Multiple sequence alignment - TraesCS7B01G387300

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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 TraesCS7B01G387300 chr7B 100.000 3377 0 0 1 3377 653221740 653218364 0.000000e+00 6237.0
1 TraesCS7B01G387300 chr7B 99.319 3377 21 1 1 3377 653281516 653278142 0.000000e+00 6107.0
2 TraesCS7B01G387300 chr7B 98.727 3377 16 4 1 3377 653170574 653167225 0.000000e+00 5973.0
3 TraesCS7B01G387300 chr7B 94.395 785 29 7 1 773 713959066 713959847 0.000000e+00 1192.0
4 TraesCS7B01G387300 chr7B 86.792 318 39 3 2516 2832 683681800 683681485 5.360000e-93 351.0
5 TraesCS7B01G387300 chr7B 88.845 251 28 0 3126 3376 50568562 50568812 3.270000e-80 309.0
6 TraesCS7B01G387300 chr7B 88.627 255 28 1 3122 3376 189711068 189711321 3.270000e-80 309.0
7 TraesCS7B01G387300 chr7B 88.492 252 27 2 3126 3376 659264340 659264090 1.520000e-78 303.0
8 TraesCS7B01G387300 chr7B 71.007 1152 285 34 1245 2367 663499034 663497903 7.290000e-57 231.0
9 TraesCS7B01G387300 chr7B 91.566 83 1 1 824 906 110322345 110322269 3.560000e-20 110.0
10 TraesCS7B01G387300 chr7B 100.000 35 0 0 2343 2377 653371675 653371641 7.820000e-07 65.8
11 TraesCS7B01G387300 chr7D 93.296 1790 77 12 906 2673 585151056 585149288 0.000000e+00 2601.0
12 TraesCS7B01G387300 chr7D 91.120 259 20 3 2873 3129 585149284 585149027 6.940000e-92 348.0
13 TraesCS7B01G387300 chr7D 85.093 322 44 4 2513 2832 164849869 164850188 3.250000e-85 326.0
14 TraesCS7B01G387300 chr7D 93.056 72 3 2 762 831 585151124 585151053 1.660000e-18 104.0
15 TraesCS7B01G387300 chr5B 93.838 779 30 6 1 764 596887967 596887192 0.000000e+00 1157.0
16 TraesCS7B01G387300 chr5B 92.737 771 30 4 1 760 693977000 693976245 0.000000e+00 1090.0
17 TraesCS7B01G387300 chr5B 90.851 787 40 7 1 760 293464474 293463693 0.000000e+00 1026.0
18 TraesCS7B01G387300 chr5B 89.541 784 42 19 1 760 268854236 268855003 0.000000e+00 957.0
19 TraesCS7B01G387300 chr5B 86.834 319 37 5 2516 2832 476574964 476574649 5.360000e-93 351.0
20 TraesCS7B01G387300 chr5B 86.164 318 42 2 2516 2832 461300910 461301226 3.230000e-90 342.0
21 TraesCS7B01G387300 chr5B 87.594 266 30 3 3113 3376 148876524 148876788 4.230000e-79 305.0
22 TraesCS7B01G387300 chr5B 88.400 250 27 2 3128 3376 92841428 92841180 1.970000e-77 300.0
23 TraesCS7B01G387300 chr5B 87.218 266 31 3 3113 3376 148882706 148882970 1.970000e-77 300.0
24 TraesCS7B01G387300 chr7A 80.943 1485 247 17 906 2374 675323787 675322323 0.000000e+00 1142.0
25 TraesCS7B01G387300 chr7A 86.628 688 48 17 2 656 3051381 3052057 0.000000e+00 721.0
26 TraesCS7B01G387300 chr7A 75.839 596 113 18 1751 2317 675332749 675332156 1.190000e-69 274.0
27 TraesCS7B01G387300 chr2B 93.167 761 41 7 1 760 480913450 480912700 0.000000e+00 1107.0
28 TraesCS7B01G387300 chr2B 87.107 318 38 3 2516 2832 125974736 125975051 1.150000e-94 357.0
29 TraesCS7B01G387300 chr2B 86.792 318 40 2 2516 2832 754706324 754706008 1.490000e-93 353.0
30 TraesCS7B01G387300 chr2B 89.286 252 25 2 3126 3376 188264404 188264154 7.030000e-82 315.0
31 TraesCS7B01G387300 chr3B 91.753 776 44 13 1 760 787502660 787503431 0.000000e+00 1061.0
32 TraesCS7B01G387300 chr3B 88.213 263 31 0 3114 3376 197773669 197773407 7.030000e-82 315.0
33 TraesCS7B01G387300 chr3B 89.286 252 24 3 3126 3376 783089303 783089552 2.530000e-81 313.0
34 TraesCS7B01G387300 chr6A 86.962 790 62 20 2 768 613086241 613085470 0.000000e+00 850.0
35 TraesCS7B01G387300 chr6A 86.364 308 40 2 2526 2832 184741235 184740929 5.400000e-88 335.0
36 TraesCS7B01G387300 chr4A 85.609 813 55 17 1 760 219189146 219188343 0.000000e+00 797.0
37 TraesCS7B01G387300 chr4A 84.848 99 9 1 808 906 662621191 662621099 9.980000e-16 95.3
38 TraesCS7B01G387300 chr6B 86.834 319 37 5 2516 2832 303056347 303056032 5.360000e-93 351.0
39 TraesCS7B01G387300 chr6B 91.250 80 1 1 827 906 525106417 525106344 1.660000e-18 104.0
40 TraesCS7B01G387300 chr6B 88.636 88 5 3 820 906 285470813 285470730 5.960000e-18 102.0
41 TraesCS7B01G387300 chr3A 86.335 322 41 3 2512 2832 629859584 629859265 6.940000e-92 348.0
42 TraesCS7B01G387300 chr3A 86.293 321 39 4 2516 2835 114189293 114189609 8.970000e-91 344.0
43 TraesCS7B01G387300 chr2A 86.520 319 38 4 2516 2832 507890346 507890031 2.490000e-91 346.0
44 TraesCS7B01G387300 chr2A 85.802 324 43 3 2512 2833 673515231 673515553 1.160000e-89 340.0
45 TraesCS7B01G387300 chr2D 85.849 318 43 2 2516 2832 102568711 102569027 1.500000e-88 337.0
46 TraesCS7B01G387300 chr2D 88.845 251 28 0 3126 3376 537516221 537516471 3.270000e-80 309.0
47 TraesCS7B01G387300 chr2D 87.795 254 27 3 3124 3376 390728551 390728801 9.160000e-76 294.0
48 TraesCS7B01G387300 chrUn 85.449 323 42 5 2516 2836 321263708 321264027 6.980000e-87 331.0
49 TraesCS7B01G387300 chrUn 87.984 258 26 5 3123 3376 2374574 2374318 1.970000e-77 300.0
50 TraesCS7B01G387300 chrUn 82.840 338 50 7 2516 2849 358202257 358202590 2.550000e-76 296.0
51 TraesCS7B01G387300 chrUn 87.059 255 33 0 3122 3376 359528277 359528531 4.260000e-74 289.0
52 TraesCS7B01G387300 chrUn 87.059 255 33 0 3122 3376 420460590 420460844 4.260000e-74 289.0
53 TraesCS7B01G387300 chrUn 86.957 253 32 1 3125 3376 282654854 282654602 1.980000e-72 283.0
54 TraesCS7B01G387300 chrUn 86.328 256 34 1 3122 3376 52969800 52970055 9.230000e-71 278.0
55 TraesCS7B01G387300 chrUn 86.454 251 33 1 3126 3376 35883030 35882781 1.190000e-69 274.0
56 TraesCS7B01G387300 chrUn 86.166 253 32 3 3125 3376 31236169 31235919 1.540000e-68 270.0
57 TraesCS7B01G387300 chrUn 100.000 28 0 0 2514 2541 30909615 30909588 6.000000e-03 52.8
58 TraesCS7B01G387300 chr5D 85.231 325 44 3 2511 2832 41244510 41244833 6.980000e-87 331.0
59 TraesCS7B01G387300 chr5D 84.877 324 42 5 2512 2832 7981060 7981379 1.510000e-83 320.0
60 TraesCS7B01G387300 chr5D 88.583 254 27 2 3125 3377 495141261 495141513 1.180000e-79 307.0
61 TraesCS7B01G387300 chr5D 88.095 252 29 1 3126 3376 315627606 315627355 7.080000e-77 298.0
62 TraesCS7B01G387300 chr5D 87.795 254 29 2 3125 3377 495198628 495198880 2.550000e-76 296.0
63 TraesCS7B01G387300 chr5D 85.818 275 38 1 2522 2796 407975844 407976117 1.190000e-74 291.0
64 TraesCS7B01G387300 chr3D 85.139 323 43 5 2516 2836 585617030 585617349 3.250000e-85 326.0
65 TraesCS7B01G387300 chr3D 85.761 309 40 4 2516 2822 189286713 189286407 1.170000e-84 324.0
66 TraesCS7B01G387300 chr4D 85.220 318 44 3 2516 2832 302342933 302343248 1.170000e-84 324.0
67 TraesCS7B01G387300 chr4D 85.938 256 32 4 3122 3376 472217852 472218104 1.540000e-68 270.0
68 TraesCS7B01G387300 chr4D 87.097 62 6 1 2511 2572 437135599 437135658 6.050000e-08 69.4
69 TraesCS7B01G387300 chr1B 89.200 250 26 1 3127 3376 610014749 610014501 9.100000e-81 311.0
70 TraesCS7B01G387300 chr4B 87.451 255 31 1 3122 3376 646813375 646813628 3.300000e-75 292.0
71 TraesCS7B01G387300 chr4B 87.698 252 28 3 3126 3376 91134172 91134421 1.190000e-74 291.0
72 TraesCS7B01G387300 chr4B 87.352 253 29 3 3125 3376 147222407 147222157 1.530000e-73 287.0
73 TraesCS7B01G387300 chr4B 86.381 257 35 0 3120 3376 37346502 37346246 7.130000e-72 281.0
74 TraesCS7B01G387300 chr4B 89.655 87 5 3 820 906 24755312 24755230 1.280000e-19 108.0
75 TraesCS7B01G387300 chr4B 89.773 88 4 3 820 906 576706132 576706215 1.280000e-19 108.0
76 TraesCS7B01G387300 chr1D 87.251 251 31 1 3126 3376 430113572 430113323 5.520000e-73 285.0
77 TraesCS7B01G387300 chr1D 87.251 251 29 3 3126 3376 490549988 490549741 1.980000e-72 283.0
78 TraesCS7B01G387300 chr1D 86.719 256 30 4 3123 3376 199563064 199563317 7.130000e-72 281.0
79 TraesCS7B01G387300 chr1D 83.562 292 37 9 2543 2828 457182787 457182501 2.580000e-66 263.0
80 TraesCS7B01G387300 chr6D 86.800 250 33 0 3127 3376 431068635 431068386 2.570000e-71 279.0
81 TraesCS7B01G387300 chr6D 86.905 252 28 5 3126 3376 154344617 154344370 9.230000e-71 278.0
82 TraesCS7B01G387300 chr6D 86.434 258 27 6 3122 3376 59177024 59176772 3.320000e-70 276.0
83 TraesCS7B01G387300 chr6D 80.496 282 52 3 2553 2832 124938631 124938351 2.640000e-51 213.0
84 TraesCS7B01G387300 chr6D 88.636 88 2 3 820 906 103322427 103322347 2.140000e-17 100.0


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 TraesCS7B01G387300 chr7B 653218364 653221740 3376 True 6237.000000 6237 100.000000 1 3377 1 chr7B.!!$R3 3376
1 TraesCS7B01G387300 chr7B 653278142 653281516 3374 True 6107.000000 6107 99.319000 1 3377 1 chr7B.!!$R4 3376
2 TraesCS7B01G387300 chr7B 653167225 653170574 3349 True 5973.000000 5973 98.727000 1 3377 1 chr7B.!!$R2 3376
3 TraesCS7B01G387300 chr7B 713959066 713959847 781 False 1192.000000 1192 94.395000 1 773 1 chr7B.!!$F3 772
4 TraesCS7B01G387300 chr7B 663497903 663499034 1131 True 231.000000 231 71.007000 1245 2367 1 chr7B.!!$R7 1122
5 TraesCS7B01G387300 chr7D 585149027 585151124 2097 True 1017.666667 2601 92.490667 762 3129 3 chr7D.!!$R1 2367
6 TraesCS7B01G387300 chr5B 596887192 596887967 775 True 1157.000000 1157 93.838000 1 764 1 chr5B.!!$R4 763
7 TraesCS7B01G387300 chr5B 693976245 693977000 755 True 1090.000000 1090 92.737000 1 760 1 chr5B.!!$R5 759
8 TraesCS7B01G387300 chr5B 293463693 293464474 781 True 1026.000000 1026 90.851000 1 760 1 chr5B.!!$R2 759
9 TraesCS7B01G387300 chr5B 268854236 268855003 767 False 957.000000 957 89.541000 1 760 1 chr5B.!!$F3 759
10 TraesCS7B01G387300 chr7A 675322323 675323787 1464 True 1142.000000 1142 80.943000 906 2374 1 chr7A.!!$R1 1468
11 TraesCS7B01G387300 chr7A 3051381 3052057 676 False 721.000000 721 86.628000 2 656 1 chr7A.!!$F1 654
12 TraesCS7B01G387300 chr7A 675332156 675332749 593 True 274.000000 274 75.839000 1751 2317 1 chr7A.!!$R2 566
13 TraesCS7B01G387300 chr2B 480912700 480913450 750 True 1107.000000 1107 93.167000 1 760 1 chr2B.!!$R2 759
14 TraesCS7B01G387300 chr3B 787502660 787503431 771 False 1061.000000 1061 91.753000 1 760 1 chr3B.!!$F2 759
15 TraesCS7B01G387300 chr6A 613085470 613086241 771 True 850.000000 850 86.962000 2 768 1 chr6A.!!$R2 766
16 TraesCS7B01G387300 chr4A 219188343 219189146 803 True 797.000000 797 85.609000 1 760 1 chr4A.!!$R1 759

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
221 231 3.787001 GGTGAAGAGGGAGCCGGG 61.787 72.222 2.18 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3009 3228 2.160219 CACACGCATTACTTCACTGCAT 59.84 45.455 0.0 0.0 35.64 3.96 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
216 226 4.821589 GCGCCGGTGAAGAGGGAG 62.822 72.222 21.76 0.0 0.00 4.30
217 227 4.821589 CGCCGGTGAAGAGGGAGC 62.822 72.222 10.20 0.0 0.00 4.70
218 228 4.475135 GCCGGTGAAGAGGGAGCC 62.475 72.222 1.90 0.0 0.00 4.70
219 229 4.148825 CCGGTGAAGAGGGAGCCG 62.149 72.222 0.00 0.0 41.82 5.52
220 230 4.148825 CGGTGAAGAGGGAGCCGG 62.149 72.222 0.00 0.0 38.86 6.13
221 231 3.787001 GGTGAAGAGGGAGCCGGG 61.787 72.222 2.18 0.0 0.00 5.73
222 232 3.787001 GTGAAGAGGGAGCCGGGG 61.787 72.222 2.18 0.0 0.00 5.73
814 974 5.712084 AATCCTAAAACTAGGTTCCTCCC 57.288 43.478 0.00 0.0 38.38 4.30
893 1053 9.533831 AATTTGGTCTCATTCACCTTTTATAGT 57.466 29.630 0.00 0.0 34.66 2.12
2837 3055 6.940831 ACCGGAAAGAAGAGAGTACTATAC 57.059 41.667 9.46 0.0 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 238 4.699522 AACTCCGCCTTCACCGGC 62.700 66.667 0.00 0.0 45.19 6.13
229 239 2.434359 GAACTCCGCCTTCACCGG 60.434 66.667 0.00 0.0 46.88 5.28
230 240 2.809601 CGAACTCCGCCTTCACCG 60.810 66.667 0.00 0.0 0.00 4.94
231 241 1.737008 GTCGAACTCCGCCTTCACC 60.737 63.158 0.00 0.0 38.37 4.02
232 242 2.087009 CGTCGAACTCCGCCTTCAC 61.087 63.158 0.00 0.0 38.37 3.18
233 243 2.257371 CGTCGAACTCCGCCTTCA 59.743 61.111 0.00 0.0 38.37 3.02
234 244 1.800713 GTCGTCGAACTCCGCCTTC 60.801 63.158 0.00 0.0 38.37 3.46
235 245 2.257676 GTCGTCGAACTCCGCCTT 59.742 61.111 0.00 0.0 38.37 4.35
236 246 4.099170 CGTCGTCGAACTCCGCCT 62.099 66.667 0.00 0.0 39.71 5.52
237 247 4.093952 TCGTCGTCGAACTCCGCC 62.094 66.667 1.37 0.0 43.34 6.13
640 761 2.799452 GGTCCCCAGGCGCGTATTA 61.799 63.158 8.43 0.0 0.00 0.98
814 974 4.143137 GCAAAACTGTTTAATGAATGCCCG 60.143 41.667 6.16 0.0 0.00 6.13
893 1053 6.251255 TCCATCAGTGTTCATATCCAATGA 57.749 37.500 0.00 0.0 39.62 2.57
3009 3228 2.160219 CACACGCATTACTTCACTGCAT 59.840 45.455 0.00 0.0 35.64 3.96


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

AutoCloner maintained by Alex Coulton.