Multiple sequence alignment - TraesCS2A01G236100

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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 TraesCS2A01G236100 chr2A 100.000 2372 0 0 1 2372 300946298 300948669 0.000000e+00 4381.0
1 TraesCS2A01G236100 chr2A 95.125 2359 114 1 1 2358 301198214 301200572 0.000000e+00 3718.0
2 TraesCS2A01G236100 chr2A 93.600 1672 104 3 1 1671 300954245 300955914 0.000000e+00 2492.0
3 TraesCS2A01G236100 chr2A 90.981 887 41 8 525 1386 654611163 654612035 0.000000e+00 1158.0
4 TraesCS2A01G236100 chr2A 94.282 682 29 2 1689 2361 669909869 669909189 0.000000e+00 1035.0
5 TraesCS2A01G236100 chr2A 94.410 644 34 2 1730 2372 324320803 324320161 0.000000e+00 989.0
6 TraesCS2A01G236100 chr2A 95.053 566 26 2 819 1383 654603390 654603954 0.000000e+00 889.0
7 TraesCS2A01G236100 chr2A 94.164 377 21 1 1 376 352177239 352177615 7.350000e-160 573.0
8 TraesCS2A01G236100 chr2A 93.634 377 21 2 1 376 352169443 352169817 5.730000e-156 560.0
9 TraesCS2A01G236100 chr2A 81.760 625 93 17 3 616 384873267 384872653 9.790000e-139 503.0
10 TraesCS2A01G236100 chr2A 94.138 290 16 1 621 909 691906141 691905852 7.780000e-120 440.0
11 TraesCS2A01G236100 chr2A 93.793 290 17 1 621 909 691898180 691897891 3.620000e-118 435.0
12 TraesCS2A01G236100 chr2A 88.344 326 14 5 525 826 654602605 654602930 1.040000e-98 370.0
13 TraesCS2A01G236100 chr2A 92.017 238 19 0 618 855 141245636 141245873 3.780000e-88 335.0
14 TraesCS2A01G236100 chr2A 90.164 244 24 0 612 855 251314451 251314694 3.800000e-83 318.0
15 TraesCS2A01G236100 chr2A 89.020 255 27 1 615 869 469142052 469142305 4.920000e-82 315.0
16 TraesCS2A01G236100 chr2A 88.660 97 3 7 1502 1593 570205162 570205069 6.930000e-21 111.0
17 TraesCS2A01G236100 chr2A 100.000 50 0 0 1625 1674 245871491 245871442 2.510000e-15 93.5
18 TraesCS2A01G236100 chr2A 90.411 73 3 3 1497 1569 460831984 460832052 2.510000e-15 93.5
19 TraesCS2A01G236100 chr3A 86.835 1428 133 24 1 1386 667921255 667919841 0.000000e+00 1544.0
20 TraesCS2A01G236100 chr3A 86.345 1428 130 28 1 1386 667909358 667907954 0.000000e+00 1496.0
21 TraesCS2A01G236100 chr3A 94.160 839 45 4 1537 2372 390613446 390614283 0.000000e+00 1275.0
22 TraesCS2A01G236100 chr3A 94.565 644 32 3 1730 2372 594367699 594368340 0.000000e+00 992.0
23 TraesCS2A01G236100 chr3A 91.160 362 24 6 1 356 390611920 390612279 3.540000e-133 484.0
24 TraesCS2A01G236100 chr3A 89.197 361 31 6 2 356 390633120 390633478 6.020000e-121 444.0
25 TraesCS2A01G236100 chr5A 95.674 809 31 4 1567 2372 317387454 317388261 0.000000e+00 1297.0
26 TraesCS2A01G236100 chr5A 93.640 849 42 11 1512 2355 317395377 317396218 0.000000e+00 1258.0
27 TraesCS2A01G236100 chr5A 94.301 737 33 9 1628 2361 193958727 193957997 0.000000e+00 1120.0
28 TraesCS2A01G236100 chr5A 91.747 727 43 8 1645 2358 275861624 275860902 0.000000e+00 994.0
29 TraesCS2A01G236100 chr5A 85.714 392 43 9 3 388 636362180 636362564 3.670000e-108 401.0
30 TraesCS2A01G236100 chr5A 84.146 82 5 6 1572 1653 547830156 547830083 3.270000e-09 73.1
31 TraesCS2A01G236100 chr6A 92.119 774 56 5 612 1383 328976022 328976792 0.000000e+00 1086.0
32 TraesCS2A01G236100 chr6A 91.656 767 60 4 619 1383 328990001 328990765 0.000000e+00 1059.0
33 TraesCS2A01G236100 chr6A 91.566 83 7 0 1385 1467 51210387 51210469 5.360000e-22 115.0
34 TraesCS2A01G236100 chr6A 91.176 68 3 1 1502 1569 467883981 467884045 3.250000e-14 89.8
35 TraesCS2A01G236100 chr6A 86.885 61 6 2 1373 1431 411636125 411636185 1.520000e-07 67.6
36 TraesCS2A01G236100 chr6A 97.143 35 1 0 1397 1431 411632959 411632993 2.550000e-05 60.2
37 TraesCS2A01G236100 chr7A 91.602 774 50 7 612 1383 378456682 378457442 0.000000e+00 1055.0
38 TraesCS2A01G236100 chr7A 82.399 892 106 30 1 855 190563870 190562993 0.000000e+00 730.0
39 TraesCS2A01G236100 chr7A 82.893 719 77 23 174 855 350852291 350851582 2.610000e-169 604.0
40 TraesCS2A01G236100 chr7A 85.260 597 59 9 286 855 350835502 350834908 2.630000e-164 588.0
41 TraesCS2A01G236100 chr7A 84.334 383 49 9 1 376 481282041 481282419 4.820000e-97 364.0
42 TraesCS2A01G236100 chr7A 90.411 73 4 2 1503 1575 286200964 286200895 2.510000e-15 93.5
43 TraesCS2A01G236100 chr4D 95.541 628 26 2 1730 2356 117373343 117372717 0.000000e+00 1003.0
44 TraesCS2A01G236100 chr4A 80.405 939 100 46 1 869 171988307 171987383 2.570000e-179 638.0
45 TraesCS2A01G236100 chr1A 86.313 358 38 8 1 352 458577082 458577434 1.720000e-101 379.0
46 TraesCS2A01G236100 chr1A 97.059 68 2 0 1667 1734 51491652 51491719 5.360000e-22 115.0
47 TraesCS2A01G236100 chr1A 90.123 81 7 1 1667 1746 368460298 368460378 1.160000e-18 104.0
48 TraesCS2A01G236100 chr1A 87.778 90 5 5 1653 1739 173779812 173779726 1.500000e-17 100.0
49 TraesCS2A01G236100 chr1A 89.041 73 6 2 1497 1569 474599624 474599694 3.250000e-14 89.8
50 TraesCS2A01G236100 chr1A 89.041 73 5 2 1503 1575 116630716 116630647 1.170000e-13 87.9
51 TraesCS2A01G236100 chr4B 92.727 55 2 2 1385 1439 311421082 311421030 7.030000e-11 78.7
52 TraesCS2A01G236100 chr4B 85.246 61 7 2 1373 1431 311567430 311567370 7.080000e-06 62.1
53 TraesCS2A01G236100 chr3D 93.333 45 3 0 1387 1431 254200119 254200075 1.520000e-07 67.6
54 TraesCS2A01G236100 chr2D 94.872 39 2 0 1393 1431 226894753 226894791 7.080000e-06 62.1


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 TraesCS2A01G236100 chr2A 300946298 300948669 2371 False 4381.0 4381 100.0000 1 2372 1 chr2A.!!$F3 2371
1 TraesCS2A01G236100 chr2A 301198214 301200572 2358 False 3718.0 3718 95.1250 1 2358 1 chr2A.!!$F5 2357
2 TraesCS2A01G236100 chr2A 300954245 300955914 1669 False 2492.0 2492 93.6000 1 1671 1 chr2A.!!$F4 1670
3 TraesCS2A01G236100 chr2A 654611163 654612035 872 False 1158.0 1158 90.9810 525 1386 1 chr2A.!!$F10 861
4 TraesCS2A01G236100 chr2A 669909189 669909869 680 True 1035.0 1035 94.2820 1689 2361 1 chr2A.!!$R5 672
5 TraesCS2A01G236100 chr2A 324320161 324320803 642 True 989.0 989 94.4100 1730 2372 1 chr2A.!!$R2 642
6 TraesCS2A01G236100 chr2A 654602605 654603954 1349 False 629.5 889 91.6985 525 1383 2 chr2A.!!$F11 858
7 TraesCS2A01G236100 chr2A 384872653 384873267 614 True 503.0 503 81.7600 3 616 1 chr2A.!!$R3 613
8 TraesCS2A01G236100 chr3A 667919841 667921255 1414 True 1544.0 1544 86.8350 1 1386 1 chr3A.!!$R2 1385
9 TraesCS2A01G236100 chr3A 667907954 667909358 1404 True 1496.0 1496 86.3450 1 1386 1 chr3A.!!$R1 1385
10 TraesCS2A01G236100 chr3A 594367699 594368340 641 False 992.0 992 94.5650 1730 2372 1 chr3A.!!$F2 642
11 TraesCS2A01G236100 chr3A 390611920 390614283 2363 False 879.5 1275 92.6600 1 2372 2 chr3A.!!$F3 2371
12 TraesCS2A01G236100 chr5A 317387454 317388261 807 False 1297.0 1297 95.6740 1567 2372 1 chr5A.!!$F1 805
13 TraesCS2A01G236100 chr5A 317395377 317396218 841 False 1258.0 1258 93.6400 1512 2355 1 chr5A.!!$F2 843
14 TraesCS2A01G236100 chr5A 193957997 193958727 730 True 1120.0 1120 94.3010 1628 2361 1 chr5A.!!$R1 733
15 TraesCS2A01G236100 chr5A 275860902 275861624 722 True 994.0 994 91.7470 1645 2358 1 chr5A.!!$R2 713
16 TraesCS2A01G236100 chr6A 328976022 328976792 770 False 1086.0 1086 92.1190 612 1383 1 chr6A.!!$F2 771
17 TraesCS2A01G236100 chr6A 328990001 328990765 764 False 1059.0 1059 91.6560 619 1383 1 chr6A.!!$F3 764
18 TraesCS2A01G236100 chr7A 378456682 378457442 760 False 1055.0 1055 91.6020 612 1383 1 chr7A.!!$F1 771
19 TraesCS2A01G236100 chr7A 190562993 190563870 877 True 730.0 730 82.3990 1 855 1 chr7A.!!$R1 854
20 TraesCS2A01G236100 chr7A 350851582 350852291 709 True 604.0 604 82.8930 174 855 1 chr7A.!!$R4 681
21 TraesCS2A01G236100 chr7A 350834908 350835502 594 True 588.0 588 85.2600 286 855 1 chr7A.!!$R3 569
22 TraesCS2A01G236100 chr4D 117372717 117373343 626 True 1003.0 1003 95.5410 1730 2356 1 chr4D.!!$R1 626
23 TraesCS2A01G236100 chr4A 171987383 171988307 924 True 638.0 638 80.4050 1 869 1 chr4A.!!$R1 868

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
517 601 0.529992 GAGCGGTAGTGGTACATGGC 60.53 60.0 0.0 0.0 44.52 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 2551 0.310543 CTCTCTTCGATCTCCCAGCG 59.689 60.0 0.0 0.0 0.0 5.18 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
58 61 6.278363 ACATGAGCATAAAATGGAGCATTTC 58.722 36.000 0.00 0.00 42.32 2.17
69 72 1.372582 GAGCATTTCTCATCGTGGCA 58.627 50.000 0.00 0.00 41.51 4.92
141 176 2.282701 CGGTTCCGGAAACTCGATTA 57.717 50.000 28.82 0.00 38.02 1.75
149 184 3.194861 CGGAAACTCGATTAAGATGCCA 58.805 45.455 0.00 0.00 0.00 4.92
197 232 1.060937 GTCATGCGATGAACGGTGC 59.939 57.895 0.00 0.00 41.69 5.01
378 461 2.030540 CCAAGGTAGTTCGAGTTCGTCA 60.031 50.000 1.07 0.00 40.80 4.35
382 465 2.227388 GGTAGTTCGAGTTCGTCAAGGA 59.773 50.000 1.07 0.00 40.80 3.36
426 509 2.932614 GCGACGGTAGTAGAAGTAGTGA 59.067 50.000 0.00 0.00 0.00 3.41
434 518 7.089538 CGGTAGTAGAAGTAGTGATCTATCGA 58.910 42.308 0.00 0.00 31.29 3.59
440 524 6.177610 AGAAGTAGTGATCTATCGATCCTCC 58.822 44.000 0.00 0.00 44.40 4.30
445 529 2.762887 TGATCTATCGATCCTCCATGGC 59.237 50.000 6.96 0.00 44.40 4.40
472 556 1.534595 AGTAGTGGTTCACGAGTCGAC 59.465 52.381 21.50 7.70 39.64 4.20
517 601 0.529992 GAGCGGTAGTGGTACATGGC 60.530 60.000 0.00 0.00 44.52 4.40
650 862 4.160329 AGAGGTACTTGATGACTCCAACA 58.840 43.478 0.00 0.00 41.55 3.33
656 868 5.233083 ACTTGATGACTCCAACATCTTCA 57.767 39.130 0.00 0.00 42.89 3.02
709 947 1.614241 AACTTGACGGATCCGAGGGG 61.614 60.000 39.55 25.56 42.83 4.79
738 1019 1.887854 TCGTGGTACTTGTTGATCCGA 59.112 47.619 0.00 0.00 0.00 4.55
765 1046 2.623889 GAGACATACTAGGCATCGGTGT 59.376 50.000 0.00 0.00 0.00 4.16
1177 2167 2.661537 CAAGGTCGTGTCGCTGCA 60.662 61.111 0.00 0.00 0.00 4.41
1344 2388 2.582498 CGCGGGATCTGGTTCGAC 60.582 66.667 0.00 0.00 0.00 4.20
1416 2460 4.882396 GGCGAGGCGAGGAGAAGC 62.882 72.222 0.00 0.00 0.00 3.86
1465 2509 1.834378 CTAGGCTGGCAGATCGGGA 60.834 63.158 20.86 0.24 0.00 5.14
1475 2519 1.152735 AGATCGGGAGCGCTTCCTA 60.153 57.895 31.76 22.77 45.98 2.94
1507 2551 4.612536 GTGTGCGTGTGTGGCAGC 62.613 66.667 0.00 0.00 41.83 5.25
1595 2640 4.493747 CGCGAGGGGACGAGGAAC 62.494 72.222 0.00 0.00 35.09 3.62
1623 2668 0.623911 AGGAGGAGGTAGGTCGAGGA 60.624 60.000 0.00 0.00 0.00 3.71
1786 2842 1.699083 CCAACAAAAGGGAAAGGCCAT 59.301 47.619 5.01 0.00 38.95 4.40
1879 2936 9.752228 ATAAAATTGGTTTGGGCATTTTTAGAT 57.248 25.926 0.00 0.00 32.42 1.98
2061 3118 4.341366 CTTGCACCAAGGAAGGAAAAAT 57.659 40.909 0.00 0.00 41.51 1.82
2084 3141 4.228237 AGTAATGGGGGAGGTGATGATA 57.772 45.455 0.00 0.00 0.00 2.15
2140 3197 2.179589 CATAATGCAAGCACAACGAGC 58.820 47.619 0.00 0.00 0.00 5.03
2145 3202 1.571460 CAAGCACAACGAGCTGGAC 59.429 57.895 1.44 0.00 42.53 4.02
2255 3316 4.241590 TGACCATGATGCAAGAAACAAC 57.758 40.909 0.00 0.00 0.00 3.32
2361 3422 1.598685 GGTCTCGGGGCGTCAAAAA 60.599 57.895 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 176 3.565307 TGTTCTTTTCCACTGGCATCTT 58.435 40.909 0.00 0.00 0.00 2.40
149 184 2.427095 GCCACACTTGTTCTTTTCCACT 59.573 45.455 0.00 0.00 0.00 4.00
378 461 5.578157 TGCCTACTTCCTTTACTTTCCTT 57.422 39.130 0.00 0.00 0.00 3.36
382 465 4.941873 CGGAATGCCTACTTCCTTTACTTT 59.058 41.667 0.00 0.00 40.07 2.66
434 518 4.506076 TCCACTGCCATGGAGGAT 57.494 55.556 18.40 0.00 44.14 3.24
440 524 1.003580 ACCACTACTTCCACTGCCATG 59.996 52.381 0.00 0.00 0.00 3.66
445 529 2.035449 TCGTGAACCACTACTTCCACTG 59.965 50.000 0.00 0.00 31.34 3.66
472 556 2.346803 ACATGAACGACCATTTCCTCG 58.653 47.619 0.00 0.00 35.96 4.63
497 581 0.248907 CCATGTACCACTACCGCTCG 60.249 60.000 0.00 0.00 0.00 5.03
517 601 0.652592 GATGCCAAGTTCGATGACGG 59.347 55.000 0.00 0.00 40.21 4.79
650 862 0.683504 ACTACCGTCGCCCTGAAGAT 60.684 55.000 0.00 0.00 0.00 2.40
656 868 2.048603 GTACCACTACCGTCGCCCT 61.049 63.158 0.00 0.00 0.00 5.19
683 895 2.033049 CGGATCCGTCAAGTTCGTCTAT 59.967 50.000 26.35 0.00 34.35 1.98
709 947 0.595095 AAGTACCACGACGTCTGGAC 59.405 55.000 29.15 22.89 32.55 4.02
738 1019 4.277174 CGATGCCTAGTATGTCTCAAGACT 59.723 45.833 11.23 0.64 44.99 3.24
765 1046 0.319555 CACGCCGAGTTCCTCAAAGA 60.320 55.000 0.00 0.00 0.00 2.52
1011 2001 1.306997 CCCTGGCCCTACTTCTCCA 60.307 63.158 0.00 0.00 0.00 3.86
1064 2054 4.430765 CAAGTACCTCGCCGCCGT 62.431 66.667 0.00 0.00 35.54 5.68
1177 2167 2.125512 CCGCCAGCTACGCTCTTT 60.126 61.111 2.88 0.00 36.40 2.52
1333 2376 2.107041 TTGCACCGGTCGAACCAGAT 62.107 55.000 2.59 0.00 38.47 2.90
1416 2460 3.775654 GCACCTCCCCGTCCTCTG 61.776 72.222 0.00 0.00 0.00 3.35
1448 2492 1.834378 CTCCCGATCTGCCAGCCTA 60.834 63.158 0.00 0.00 0.00 3.93
1457 2501 1.152735 TAGGAAGCGCTCCCGATCT 60.153 57.895 12.06 4.90 46.81 2.75
1468 2512 0.384669 ATACACCGTCGCTAGGAAGC 59.615 55.000 0.00 0.00 45.86 3.86
1475 2519 2.506217 CACGCATACACCGTCGCT 60.506 61.111 0.00 0.00 36.69 4.93
1507 2551 0.310543 CTCTCTTCGATCTCCCAGCG 59.689 60.000 0.00 0.00 0.00 5.18
1595 2640 0.397187 TACCTCCTCCTCTCGATCCG 59.603 60.000 0.00 0.00 0.00 4.18
1623 2668 0.919710 GCACCCCTTCTCAACCCTAT 59.080 55.000 0.00 0.00 0.00 2.57
1915 2972 5.129485 TGGTTAGGTTCAAAAATGCCTCAAA 59.871 36.000 0.00 0.00 32.90 2.69
1993 3050 9.681692 TTAATGTTCAATCTTTGTCAATGAGTG 57.318 29.630 17.99 17.99 33.56 3.51
2061 3118 4.015617 TCATCACCTCCCCCATTACTTA 57.984 45.455 0.00 0.00 0.00 2.24
2084 3141 1.002315 GGCTTTGCATTTGACCCATGT 59.998 47.619 0.00 0.00 0.00 3.21
2140 3197 1.068125 CATGTGCATTGTGGTGTCCAG 60.068 52.381 0.00 0.00 32.34 3.86
2145 3202 3.579335 TTCATCATGTGCATTGTGGTG 57.421 42.857 0.00 0.00 0.00 4.17
2232 3290 4.443913 TGTTTCTTGCATCATGGTCATG 57.556 40.909 4.67 4.67 40.09 3.07
2255 3316 4.641541 TCTTGATGGTGCCTTTGTCATATG 59.358 41.667 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.