Multiple sequence alignment - TraesCS1B01G427600

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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 TraesCS1B01G427600 chr1B 100.000 2873 0 0 1 2873 653040813 653037941 0.000000e+00 5306.0
1 TraesCS1B01G427600 chr1B 92.453 795 58 2 2080 2873 65711127 65710334 0.000000e+00 1134.0
2 TraesCS1B01G427600 chr1B 83.492 1048 112 30 1035 2071 652925832 652924835 0.000000e+00 920.0
3 TraesCS1B01G427600 chr1B 85.670 321 11 5 610 920 652926193 652925898 3.600000e-79 305.0
4 TraesCS1B01G427600 chr1A 92.189 1485 101 9 607 2082 564041240 564039762 0.000000e+00 2085.0
5 TraesCS1B01G427600 chr1A 90.316 506 40 3 1375 1871 563989677 563989172 0.000000e+00 654.0
6 TraesCS1B01G427600 chr1D 91.385 1393 92 11 607 1994 470339950 470338581 0.000000e+00 1882.0
7 TraesCS1B01G427600 chr1D 84.483 1044 100 27 1035 2071 470311984 470310996 0.000000e+00 974.0
8 TraesCS1B01G427600 chr1D 82.353 323 17 5 607 920 470312369 470312078 7.950000e-61 244.0
9 TraesCS1B01G427600 chr6D 93.977 797 46 2 2078 2873 83111490 83110695 0.000000e+00 1205.0
10 TraesCS1B01G427600 chr6D 90.704 796 72 2 2078 2872 414204534 414205328 0.000000e+00 1059.0
11 TraesCS1B01G427600 chr6D 81.461 178 27 5 1357 1531 317105970 317105796 1.070000e-29 141.0
12 TraesCS1B01G427600 chr2D 92.579 795 58 1 2078 2871 599459938 599459144 0.000000e+00 1140.0
13 TraesCS1B01G427600 chr5D 92.356 798 55 4 2078 2873 116031391 116030598 0.000000e+00 1131.0
14 TraesCS1B01G427600 chr5B 92.346 797 56 4 2078 2873 251341679 251342471 0.000000e+00 1129.0
15 TraesCS1B01G427600 chr5B 100.000 29 0 0 740 768 3901271 3901243 1.000000e-03 54.7
16 TraesCS1B01G427600 chr4A 92.085 796 60 2 2078 2872 618068143 618067350 0.000000e+00 1118.0
17 TraesCS1B01G427600 chr6A 91.217 797 68 2 2078 2873 408869726 408870521 0.000000e+00 1083.0
18 TraesCS1B01G427600 chr6A 80.337 178 29 5 1357 1531 454712224 454712050 2.320000e-26 130.0
19 TraesCS1B01G427600 chr7A 90.715 797 72 2 2078 2873 149428728 149427933 0.000000e+00 1061.0
20 TraesCS1B01G427600 chr7B 96.260 615 14 3 1 607 596679298 596679911 0.000000e+00 1000.0
21 TraesCS1B01G427600 chr7D 79.516 620 63 39 1 602 28028802 28029375 1.620000e-102 383.0
22 TraesCS1B01G427600 chr2A 81.356 177 29 3 1354 1528 673327381 673327555 1.070000e-29 141.0
23 TraesCS1B01G427600 chr2B 80.791 177 30 4 1354 1528 627073520 627073694 4.990000e-28 135.0
24 TraesCS1B01G427600 chr6B 97.959 49 1 0 720 768 502021976 502021928 5.100000e-13 86.1
25 TraesCS1B01G427600 chr4B 90.769 65 5 1 23 86 69464245 69464309 5.100000e-13 86.1


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 TraesCS1B01G427600 chr1B 653037941 653040813 2872 True 5306.0 5306 100.000 1 2873 1 chr1B.!!$R2 2872
1 TraesCS1B01G427600 chr1B 65710334 65711127 793 True 1134.0 1134 92.453 2080 2873 1 chr1B.!!$R1 793
2 TraesCS1B01G427600 chr1B 652924835 652926193 1358 True 612.5 920 84.581 610 2071 2 chr1B.!!$R3 1461
3 TraesCS1B01G427600 chr1A 564039762 564041240 1478 True 2085.0 2085 92.189 607 2082 1 chr1A.!!$R2 1475
4 TraesCS1B01G427600 chr1A 563989172 563989677 505 True 654.0 654 90.316 1375 1871 1 chr1A.!!$R1 496
5 TraesCS1B01G427600 chr1D 470338581 470339950 1369 True 1882.0 1882 91.385 607 1994 1 chr1D.!!$R1 1387
6 TraesCS1B01G427600 chr1D 470310996 470312369 1373 True 609.0 974 83.418 607 2071 2 chr1D.!!$R2 1464
7 TraesCS1B01G427600 chr6D 83110695 83111490 795 True 1205.0 1205 93.977 2078 2873 1 chr6D.!!$R1 795
8 TraesCS1B01G427600 chr6D 414204534 414205328 794 False 1059.0 1059 90.704 2078 2872 1 chr6D.!!$F1 794
9 TraesCS1B01G427600 chr2D 599459144 599459938 794 True 1140.0 1140 92.579 2078 2871 1 chr2D.!!$R1 793
10 TraesCS1B01G427600 chr5D 116030598 116031391 793 True 1131.0 1131 92.356 2078 2873 1 chr5D.!!$R1 795
11 TraesCS1B01G427600 chr5B 251341679 251342471 792 False 1129.0 1129 92.346 2078 2873 1 chr5B.!!$F1 795
12 TraesCS1B01G427600 chr4A 618067350 618068143 793 True 1118.0 1118 92.085 2078 2872 1 chr4A.!!$R1 794
13 TraesCS1B01G427600 chr6A 408869726 408870521 795 False 1083.0 1083 91.217 2078 2873 1 chr6A.!!$F1 795
14 TraesCS1B01G427600 chr7A 149427933 149428728 795 True 1061.0 1061 90.715 2078 2873 1 chr7A.!!$R1 795
15 TraesCS1B01G427600 chr7B 596679298 596679911 613 False 1000.0 1000 96.260 1 607 1 chr7B.!!$F1 606
16 TraesCS1B01G427600 chr7D 28028802 28029375 573 False 383.0 383 79.516 1 602 1 chr7D.!!$F1 601

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
420 430 0.104725 AATGGAAAAGGCCCCAACCA 60.105 50.0 0.00 5.34 35.85 3.67 F
675 712 0.233590 GCACATGCACACGTACGAAA 59.766 50.0 24.41 2.39 41.59 3.46 F
1665 1737 0.391661 ACGCCGATCATGCAAGAACT 60.392 50.0 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1718 0.391661 AGTTCTTGCATGATCGGCGT 60.392 50.0 6.85 0.0 0.00 5.68 R
1749 1824 0.447801 GATCTTGCATCGTTGGCGTT 59.552 50.0 0.00 0.0 39.49 4.84 R
2474 2562 1.057851 AACCCACCTCGGTCCTTTGA 61.058 55.0 0.00 0.0 33.98 2.69 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
157 162 3.788434 ACAGAATGCGTGTTAAGAACG 57.212 42.857 6.31 6.31 42.53 3.95
420 430 0.104725 AATGGAAAAGGCCCCAACCA 60.105 50.000 0.00 5.34 35.85 3.67
675 712 0.233590 GCACATGCACACGTACGAAA 59.766 50.000 24.41 2.39 41.59 3.46
967 1009 2.990667 CGATTGGTGTCGATCTGCAAGA 60.991 50.000 0.00 0.00 44.06 3.02
1054 1111 3.862124 GCGACACGAGCAACATCT 58.138 55.556 0.00 0.00 34.19 2.90
1071 1128 1.227823 CTTGGAGAACGTGTGGGCA 60.228 57.895 0.00 0.00 0.00 5.36
1155 1212 1.556911 ACATCTTTCGTGGATCAGGCT 59.443 47.619 0.00 0.00 0.00 4.58
1159 1216 1.841302 TTTCGTGGATCAGGCTGGCT 61.841 55.000 15.73 0.00 0.00 4.75
1168 1225 2.132996 CAGGCTGGCTCGGAGATCT 61.133 63.158 9.69 0.00 33.89 2.75
1228 1285 3.054503 CCGACGAGTGGGACGAGT 61.055 66.667 0.00 0.00 34.70 4.18
1230 1287 1.154263 CGACGAGTGGGACGAGTTC 60.154 63.158 0.00 0.00 34.70 3.01
1312 1372 3.474570 CTCGGGGAGAAGGCCAGG 61.475 72.222 5.01 0.00 0.00 4.45
1485 1548 4.849329 CTCGCCTACGACGTGGCC 62.849 72.222 25.46 8.75 45.12 5.36
1543 1606 1.513158 CCGATCGAGAAGGTGCAGT 59.487 57.895 18.66 0.00 0.00 4.40
1590 1653 4.003788 CAGTTCCTGGACGCCGGT 62.004 66.667 1.90 0.00 0.00 5.28
1607 1679 2.933287 TGACCATTCCACGGGCCT 60.933 61.111 0.84 0.00 0.00 5.19
1608 1680 2.438434 GACCATTCCACGGGCCTG 60.438 66.667 11.02 11.02 0.00 4.85
1646 1718 3.695606 GAGGAGCAGTGCCACCGA 61.696 66.667 12.58 0.00 32.55 4.69
1665 1737 0.391661 ACGCCGATCATGCAAGAACT 60.392 50.000 0.00 0.00 0.00 3.01
1743 1818 3.844090 GCCAGCTCGAGGAGGGAC 61.844 72.222 15.58 0.00 0.00 4.46
1778 1853 4.210304 GCAAGATCGGCGCGTGAC 62.210 66.667 8.43 0.00 0.00 3.67
1811 1886 1.086634 GGAGGTGCTGTGAATCGAGC 61.087 60.000 0.00 0.00 35.65 5.03
1835 1910 1.134280 CGAGGTTGAGGAGATTGGCAT 60.134 52.381 0.00 0.00 0.00 4.40
1836 1911 2.103094 CGAGGTTGAGGAGATTGGCATA 59.897 50.000 0.00 0.00 0.00 3.14
1941 2016 4.698575 GGGGAGTGATGATCAAGTAGTTC 58.301 47.826 0.00 0.00 0.00 3.01
2012 2097 6.692486 CAAGTTAGTTACAGTGATCTCCTGT 58.308 40.000 18.42 18.42 44.90 4.00
2046 2131 6.923012 TGCAGTTTCAGTAATTTGTATGCAT 58.077 32.000 3.79 3.79 35.24 3.96
2048 2133 7.871973 TGCAGTTTCAGTAATTTGTATGCATTT 59.128 29.630 3.54 0.00 35.24 2.32
2157 2242 4.752101 CAGGATCGTGGATAACCTCAATTC 59.248 45.833 7.54 0.00 37.04 2.17
2243 2328 1.134521 GTGGGTATGATCCGCTTGTGA 60.135 52.381 0.00 0.00 32.41 3.58
2305 2392 5.705609 TCACATCTAAAGGAAGCAAAACC 57.294 39.130 0.00 0.00 0.00 3.27
2382 2469 2.513897 GCCCGAGGGTGTGCATAC 60.514 66.667 10.26 4.79 37.65 2.39
2467 2555 3.668141 ATGGTGAAATGGGCTGACATA 57.332 42.857 0.00 0.00 0.00 2.29
2474 2562 2.742428 ATGGGCTGACATATGCTTGT 57.258 45.000 1.58 0.00 0.00 3.16
2547 2635 1.810151 GCTCATGCTTCGTTGGGTTTA 59.190 47.619 0.00 0.00 36.03 2.01
2585 2673 1.529244 GGAGGTTTGTGGCTGCAGT 60.529 57.895 16.64 0.00 0.00 4.40
2591 2679 2.295909 GGTTTGTGGCTGCAGTTGATTA 59.704 45.455 16.64 0.00 0.00 1.75
2608 2696 8.041323 CAGTTGATTAAGTCCAAGTACCTACAT 58.959 37.037 0.00 0.00 0.00 2.29
2609 2697 9.263446 AGTTGATTAAGTCCAAGTACCTACATA 57.737 33.333 0.00 0.00 0.00 2.29
2611 2699 9.483489 TTGATTAAGTCCAAGTACCTACATAGA 57.517 33.333 0.00 0.00 0.00 1.98
2631 2719 0.829182 CAACCCCTCTTGGCTTGCTT 60.829 55.000 0.00 0.00 0.00 3.91
2651 2739 1.379176 CTCTCGGCTGAGTCCCAGA 60.379 63.158 21.88 1.02 45.78 3.86
2698 2786 3.046374 GGAGGAGATTAGGCTGGGTTTA 58.954 50.000 0.00 0.00 0.00 2.01
2707 2795 0.035739 GGCTGGGTTTACGGTTCTCA 59.964 55.000 0.00 0.00 0.00 3.27
2809 2898 0.321210 TGCGATTTGTGATGACCCGT 60.321 50.000 0.00 0.00 0.00 5.28
2856 2945 3.398629 TGGATGAGGGATGGAATATTGCA 59.601 43.478 12.37 12.37 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.586541 GCTTACAACTGCAAGGGGC 59.413 57.895 0.00 0.00 45.13 5.80
92 93 1.032014 GGTGCGTGAATGCCCATAAT 58.968 50.000 0.00 0.00 0.00 1.28
675 712 2.848694 TCTCTGCAGGAATTCAGGGATT 59.151 45.455 15.13 0.00 35.08 3.01
968 1010 9.820229 CGCTACACAAATTCTCAAGTAATTTTA 57.180 29.630 0.00 0.00 35.00 1.52
970 1012 6.801862 GCGCTACACAAATTCTCAAGTAATTT 59.198 34.615 0.00 0.00 37.08 1.82
976 1018 3.187227 ACAGCGCTACACAAATTCTCAAG 59.813 43.478 10.99 0.00 0.00 3.02
1044 1101 2.158449 CACGTTCTCCAAGATGTTGCTC 59.842 50.000 0.00 0.00 31.64 4.26
1054 1111 1.098712 GTTGCCCACACGTTCTCCAA 61.099 55.000 0.00 0.00 0.00 3.53
1071 1128 0.460284 GCGTCTCGGTCATGATGGTT 60.460 55.000 0.00 0.00 0.00 3.67
1155 1212 1.519246 CTGCAAGATCTCCGAGCCA 59.481 57.895 0.00 0.00 34.07 4.75
1159 1216 2.496341 CCGCTGCAAGATCTCCGA 59.504 61.111 0.00 0.00 34.07 4.55
1228 1285 4.373116 GTCCGCCACGCTGAGGAA 62.373 66.667 0.00 0.00 34.17 3.36
1299 1356 3.011517 TGCTCCTGGCCTTCTCCC 61.012 66.667 3.32 0.00 40.92 4.30
1590 1653 2.933287 AGGCCCGTGGAATGGTCA 60.933 61.111 0.00 0.00 43.26 4.02
1646 1718 0.391661 AGTTCTTGCATGATCGGCGT 60.392 50.000 6.85 0.00 0.00 5.68
1665 1737 1.134694 CGTGAGATCAGCGTCGACA 59.865 57.895 17.16 0.00 0.00 4.35
1743 1818 2.740826 ATCGTTGGCGTTCCGTGG 60.741 61.111 0.00 0.00 39.49 4.94
1749 1824 0.447801 GATCTTGCATCGTTGGCGTT 59.552 50.000 0.00 0.00 39.49 4.84
1797 1872 2.963499 GATCGCTCGATTCACAGCA 58.037 52.632 6.22 0.00 35.15 4.41
1811 1886 2.544694 CCAATCTCCTCAACCTCGATCG 60.545 54.545 9.36 9.36 0.00 3.69
1835 1910 6.075984 GGGAACAGATAGTCCCAATACTCTA 58.924 44.000 3.79 0.00 37.46 2.43
1836 1911 4.902448 GGGAACAGATAGTCCCAATACTCT 59.098 45.833 3.79 0.00 37.46 3.24
1941 2016 7.978975 CCCAAATTAACATAACCACACCTAATG 59.021 37.037 0.00 0.00 0.00 1.90
2083 2168 4.892934 ACCACAACCTTGCTCTTATCAAAA 59.107 37.500 0.00 0.00 0.00 2.44
2157 2242 1.284785 TGGGGAATGAAGCCAACCTAG 59.715 52.381 0.00 0.00 0.00 3.02
2202 2287 3.138283 ACTCACCAAAATCCTGGACTCAA 59.862 43.478 0.00 0.00 38.96 3.02
2305 2392 4.567159 GCAAGGTTAGAACTAATGAGGACG 59.433 45.833 0.00 0.00 0.00 4.79
2416 2503 3.402681 CGACCATCCCCTGCCTGT 61.403 66.667 0.00 0.00 0.00 4.00
2467 2555 1.611673 CCTCGGTCCTTTGACAAGCAT 60.612 52.381 0.00 0.00 43.65 3.79
2474 2562 1.057851 AACCCACCTCGGTCCTTTGA 61.058 55.000 0.00 0.00 33.98 2.69
2547 2635 3.854669 CTCCCCGCAAGATCCGCT 61.855 66.667 3.48 0.00 43.02 5.52
2585 2673 9.483489 TCTATGTAGGTACTTGGACTTAATCAA 57.517 33.333 0.00 0.00 41.75 2.57
2591 2679 6.070938 GGTTGTCTATGTAGGTACTTGGACTT 60.071 42.308 15.77 0.00 40.26 3.01
2651 2739 6.914665 TGATGTCCTGGATAGATTTCCAAAT 58.085 36.000 0.00 0.00 45.03 2.32
2698 2786 2.290071 CCCATTACCAACTGAGAACCGT 60.290 50.000 0.00 0.00 0.00 4.83
2707 2795 1.633945 GTCCCAGACCCATTACCAACT 59.366 52.381 0.00 0.00 0.00 3.16
2809 2898 3.253188 GCAGCCACAGAAACAAGAACATA 59.747 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.