Multiple sequence alignment - TraesCS7A01G078700

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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 TraesCS7A01G078700 chr7A 100.000 2969 0 0 1 2969 43459371 43456403 0.000000e+00 5483.0
1 TraesCS7A01G078700 chr7A 97.785 1580 19 4 1185 2764 43439511 43437948 0.000000e+00 2710.0
2 TraesCS7A01G078700 chr7A 93.068 1154 35 10 1837 2969 43258423 43257294 0.000000e+00 1646.0
3 TraesCS7A01G078700 chr7A 88.160 1174 100 23 901 2047 45603315 45602154 0.000000e+00 1362.0
4 TraesCS7A01G078700 chr7A 87.500 1176 107 24 901 2047 45574615 45573451 0.000000e+00 1321.0
5 TraesCS7A01G078700 chr7A 87.415 1176 108 24 901 2047 45594305 45593141 0.000000e+00 1315.0
6 TraesCS7A01G078700 chr7A 80.541 1331 175 53 1658 2969 44877557 44876292 0.000000e+00 946.0
7 TraesCS7A01G078700 chr7A 87.883 652 52 16 1348 1978 45067710 45067065 0.000000e+00 741.0
8 TraesCS7A01G078700 chr7A 87.423 652 55 16 1348 1978 45020893 45020248 0.000000e+00 725.0
9 TraesCS7A01G078700 chr7A 97.619 252 5 1 901 1151 43439855 43439604 5.880000e-117 431.0
10 TraesCS7A01G078700 chr7A 85.450 378 33 11 1230 1585 45186500 45186123 1.000000e-99 374.0
11 TraesCS7A01G078700 chr7A 89.020 255 27 1 2716 2969 45015642 45015388 6.180000e-82 315.0
12 TraesCS7A01G078700 chr7A 84.024 338 29 15 1342 1658 44884948 44884615 4.810000e-78 302.0
13 TraesCS7A01G078700 chr7A 87.843 255 30 1 2716 2969 45062422 45062168 6.220000e-77 298.0
14 TraesCS7A01G078700 chr7A 78.348 448 62 20 2394 2817 287246501 287246065 1.060000e-64 257.0
15 TraesCS7A01G078700 chr7D 92.102 1760 86 29 1228 2969 43430357 43428633 0.000000e+00 2431.0
16 TraesCS7A01G078700 chr7D 88.848 816 55 16 1248 2046 43384815 43384019 0.000000e+00 970.0
17 TraesCS7A01G078700 chr7D 95.288 191 7 2 907 1096 43430548 43430359 4.810000e-78 302.0
18 TraesCS7A01G078700 chr7D 88.841 233 21 4 671 899 232325043 232325274 6.270000e-72 281.0
19 TraesCS7A01G078700 chr7D 86.466 133 11 3 1096 1227 447766828 447766702 3.990000e-29 139.0
20 TraesCS7A01G078700 chr4A 92.420 752 43 8 167 905 740855689 740854939 0.000000e+00 1061.0
21 TraesCS7A01G078700 chr4A 89.343 807 62 13 1259 2047 651986141 651985341 0.000000e+00 992.0
22 TraesCS7A01G078700 chr4A 90.025 401 34 5 1652 2047 651637816 651637417 5.670000e-142 514.0
23 TraesCS7A01G078700 chr4A 86.637 449 27 14 1228 1659 651638675 651638243 1.610000e-127 466.0
24 TraesCS7A01G078700 chr4A 95.217 230 11 0 1 230 740855892 740855663 6.050000e-97 364.0
25 TraesCS7A01G078700 chr4A 89.370 254 27 0 2716 2969 651984675 651984422 1.330000e-83 320.0
26 TraesCS7A01G078700 chr4A 89.316 234 21 3 674 903 45345685 45345452 1.040000e-74 291.0
27 TraesCS7A01G078700 chr4A 85.507 138 12 6 1095 1231 556761756 556761626 1.440000e-28 137.0
28 TraesCS7A01G078700 chr4A 78.710 155 19 14 2360 2505 708031434 708031583 1.130000e-14 91.6
29 TraesCS7A01G078700 chr5B 91.523 696 37 3 1 674 179222803 179222108 0.000000e+00 939.0
30 TraesCS7A01G078700 chr5B 81.602 462 75 10 2513 2969 661315347 661314891 1.000000e-99 374.0
31 TraesCS7A01G078700 chr5B 94.273 227 13 0 674 900 179221911 179221685 6.090000e-92 348.0
32 TraesCS7A01G078700 chr5B 89.744 234 20 3 674 903 555192823 555192590 2.240000e-76 296.0
33 TraesCS7A01G078700 chr5B 88.034 234 23 5 674 903 552265753 552265521 3.770000e-69 272.0
34 TraesCS7A01G078700 chr5B 87.712 236 23 5 671 901 387760341 387760575 1.360000e-68 270.0
35 TraesCS7A01G078700 chr5B 84.247 146 14 5 1088 1230 581144378 581144517 1.860000e-27 134.0
36 TraesCS7A01G078700 chr5B 76.978 139 22 10 2364 2495 220707831 220707696 1.480000e-08 71.3
37 TraesCS7A01G078700 chr6B 80.624 929 110 37 1 902 520107489 520106604 0.000000e+00 654.0
38 TraesCS7A01G078700 chr3B 80.165 726 111 18 2245 2965 16128976 16128279 2.040000e-141 512.0
39 TraesCS7A01G078700 chr2B 81.013 474 74 15 2503 2969 67272752 67273216 2.180000e-96 363.0
40 TraesCS7A01G078700 chr2B 83.221 149 19 5 1095 1238 434723597 434723744 6.680000e-27 132.0
41 TraesCS7A01G078700 chr2B 85.057 87 5 7 2361 2443 787938473 787938391 6.820000e-12 82.4
42 TraesCS7A01G078700 chr3A 81.104 471 72 14 2503 2969 37645660 37646117 7.820000e-96 361.0
43 TraesCS7A01G078700 chr7B 89.873 237 20 3 671 903 673660579 673660815 4.810000e-78 302.0
44 TraesCS7A01G078700 chr7B 83.784 148 17 5 1092 1238 678632488 678632347 1.860000e-27 134.0
45 TraesCS7A01G078700 chr4B 77.938 485 70 24 2356 2815 554022648 554022176 4.880000e-68 268.0
46 TraesCS7A01G078700 chr4B 75.330 454 74 23 22 459 47648906 47648475 1.820000e-42 183.0
47 TraesCS7A01G078700 chr4B 81.461 178 31 2 497 674 47648185 47648010 8.580000e-31 145.0
48 TraesCS7A01G078700 chr6D 76.829 492 72 27 2356 2817 45488781 45489260 3.820000e-59 239.0
49 TraesCS7A01G078700 chr3D 85.926 135 12 3 1094 1227 327739364 327739492 1.440000e-28 137.0
50 TraesCS7A01G078700 chr3D 85.075 134 18 2 1096 1227 177243835 177243968 5.160000e-28 135.0
51 TraesCS7A01G078700 chr2A 84.138 145 15 6 1093 1235 628066438 628066300 1.860000e-27 134.0
52 TraesCS7A01G078700 chr2D 84.028 144 15 6 1093 1235 591951779 591951915 6.680000e-27 132.0
53 TraesCS7A01G078700 chr4D 79.130 115 16 8 2375 2486 390914772 390914663 4.110000e-09 73.1
54 TraesCS7A01G078700 chr4D 97.222 36 0 1 2368 2403 90844271 90844305 3.200000e-05 60.2


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 TraesCS7A01G078700 chr7A 43456403 43459371 2968 True 5483.0 5483 100.0000 1 2969 1 chr7A.!!$R2 2968
1 TraesCS7A01G078700 chr7A 43257294 43258423 1129 True 1646.0 1646 93.0680 1837 2969 1 chr7A.!!$R1 1132
2 TraesCS7A01G078700 chr7A 43437948 43439855 1907 True 1570.5 2710 97.7020 901 2764 2 chr7A.!!$R14 1863
3 TraesCS7A01G078700 chr7A 45602154 45603315 1161 True 1362.0 1362 88.1600 901 2047 1 chr7A.!!$R12 1146
4 TraesCS7A01G078700 chr7A 45573451 45574615 1164 True 1321.0 1321 87.5000 901 2047 1 chr7A.!!$R10 1146
5 TraesCS7A01G078700 chr7A 45593141 45594305 1164 True 1315.0 1315 87.4150 901 2047 1 chr7A.!!$R11 1146
6 TraesCS7A01G078700 chr7A 44876292 44877557 1265 True 946.0 946 80.5410 1658 2969 1 chr7A.!!$R3 1311
7 TraesCS7A01G078700 chr7A 45067065 45067710 645 True 741.0 741 87.8830 1348 1978 1 chr7A.!!$R8 630
8 TraesCS7A01G078700 chr7A 45020248 45020893 645 True 725.0 725 87.4230 1348 1978 1 chr7A.!!$R6 630
9 TraesCS7A01G078700 chr7D 43428633 43430548 1915 True 1366.5 2431 93.6950 907 2969 2 chr7D.!!$R3 2062
10 TraesCS7A01G078700 chr7D 43384019 43384815 796 True 970.0 970 88.8480 1248 2046 1 chr7D.!!$R1 798
11 TraesCS7A01G078700 chr4A 740854939 740855892 953 True 712.5 1061 93.8185 1 905 2 chr4A.!!$R5 904
12 TraesCS7A01G078700 chr4A 651984422 651986141 1719 True 656.0 992 89.3565 1259 2969 2 chr4A.!!$R4 1710
13 TraesCS7A01G078700 chr4A 651637417 651638675 1258 True 490.0 514 88.3310 1228 2047 2 chr4A.!!$R3 819
14 TraesCS7A01G078700 chr5B 179221685 179222803 1118 True 643.5 939 92.8980 1 900 2 chr5B.!!$R5 899
15 TraesCS7A01G078700 chr6B 520106604 520107489 885 True 654.0 654 80.6240 1 902 1 chr6B.!!$R1 901
16 TraesCS7A01G078700 chr3B 16128279 16128976 697 True 512.0 512 80.1650 2245 2965 1 chr3B.!!$R1 720

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
151 157 1.153989 CCTCTATCCCTGCTCCGGA 59.846 63.158 2.93 2.93 0.0 5.14 F
509 555 2.036992 CAGAGACCAGAGTTGCTTGAGT 59.963 50.000 0.00 0.00 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1810 1.336887 GCGAAGGTTACTGACTGCTGA 60.337 52.381 0.0 0.0 0.0 4.26 R
2102 2975 2.093658 ACGTCGGCTCTTTGGTTATCAT 60.094 45.455 0.0 0.0 0.0 2.45 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
77 78 2.544698 GCCTATCTCGTCCGTCGCT 61.545 63.158 0.00 0.00 39.67 4.93
86 87 1.158484 CGTCCGTCGCTCATCTCCTA 61.158 60.000 0.00 0.00 0.00 2.94
151 157 1.153989 CCTCTATCCCTGCTCCGGA 59.846 63.158 2.93 2.93 0.00 5.14
270 315 3.360249 AAAACATGTCTTGCTGCAGTC 57.640 42.857 16.64 8.39 0.00 3.51
327 372 7.147958 TGATCTGGATGTTATCAATTGGGTA 57.852 36.000 5.42 0.00 0.00 3.69
328 373 7.226441 TGATCTGGATGTTATCAATTGGGTAG 58.774 38.462 5.42 0.00 0.00 3.18
353 398 6.237915 GCTATAAATTGTTTGCTGGCATCAAC 60.238 38.462 2.77 8.71 0.00 3.18
362 407 4.335400 TGCTGGCATCAACTCGAATATA 57.665 40.909 0.00 0.00 0.00 0.86
371 416 9.760660 GGCATCAACTCGAATATATATTTTGTC 57.239 33.333 9.33 0.00 0.00 3.18
486 531 5.319453 TGCTTCAGAAGGACATTTCTTCAT 58.681 37.500 12.30 0.00 42.09 2.57
487 532 5.413833 TGCTTCAGAAGGACATTTCTTCATC 59.586 40.000 12.30 0.00 42.09 2.92
488 533 5.163673 GCTTCAGAAGGACATTTCTTCATCC 60.164 44.000 12.30 0.00 42.09 3.51
489 534 5.503634 TCAGAAGGACATTTCTTCATCCA 57.496 39.130 6.60 0.00 42.09 3.41
490 535 5.494724 TCAGAAGGACATTTCTTCATCCAG 58.505 41.667 6.60 0.00 42.09 3.86
492 537 5.585445 CAGAAGGACATTTCTTCATCCAGAG 59.415 44.000 6.60 0.00 42.09 3.35
494 539 5.096443 AGGACATTTCTTCATCCAGAGAC 57.904 43.478 0.00 0.00 33.33 3.36
509 555 2.036992 CAGAGACCAGAGTTGCTTGAGT 59.963 50.000 0.00 0.00 0.00 3.41
558 604 9.647797 AGGATTTTTCTTTAGTTTTTGTTCGTT 57.352 25.926 0.00 0.00 0.00 3.85
572 618 8.950961 GTTTTTGTTCGTTTGTTATAGAAGACC 58.049 33.333 0.00 0.00 0.00 3.85
780 1035 3.668821 ACCTCACATAGATTCCATGGGA 58.331 45.455 13.02 2.34 34.67 4.37
829 1084 7.063456 CGAATTCGTATTCATGTCCATTACAC 58.937 38.462 19.67 0.00 40.17 2.90
1183 1498 8.127327 TCTTGTTTTAGATTCGTCTAGATACGG 58.873 37.037 0.00 0.00 43.05 4.02
1216 1531 7.611855 ACGAATCTAAGACAAGAATTTTGGGAT 59.388 33.333 0.00 0.00 0.00 3.85
1217 1532 9.109393 CGAATCTAAGACAAGAATTTTGGGATA 57.891 33.333 5.68 0.00 0.00 2.59
1464 1810 6.317140 CACAACCATTAGCTGAATACACATCT 59.683 38.462 0.00 0.00 0.00 2.90
2102 2975 3.704566 ACATAAGGACGGCTGAGATTACA 59.295 43.478 0.00 0.00 0.00 2.41
2508 3410 7.969536 TGGTGAACTTTGTTTTTCAAAATCA 57.030 28.000 0.00 0.00 44.08 2.57
2732 3637 2.992124 TGGTTGAACCACGAAGAAGA 57.008 45.000 14.05 0.00 44.79 2.87
2803 3708 2.445155 GGCCCCATGAAAGGTGGT 59.555 61.111 0.00 0.00 34.87 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.722034 GGCCATGGAGTAGGAGATGA 58.278 55.000 18.40 0.00 0.00 2.92
151 157 2.038490 GAGGGGGTACGGTGGACT 59.962 66.667 0.00 0.00 0.00 3.85
179 185 2.277072 CGGCAGAGGAGGAGAGGA 59.723 66.667 0.00 0.00 0.00 3.71
270 315 9.029243 CAATAAAAGAGACATAGCAGTACTCAG 57.971 37.037 0.00 0.00 0.00 3.35
327 372 5.127519 TGATGCCAGCAAACAATTTATAGCT 59.872 36.000 0.00 0.00 0.00 3.32
328 373 5.350633 TGATGCCAGCAAACAATTTATAGC 58.649 37.500 0.00 0.00 0.00 2.97
353 398 8.223769 GGTGCTGTGACAAAATATATATTCGAG 58.776 37.037 8.42 4.73 0.00 4.04
362 407 5.243507 TCATGTTGGTGCTGTGACAAAATAT 59.756 36.000 0.00 0.00 0.00 1.28
371 416 1.265095 GACTGTCATGTTGGTGCTGTG 59.735 52.381 2.24 0.00 0.00 3.66
486 531 1.345741 CAAGCAACTCTGGTCTCTGGA 59.654 52.381 0.00 0.00 31.28 3.86
487 532 1.345741 TCAAGCAACTCTGGTCTCTGG 59.654 52.381 0.00 0.00 31.28 3.86
488 533 2.036992 ACTCAAGCAACTCTGGTCTCTG 59.963 50.000 0.00 0.00 31.28 3.35
489 534 2.324541 ACTCAAGCAACTCTGGTCTCT 58.675 47.619 0.00 0.00 31.28 3.10
490 535 2.805099 CAACTCAAGCAACTCTGGTCTC 59.195 50.000 0.00 0.00 31.28 3.36
492 537 1.265365 GCAACTCAAGCAACTCTGGTC 59.735 52.381 0.00 0.00 31.28 4.02
494 539 1.311859 TGCAACTCAAGCAACTCTGG 58.688 50.000 0.00 0.00 39.39 3.86
572 618 7.525688 TCTGTGCTAAACTGAATAATTCTCG 57.474 36.000 0.00 0.00 34.15 4.04
700 955 5.105351 GGGTTTGCATAGTGCCTTTTCTATT 60.105 40.000 0.00 0.00 44.23 1.73
704 959 2.298729 TGGGTTTGCATAGTGCCTTTTC 59.701 45.455 0.00 0.00 44.23 2.29
709 964 0.527565 CTGTGGGTTTGCATAGTGCC 59.472 55.000 0.00 0.00 44.23 5.01
780 1035 5.471556 TTGTTTGGATGCTCATGAATTGT 57.528 34.783 0.00 0.00 0.00 2.71
829 1084 4.157656 TCAATACCAATTCGGCAAGGAAAG 59.842 41.667 0.00 0.00 39.03 2.62
1157 1413 8.127327 CCGTATCTAGACGAATCTAAAACAAGA 58.873 37.037 5.60 0.00 45.82 3.02
1159 1415 7.988737 TCCGTATCTAGACGAATCTAAAACAA 58.011 34.615 5.60 0.00 45.82 2.83
1161 1417 8.505625 AGATCCGTATCTAGACGAATCTAAAAC 58.494 37.037 4.23 0.00 45.82 2.43
1162 1418 8.618702 AGATCCGTATCTAGACGAATCTAAAA 57.381 34.615 4.23 0.00 45.82 1.52
1175 1431 8.747471 TCTTAGATTCGTCTAGATCCGTATCTA 58.253 37.037 19.32 19.32 42.61 1.98
1176 1432 7.546667 GTCTTAGATTCGTCTAGATCCGTATCT 59.453 40.741 20.71 20.71 44.80 1.98
1177 1433 7.331440 TGTCTTAGATTCGTCTAGATCCGTATC 59.669 40.741 11.86 11.86 32.96 2.24
1180 1495 5.366460 TGTCTTAGATTCGTCTAGATCCGT 58.634 41.667 0.00 0.00 0.00 4.69
1183 1498 9.959749 AATTCTTGTCTTAGATTCGTCTAGATC 57.040 33.333 0.00 0.00 0.00 2.75
1302 1631 4.439563 GGTGGAATGTAATTAAGGGTTGCG 60.440 45.833 0.00 0.00 36.07 4.85
1464 1810 1.336887 GCGAAGGTTACTGACTGCTGA 60.337 52.381 0.00 0.00 0.00 4.26
2102 2975 2.093658 ACGTCGGCTCTTTGGTTATCAT 60.094 45.455 0.00 0.00 0.00 2.45
2732 3637 0.392336 GAGGAGAATGCGCCTGATCT 59.608 55.000 0.00 2.60 45.01 2.75


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

AutoCloner maintained by Alex Coulton.