 90.166 722 35 10 1285 1982 497909245 497909954 0.000000e+00 907.0
53 TraesCS4D01G190000 chr7A 89.335 722 41 10 1285 1982 689071522 689072231 0.000000e+00 874.0
54 TraesCS4D01G190000 chr7A 97.391 115 3 0 664 778 25226169 25226055 2.540000e-46 196.0
55 TraesCS4D01G190000 chr2A 89.266 708 41 11 1285 1968 687143991 687143295 0.000000e+00 854.0
56 TraesCS4D01G190000 chr2A 89.358 639 35 10 1368 1982 539388007 539387378 0.000000e+00 773.0
57 TraesCS4D01G190000 chrUn 88.824 680 41 11 1285 1939 219488144 219487475 0.000000e+00 802.0
58 TraesCS4D01G190000 chrUn 88.580 683 40 11 1285 1939 237806492 237805820 0.000000e+00 795.0
59 TraesCS4D01G190000 chrUn 86.645 307 23 6 1685 1982 306377778 306378075 1.120000e-84 324.0
60 TraesCS4D01G190000 chrUn 84.530 362 19 13 2192 2536 306378213 306378554 1.120000e-84 324.0
61 TraesCS4D01G190000 chrUn 84.530 362 19 13 2192 2536 310663529 310663188 1.120000e-84 324.0
62 TraesCS4D01G190000 chrUn 86.645 307 23 6 1685 1982 310663964 310663667 1.120000e-84 324.0
63 TraesCS4D01G190000 chr6B 91.600 500 28 7 1685 2175 651365031 651364537 0.000000e+00 678.0
64 TraesCS4D01G190000 chr6B 91.400 500 29 7 1685 2175 671659251 671659745 0.000000e+00 673.0
65 TraesCS4D01G190000 chr6B 91.200 500 30 7 1685 2175 76226179 76225685 0.000000e+00 667.0
66 TraesCS4D01G190000 chr6B 93.443 183 10 2 2192 2373 651364475 651364294 1.480000e-68 270.0
67 TraesCS4D01G190000 chr6B 92.350 183 12 2 2192 2373 671659807 671659988 3.200000e-65 259.0
68 TraesCS4D01G190000 chr1D 88.828 367 16 5 2192 2537 425477224 425477586 8.280000e-116 427.0
69 TraesCS4D01G190000 chr1D 85.714 343 31 8 2535 2874 386165921 386165594 2.390000e-91 346.0
70 TraesCS4D01G190000 chr1D 94.286 175 9 1 2889 3063 386164891 386164718 1.910000e-67 267.0
71 TraesCS4D01G190000 chr1D 93.243 74 5 0 3063 3136 473554899 473554972 3.410000e-20 110.0
72 TraesCS4D01G190000 chr6A 88.688 221 14 4 1763 1982 166116246 166116456 3.200000e-65 259.0
73 TraesCS4D01G190000 chr5A 94.915 118 5 1 664 780 539826826 539826709 1.980000e-42 183.0
74 TraesCS4D01G190000 chr5A 91.304 115 10 0 664 778 374025606 374025492 1.200000e-34 158.0
75 TraesCS4D01G190000 chr4B 86.400 125 5 6 762 886 639151250 639151138 3.380000e-25 126.0


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 TraesCS4D01G190000 chr4D 332128795 332132025 3230 False 5967.000000 5967 100.000000 1 3231 1 chr4D.!!$F1 3230
1 TraesCS4D01G190000 chr7D 594650008 594653230 3222 False 5179.000000 5179 95.652000 1 3231 1 chr7D.!!$F1 3230
2 TraesCS4D01G190000 chr6D 73252090 73255330 3240 True 5134.000000 5134 95.326000 1 3231 1 chr6D.!!$R2 3230
3 TraesCS4D01G190000 chr5D 339382186 339384745 2559 False 4185.000000 4185 96.091000 653 3231 1 chr5D.!!$F2 2578
4 TraesCS4D01G190000 chr5D 29627295 29630220 2925 False 2126.000000 3186 95.999000 1 2658 2 chr5D.!!$F3 2657
5 TraesCS4D01G190000 chr2D 147700265 147703853 3588 False 2622.000000 4183 96.111500 1 3231 2 chr2D.!!$F2 3230
6 TraesCS4D01G190000 chr2D 92456481 92457192 711 False 1094.000000 1094 94.553000 1 706 1 chr2D.!!$F1 705
7 TraesCS4D01G190000 chr2D 233888319 233890092 1773 False 1009.000000 1594 89.313500 756 2537 2 chr2D.!!$F3 1781
8 TraesCS4D01G190000 chr3D 231531507 231534696 3189 True 2619.500000 3107 96.442500 1 3231 2 chr3D.!!$R4 3230
9 TraesCS4D01G190000 chr1B 151148293 151150013 1720 True 724.000000 1572 93.856333 815 2343 3 chr1B.!!$R2 1528
10 TraesCS4D01G190000 chr4A 322881875 322884874 2999 False 995.333333 1373 93.388000 756 3231 3 chr4A.!!$F1 2475
11 TraesCS4D01G190000 chr1A 522944406 522945122 716 False 998.000000 998 91.806000 1 717 1 chr1A.!!$F3 716
12 TraesCS4D01G190000 chr1A 522936338 522937055 717 False 981.000000 981 91.401000 1 717 1 chr1A.!!$F2 716
13 TraesCS4D01G190000 chr1A 486052877 486054149 1272 True 273.000000 289 88.042000 2535 3063 2 chr1A.!!$R2 528
14 TraesCS4D01G190000 chr5B 415392444 415393165 721 False 974.000000 974 91.185000 1 717 1 chr5B.!!$F2 716
15 TraesCS4D01G190000 chr5B 25484517 25485253 736 False 448.500000 623 91.778000 1685 2373 2 chr5B.!!$F4 688
16 TraesCS4D01G190000 chr2B 306847399 306848658 1259 True 732.500000 920 94.443500 2256 3231 2 chr2B.!!$R1 975
17 TraesCS4D01G190000 chr3A 497909245 497909954 709 False 907.000000 907 90.166000 1285 1982 1 chr3A.!!$F1 697
18 TraesCS4D01G190000 chr7A 689071522 689072231 709 False 874.000000 874 89.335000 1285 1982 1 chr7A.!!$F1 697
19 TraesCS4D01G190000 chr2A 687143295 687143991 696 True 854.000000 854 89.266000 1285 1968 1 chr2A.!!$R2 683
20 TraesCS4D01G190000 chr2A 539387378 539388007 629 True 773.000000 773 89.358000 1368 1982 1 chr2A.!!$R1 614
21 TraesCS4D01G190000 chrUn 219487475 219488144 669 True 802.000000 802 88.824000 1285 1939 1 chrUn.!!$R1 654
22 TraesCS4D01G190000 chrUn 237805820 237806492 672 True 795.000000 795 88.580000 1285 1939 1 chrUn.!!$R2 654
23 TraesCS4D01G190000 chrUn 306377778 306378554 776 False 324.000000 324 85.587500 1685 2536 2 chrUn.!!$F1 851
24 TraesCS4D01G190000 chrUn 310663188 310663964 776 True 324.000000 324 85.587500 1685 2536 2 chrUn.!!$R3 851
25 TraesCS4D01G190000 chr6B 651364294 651365031 737 True 474.000000 678 92.521500 1685 2373 2 chr6B.!!$R2 688
26 TraesCS4D01G190000 chr6B 671659251 671659988 737 False 466.000000 673 91.875000 1685 2373 2 chr6B.!!$F1 688
27 TraesCS4D01G190000 chr1D 386164718 386165921 1203 True 306.500000 346 90.000000 2535 3063 2 chr1D.!!$R1 528

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
818 1211 0.610687 CGCTCCTCTCCAACTTCCTT 59.389 55.000 0.0 0.0 0.0 3.36 F
1099 1495 1.078848 GAGGGCTGCAACATCGAGT 60.079 57.895 0.5 0.0 0.0 4.18 F
1869 2293 2.581354 GATCTCACAGTGGCGCCT 59.419 61.111 29.7 4.8 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2293 0.037590 AGCATGTCCTAAACCGCCAA 59.962 50.000 0.00 0.0 0.00 4.52 R
2045 2608 1.148157 CGTCGATCGCAGCATCCTTT 61.148 55.000 11.09 0.0 0.00 3.11 R
3180 4622 1.900486 AGTACCCAGTTGTACTCCAGC 59.100 52.381 0.00 0.0 46.48 4.85 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
190 194 8.076178 ACTCATTTTGGACACTCGAAAAATAAG 58.924 33.333 3.59 2.32 37.55 1.73
441 450 2.367512 GGTCCAGGGGCCTCTCAT 60.368 66.667 0.00 0.00 0.00 2.90
463 472 1.604438 CGGATCGCGGATAAATCACCA 60.604 52.381 6.13 0.00 0.00 4.17
507 524 2.935740 CGCAGCTCACCCTCTCACA 61.936 63.158 0.00 0.00 0.00 3.58
522 539 4.250305 ACACACCCACCGTGAGCC 62.250 66.667 0.00 0.00 46.20 4.70
562 583 0.808125 CACACCACTCCTCTCTCTCG 59.192 60.000 0.00 0.00 0.00 4.04
727 1108 1.022903 ACTCCCTCCCTCTGGATCTT 58.977 55.000 0.00 0.00 40.80 2.40
818 1211 0.610687 CGCTCCTCTCCAACTTCCTT 59.389 55.000 0.00 0.00 0.00 3.36
828 1221 3.509137 AACTTCCTTCGCGTCGGCA 62.509 57.895 5.77 0.00 39.92 5.69
893 1286 2.317609 CCACTTCCACTTCCGCACG 61.318 63.158 0.00 0.00 0.00 5.34
935 1328 4.351054 CCCCACTGCTTCCGCCTT 62.351 66.667 0.00 0.00 34.43 4.35
1099 1495 1.078848 GAGGGCTGCAACATCGAGT 60.079 57.895 0.50 0.00 0.00 4.18
1150 1551 4.503817 CGATTTGATCCAATCTAGGGCTCA 60.504 45.833 15.39 0.00 0.00 4.26
1319 1720 9.174166 GCTAATTTACTGATTTGGTTTCCTCTA 57.826 33.333 0.00 0.00 0.00 2.43
1380 1781 2.750350 CAGTCCAGGAAGGCGGTT 59.250 61.111 0.00 0.00 37.29 4.44
1841 2265 7.893124 ATTCATTCTTACATTCTGGCATCTT 57.107 32.000 0.00 0.00 0.00 2.40
1869 2293 2.581354 GATCTCACAGTGGCGCCT 59.419 61.111 29.70 4.80 0.00 5.52
1926 2364 2.871182 TGAGCTCAGGCAATACTACG 57.129 50.000 13.74 0.00 41.70 3.51
1930 2368 3.522553 AGCTCAGGCAATACTACGTTTC 58.477 45.455 0.00 0.00 41.70 2.78
2045 2608 6.602410 TGAAAAATATCTGACCATGGCAAA 57.398 33.333 13.04 0.00 0.00 3.68
2046 2609 7.002250 TGAAAAATATCTGACCATGGCAAAA 57.998 32.000 13.04 2.79 0.00 2.44
2281 2895 2.309613 AGGTGCTGACTTGATGCAAAA 58.690 42.857 0.00 0.00 38.50 2.44
2282 2896 2.694628 AGGTGCTGACTTGATGCAAAAA 59.305 40.909 0.00 0.00 38.50 1.94
2452 3084 3.981071 TCCCATTCACTAGACAACCAG 57.019 47.619 0.00 0.00 0.00 4.00
2749 3389 9.799106 CATGTTTAGAATATATCCACCTCCTTT 57.201 33.333 0.00 0.00 0.00 3.11
3180 4622 0.677731 TTTTGGGCTGATGCTCTCCG 60.678 55.000 0.00 0.00 41.13 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.934457 AAGACAAATTTCCGCCGATTT 57.066 38.095 0.00 0.00 0.00 2.17
406 415 4.081365 TGGACCAATCAGAACGCAGTATAA 60.081 41.667 0.00 0.00 45.00 0.98
839 1232 3.005539 AGGAGGCTGTGTGCGGAT 61.006 61.111 0.00 0.00 44.05 4.18
893 1286 1.304509 GGAGAAGGAGTTGCTGCTGC 61.305 60.000 8.89 8.89 31.17 5.25
935 1328 1.897137 CTCCGGTGGGATCGATCGA 60.897 63.158 21.86 21.86 42.83 3.59
1099 1495 3.309582 GGAACCTCGGATCTGGCA 58.690 61.111 0.62 0.00 0.00 4.92
1150 1551 0.106015 AGCAACCAGTTGAAGGCCTT 60.106 50.000 20.65 20.65 42.93 4.35
1319 1720 1.421268 TCAGGAACAAGCATCACCAGT 59.579 47.619 0.00 0.00 0.00 4.00
1352 1753 2.848679 TGGACTGCACCAGCTCCA 60.849 61.111 10.44 10.44 42.74 3.86
1841 2265 4.546570 CACTGTGAGATCGTTCAAGTACA 58.453 43.478 0.32 0.00 0.00 2.90
1869 2293 0.037590 AGCATGTCCTAAACCGCCAA 59.962 50.000 0.00 0.00 0.00 4.52
2045 2608 1.148157 CGTCGATCGCAGCATCCTTT 61.148 55.000 11.09 0.00 0.00 3.11
2046 2609 1.589993 CGTCGATCGCAGCATCCTT 60.590 57.895 11.09 0.00 0.00 3.36
2313 2944 2.977914 ACAACAGCTAGCATCGTTCAT 58.022 42.857 18.83 5.05 0.00 2.57
2452 3084 9.755064 CAAACATGCAAATACAAGTAGTAGTAC 57.245 33.333 0.00 0.00 35.85 2.73
2502 3142 5.778241 TCCTAGTACTGAATTTCCTCACACA 59.222 40.000 5.39 0.00 0.00 3.72
2920 4362 9.213777 TGTCTTACTGTAATAAGAATCCATCCT 57.786 33.333 0.00 0.00 41.67 3.24
3180 4622 1.900486 AGTACCCAGTTGTACTCCAGC 59.100 52.381 0.00 0.00 46.48 4.85
3191 4633 4.074970 CAAAAAGAGATGCAGTACCCAGT 58.925 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.