Multiple sequence alignment - TraesCS4D01G108800

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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 TraesCS4D01G108800 chr4D 100.000 3544 0 0 1 3544 88120810 88124353 0.000000e+00 6545
1 TraesCS4D01G108800 chr4D 84.009 444 64 7 1881 2322 386436134 386435696 1.520000e-113 420
2 TraesCS4D01G108800 chr4D 90.517 116 11 0 1394 1509 386437956 386437841 1.700000e-33 154
3 TraesCS4D01G108800 chr4D 93.590 78 5 0 1718 1795 386437275 386437198 2.240000e-22 117
4 TraesCS4D01G108800 chr4B 94.973 2924 90 18 26 2917 124740548 124743446 0.000000e+00 4532
5 TraesCS4D01G108800 chr4B 96.491 285 5 5 2985 3265 124743450 124743733 1.930000e-127 466
6 TraesCS4D01G108800 chr4B 84.234 444 63 7 1881 2322 473569981 473569543 3.270000e-115 425
7 TraesCS4D01G108800 chr4B 96.680 241 1 2 3258 3492 124743892 124744131 9.220000e-106 394
8 TraesCS4D01G108800 chr4B 90.517 116 11 0 1394 1509 473571692 473571577 1.700000e-33 154
9 TraesCS4D01G108800 chr4B 93.590 78 5 0 1718 1795 473570981 473570904 2.240000e-22 117
10 TraesCS4D01G108800 chr4A 92.818 3077 104 47 1 3008 500899807 500902835 0.000000e+00 4349
11 TraesCS4D01G108800 chr4A 93.717 573 21 6 2986 3544 500902854 500903425 0.000000e+00 845
12 TraesCS4D01G108800 chr4A 84.459 444 62 7 1881 2322 67892522 67892084 7.030000e-117 431
13 TraesCS4D01G108800 chr4A 90.517 116 11 0 1394 1509 67894297 67894182 1.700000e-33 154
14 TraesCS4D01G108800 chr4A 83.019 159 25 2 1208 1365 197971118 197971275 3.690000e-30 143
15 TraesCS4D01G108800 chr1D 87.345 403 49 2 1394 1795 62600891 62600490 8.960000e-126 460
16 TraesCS4D01G108800 chr1D 83.596 445 64 8 1881 2322 374471503 374471065 3.290000e-110 409
17 TraesCS4D01G108800 chr1D 91.489 188 15 1 1507 1693 374473269 374473082 1.260000e-64 257
18 TraesCS4D01G108800 chr1D 86.076 158 22 0 1208 1365 374474030 374473873 1.690000e-38 171
19 TraesCS4D01G108800 chr1B 86.600 403 52 2 1394 1795 99755109 99754708 9.030000e-121 444
20 TraesCS4D01G108800 chr1B 84.375 448 57 9 1881 2323 99753564 99753125 9.090000e-116 427
21 TraesCS4D01G108800 chr1B 83.929 448 57 12 1881 2322 499469116 499468678 7.080000e-112 414
22 TraesCS4D01G108800 chr1B 85.911 291 37 4 1507 1795 499470716 499470428 1.240000e-79 307
23 TraesCS4D01G108800 chr1B 86.709 158 21 0 1208 1365 499471527 499471370 3.640000e-40 176
24 TraesCS4D01G108800 chr1B 84.615 117 16 2 1394 1509 499470945 499470830 8.040000e-22 115
25 TraesCS4D01G108800 chr1A 86.241 407 54 2 1390 1795 60735590 60735995 1.170000e-119 440
26 TraesCS4D01G108800 chr1A 84.375 448 57 9 1881 2323 60737113 60737552 9.090000e-116 427
27 TraesCS4D01G108800 chr1A 83.445 447 61 9 1881 2322 474226181 474225743 1.530000e-108 403
28 TraesCS4D01G108800 chr1A 86.709 158 21 0 1208 1365 474228844 474228687 3.640000e-40 176
29 TraesCS4D01G108800 chr1A 83.146 178 28 2 2355 2531 60738595 60738771 1.020000e-35 161
30 TraesCS4D01G108800 chr3D 83.372 433 63 9 1881 2310 476553623 476554049 3.320000e-105 392
31 TraesCS4D01G108800 chr3D 87.241 290 35 2 1507 1795 476551514 476551802 2.640000e-86 329
32 TraesCS4D01G108800 chr3D 85.714 154 20 2 1208 1360 476550594 476550746 1.020000e-35 161
33 TraesCS4D01G108800 chr3B 82.743 452 67 11 1875 2322 635220430 635220874 3.320000e-105 392
34 TraesCS4D01G108800 chr3B 85.714 154 20 2 1208 1360 635217462 635217614 1.020000e-35 161
35 TraesCS4D01G108800 chr3A 82.472 445 69 8 1881 2322 620218449 620218011 7.180000e-102 381
36 TraesCS4D01G108800 chr3A 87.500 288 34 2 1507 1793 620220605 620220319 7.330000e-87 331
37 TraesCS4D01G108800 chr3A 85.714 154 20 2 1208 1360 620221447 620221295 1.020000e-35 161


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 TraesCS4D01G108800 chr4D 88120810 88124353 3543 False 6545.000000 6545 100.000000 1 3544 1 chr4D.!!$F1 3543
1 TraesCS4D01G108800 chr4D 386435696 386437956 2260 True 230.333333 420 89.372000 1394 2322 3 chr4D.!!$R1 928
2 TraesCS4D01G108800 chr4B 124740548 124744131 3583 False 1797.333333 4532 96.048000 26 3492 3 chr4B.!!$F1 3466
3 TraesCS4D01G108800 chr4B 473569543 473571692 2149 True 232.000000 425 89.447000 1394 2322 3 chr4B.!!$R1 928
4 TraesCS4D01G108800 chr4A 500899807 500903425 3618 False 2597.000000 4349 93.267500 1 3544 2 chr4A.!!$F2 3543
5 TraesCS4D01G108800 chr4A 67892084 67894297 2213 True 292.500000 431 87.488000 1394 2322 2 chr4A.!!$R1 928
6 TraesCS4D01G108800 chr1D 374471065 374474030 2965 True 279.000000 409 87.053667 1208 2322 3 chr1D.!!$R2 1114
7 TraesCS4D01G108800 chr1B 99753125 99755109 1984 True 435.500000 444 85.487500 1394 2323 2 chr1B.!!$R1 929
8 TraesCS4D01G108800 chr1B 499468678 499471527 2849 True 253.000000 414 85.291000 1208 2322 4 chr1B.!!$R2 1114
9 TraesCS4D01G108800 chr1A 60735590 60738771 3181 False 342.666667 440 84.587333 1390 2531 3 chr1A.!!$F1 1141
10 TraesCS4D01G108800 chr1A 474225743 474228844 3101 True 289.500000 403 85.077000 1208 2322 2 chr1A.!!$R1 1114
11 TraesCS4D01G108800 chr3D 476550594 476554049 3455 False 294.000000 392 85.442333 1208 2310 3 chr3D.!!$F1 1102
12 TraesCS4D01G108800 chr3B 635217462 635220874 3412 False 276.500000 392 84.228500 1208 2322 2 chr3B.!!$F1 1114
13 TraesCS4D01G108800 chr3A 620218011 620221447 3436 True 291.000000 381 85.228667 1208 2322 3 chr3A.!!$R1 1114

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
971 1026 0.326522 TGCCATAGCAGGGGAGAGAA 60.327 55.0 0.0 0.0 46.52 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2739 8778 0.871722 ACACACACACACACACACAC 59.128 50.0 0.0 0.0 0.0 3.82 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
95 99 7.195374 ACTATGAATGCCCTGTTCTAAGTTA 57.805 36.000 0.00 0.00 0.00 2.24
96 100 7.806180 ACTATGAATGCCCTGTTCTAAGTTAT 58.194 34.615 0.00 0.00 0.00 1.89
399 406 3.325135 ACATTTCCGGGTTAATTGCCAAA 59.675 39.130 0.00 0.00 0.00 3.28
434 445 4.028825 TCACCTTAAAGCCTAGTACTCCC 58.971 47.826 0.00 0.00 0.00 4.30
446 457 5.661458 CCTAGTACTCCCAACTACACATTG 58.339 45.833 0.00 0.00 0.00 2.82
453 468 2.159627 CCCAACTACACATTGCGAACTC 59.840 50.000 0.00 0.00 0.00 3.01
454 469 2.805671 CCAACTACACATTGCGAACTCA 59.194 45.455 0.00 0.00 0.00 3.41
455 470 3.436704 CCAACTACACATTGCGAACTCAT 59.563 43.478 0.00 0.00 0.00 2.90
456 471 4.436050 CCAACTACACATTGCGAACTCATC 60.436 45.833 0.00 0.00 0.00 2.92
494 509 3.873361 AGTGGACATCATATTTGTGCGAG 59.127 43.478 0.00 0.00 38.16 5.03
513 532 5.154222 GCGAGGAAAACCTTTTGATTGTAG 58.846 41.667 0.00 0.00 0.00 2.74
521 540 9.543018 GAAAACCTTTTGATTGTAGACTAATCG 57.457 33.333 0.00 0.00 37.36 3.34
563 582 1.275856 TCCAAGCAATGATGGGTTTGC 59.724 47.619 5.81 0.00 46.68 3.68
616 635 1.740025 GCCACTAAGCTCCAATCACAC 59.260 52.381 0.00 0.00 0.00 3.82
716 738 0.755686 ACATTCGCCCATCTCTCTCC 59.244 55.000 0.00 0.00 0.00 3.71
725 747 4.411927 GCCCATCTCTCTCCTACTATTCA 58.588 47.826 0.00 0.00 0.00 2.57
732 754 5.818336 TCTCTCTCCTACTATTCACTGAACG 59.182 44.000 0.00 0.00 0.00 3.95
779 806 3.165875 GGAAAAGGAAAAAGGGAGAGGG 58.834 50.000 0.00 0.00 0.00 4.30
799 826 4.599241 AGGGGAGAAGAGAAAGATCACAAA 59.401 41.667 0.00 0.00 0.00 2.83
949 993 5.944007 TGCTTGCTCGATCCTATATAGTACA 59.056 40.000 8.92 0.00 0.00 2.90
971 1026 0.326522 TGCCATAGCAGGGGAGAGAA 60.327 55.000 0.00 0.00 46.52 2.87
995 1050 2.418609 GGAGGAGCAGAGAAAGAAGAGC 60.419 54.545 0.00 0.00 0.00 4.09
1062 1117 2.685224 CGTGGAGATGGAGAGAGAAGGA 60.685 54.545 0.00 0.00 0.00 3.36
1803 3112 5.004821 CGCTGTCACTGTGTAATCATCTTAC 59.995 44.000 7.79 0.00 0.00 2.34
2629 8668 8.556213 AAAGATTATTCAACACGCCTAGTTAA 57.444 30.769 0.00 0.00 0.00 2.01
2630 8669 8.732746 AAGATTATTCAACACGCCTAGTTAAT 57.267 30.769 0.00 0.00 0.00 1.40
2631 8670 8.732746 AGATTATTCAACACGCCTAGTTAATT 57.267 30.769 0.00 0.00 0.00 1.40
2632 8671 9.826574 AGATTATTCAACACGCCTAGTTAATTA 57.173 29.630 0.00 0.00 0.00 1.40
2641 8680 6.592994 ACACGCCTAGTTAATTAGTTTCTTCC 59.407 38.462 4.51 0.00 0.00 3.46
2673 8712 9.567848 GAAGAAACTCTAGTTAATCTCTCACAG 57.432 37.037 0.00 0.00 37.25 3.66
2676 8715 8.871629 AAACTCTAGTTAATCTCTCACAGAGA 57.128 34.615 5.71 5.71 45.33 3.10
2677 8716 8.871629 AACTCTAGTTAATCTCTCACAGAGAA 57.128 34.615 7.31 0.00 44.32 2.87
2678 8717 9.303116 AACTCTAGTTAATCTCTCACAGAGAAA 57.697 33.333 7.31 0.00 44.32 2.52
2726 8765 4.768145 TGAATTTTGATCGTGTCGTGTTC 58.232 39.130 0.00 0.00 0.00 3.18
2739 8778 3.160545 GTCGTGTTCTGTTTTGTGTGTG 58.839 45.455 0.00 0.00 0.00 3.82
2783 8822 7.698550 GTGTGTGTGTGTCATGTTTGTAATTAA 59.301 33.333 0.00 0.00 0.00 1.40
2795 8851 9.345517 CATGTTTGTAATTAACAGTTCATGAGG 57.654 33.333 0.00 0.00 40.51 3.86
2886 8947 3.490078 CGCTCTGTTCTTCTCCCATCTAC 60.490 52.174 0.00 0.00 0.00 2.59
2917 8978 7.512130 TCACATGCAGTTCTCCTATATGATTT 58.488 34.615 0.00 0.00 0.00 2.17
2920 8981 5.624159 TGCAGTTCTCCTATATGATTTGGG 58.376 41.667 0.00 0.00 0.00 4.12
2921 8982 5.006386 GCAGTTCTCCTATATGATTTGGGG 58.994 45.833 0.00 0.00 0.00 4.96
2949 9011 9.638176 AAAAATCCATCTCTGAATTACTATGCT 57.362 29.630 0.00 0.00 0.00 3.79
2951 9013 9.717942 AAATCCATCTCTGAATTACTATGCTAC 57.282 33.333 0.00 0.00 0.00 3.58
2952 9014 8.663209 ATCCATCTCTGAATTACTATGCTACT 57.337 34.615 0.00 0.00 0.00 2.57
3108 9228 8.293867 TGTTTATTTAGCTTAATTGTTGCGAGT 58.706 29.630 2.87 0.00 0.00 4.18
3327 9620 2.175499 GGTGATGATCCATCCCCTTCAA 59.825 50.000 4.69 0.00 39.87 2.69
3417 9710 7.176690 ACCCACAGGACAACTAAATAATTTCAG 59.823 37.037 0.00 0.00 36.73 3.02
3496 9789 2.814336 GTCCCAGAAAATCAAAGCGAGT 59.186 45.455 0.00 0.00 0.00 4.18
3518 9811 6.075918 AGTATATATCTGTTTACACGTCGCG 58.924 40.000 0.00 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 45 8.028938 ACAAACTGGATGAAAATGTTATAGTGC 58.971 33.333 0.00 0.00 0.00 4.40
399 406 7.888546 AGGCTTTAAGGTGAATGTTGTAATAGT 59.111 33.333 0.00 0.00 0.00 2.12
434 445 4.152223 TGATGAGTTCGCAATGTGTAGTTG 59.848 41.667 0.00 0.00 0.00 3.16
446 457 9.554724 TTTAGTTAATTTGATTGATGAGTTCGC 57.445 29.630 0.00 0.00 0.00 4.70
494 509 9.841880 GATTAGTCTACAATCAAAAGGTTTTCC 57.158 33.333 0.00 0.00 35.08 3.13
513 532 3.442273 AGATAGCTAGCTGCCGATTAGTC 59.558 47.826 27.68 10.25 44.23 2.59
521 540 3.576550 AGGTTTAGAGATAGCTAGCTGCC 59.423 47.826 27.68 17.50 44.23 4.85
563 582 1.138036 CGCATGGCATGTCCTTGTG 59.862 57.895 26.94 16.53 41.92 3.33
616 635 1.600023 TTGCGTTGGTAACCAGAAGG 58.400 50.000 0.00 0.00 42.21 3.46
716 738 2.460918 CGGCCGTTCAGTGAATAGTAG 58.539 52.381 19.50 0.00 0.00 2.57
725 747 1.447838 CATACAGCGGCCGTTCAGT 60.448 57.895 28.70 18.30 0.00 3.41
732 754 0.391927 TTGGTACACATACAGCGGCC 60.392 55.000 0.00 0.00 39.29 6.13
779 806 7.382898 ACTAGTTTGTGATCTTTCTCTTCTCC 58.617 38.462 0.00 0.00 0.00 3.71
799 826 0.890996 GCACCAGCTGGCAAACTAGT 60.891 55.000 33.06 7.63 39.32 2.57
971 1026 2.917713 TCTTTCTCTGCTCCTCCTCT 57.082 50.000 0.00 0.00 0.00 3.69
995 1050 0.319383 CTTCTCCGATGCCATCCTCG 60.319 60.000 0.00 0.00 34.73 4.63
2387 8420 2.510906 GCGTACATCCCTGCCCAT 59.489 61.111 0.00 0.00 0.00 4.00
2393 8426 3.395702 TTGGCGGCGTACATCCCT 61.396 61.111 9.37 0.00 0.00 4.20
2619 8658 7.039882 TCAGGAAGAAACTAATTAACTAGGCG 58.960 38.462 0.00 0.00 0.00 5.52
2726 8765 2.979151 CACACACACACACACAAAACAG 59.021 45.455 0.00 0.00 0.00 3.16
2739 8778 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2783 8822 6.155221 ACATACATACAGTCCTCATGAACTGT 59.845 38.462 27.68 27.68 44.45 3.55
2886 8947 3.567164 AGGAGAACTGCATGTGAACTTTG 59.433 43.478 0.00 0.00 0.00 2.77
2949 9011 7.498239 ACAAGAGCAGATCAATACTACGTAGTA 59.502 37.037 31.69 31.69 45.11 1.82
2951 9013 6.730175 ACAAGAGCAGATCAATACTACGTAG 58.270 40.000 20.97 20.97 0.00 3.51
2952 9014 6.694877 ACAAGAGCAGATCAATACTACGTA 57.305 37.500 0.00 0.00 0.00 3.57
3039 9158 4.161001 AGCCAAACAATCTTTGATCATCCC 59.839 41.667 0.00 0.00 0.00 3.85
3049 9168 7.121020 ACAAAAACAATTGAGCCAAACAATCTT 59.879 29.630 13.59 0.00 37.04 2.40
3108 9228 2.371910 CATGCATGCCACATCACAAA 57.628 45.000 14.93 0.00 0.00 2.83
3327 9620 3.646162 TCACCATAGGATGTCCGCTTTAT 59.354 43.478 0.00 0.00 42.08 1.40
3417 9710 1.125021 CACACGTGATTCTTCGACAGC 59.875 52.381 25.01 0.00 0.00 4.40
3496 9789 4.847757 GCGCGACGTGTAAACAGATATATA 59.152 41.667 12.10 0.00 0.00 0.86
3518 9811 6.925211 TGCAAGTGAGAGTACCATATATAGC 58.075 40.000 0.00 0.00 0.00 2.97


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

AutoCloner maintained by Alex Coulton.