Multiple sequence alignment - TraesCS1A01G231400

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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 TraesCS1A01G231400 chr1A 100.000 3613 0 0 1 3613 404391160 404387548 0.000000e+00 6673.0
1 TraesCS1A01G231400 chr1A 91.562 2157 167 12 631 2780 343290638 343292786 0.000000e+00 2961.0
2 TraesCS1A01G231400 chr1A 94.118 833 49 0 2781 3613 384857226 384858058 0.000000e+00 1267.0
3 TraesCS1A01G231400 chr1A 93.998 833 50 0 2781 3613 254227491 254226659 0.000000e+00 1262.0
4 TraesCS1A01G231400 chr1A 93.878 833 51 0 2781 3613 249225041 249224209 0.000000e+00 1256.0
5 TraesCS1A01G231400 chr1A 93.758 833 52 0 2781 3613 94071268 94072100 0.000000e+00 1251.0
6 TraesCS1A01G231400 chr7A 93.274 2126 130 11 660 2780 384157817 384155700 0.000000e+00 3121.0
7 TraesCS1A01G231400 chr7A 92.807 2127 137 13 660 2780 384149922 384147806 0.000000e+00 3066.0
8 TraesCS1A01G231400 chr7A 91.998 2137 153 17 652 2780 252543000 252545126 0.000000e+00 2983.0
9 TraesCS1A01G231400 chr7A 91.815 2138 156 18 652 2780 283236327 283238454 0.000000e+00 2961.0
10 TraesCS1A01G231400 chr7A 91.000 2189 173 18 596 2781 648899570 648897403 0.000000e+00 2929.0
11 TraesCS1A01G231400 chr7A 86.178 1201 106 40 500 1668 176873262 176872090 0.000000e+00 1243.0
12 TraesCS1A01G231400 chr7A 96.377 414 13 1 1 414 169390061 169390472 0.000000e+00 680.0
13 TraesCS1A01G231400 chr6A 93.162 2135 128 17 653 2780 8353200 8355323 0.000000e+00 3118.0
14 TraesCS1A01G231400 chr6A 92.416 2136 145 16 653 2781 8361021 8363146 0.000000e+00 3031.0
15 TraesCS1A01G231400 chr6A 89.711 1351 114 20 1 1332 420047378 420046034 0.000000e+00 1701.0
16 TraesCS1A01G231400 chr6A 94.598 833 45 0 2781 3613 210891484 210890652 0.000000e+00 1290.0
17 TraesCS1A01G231400 chr6A 94.238 833 48 0 2781 3613 504433414 504434246 0.000000e+00 1273.0
18 TraesCS1A01G231400 chr6A 96.970 33 0 1 501 532 207001116 207001084 2.000000e-03 54.7
19 TraesCS1A01G231400 chr2A 91.783 2154 157 17 630 2780 59186487 59188623 0.000000e+00 2979.0
20 TraesCS1A01G231400 chr2D 87.709 2514 233 42 238 2718 344671357 344668887 0.000000e+00 2861.0
21 TraesCS1A01G231400 chr2D 87.082 2570 254 45 238 2780 344679726 344677208 0.000000e+00 2835.0
22 TraesCS1A01G231400 chr4A 94.118 833 49 0 2781 3613 582618025 582618857 0.000000e+00 1267.0
23 TraesCS1A01G231400 chr4A 93.758 833 52 0 2781 3613 231143023 231142191 0.000000e+00 1251.0
24 TraesCS1A01G231400 chr4A 93.758 833 52 0 2781 3613 545290953 545290121 0.000000e+00 1251.0
25 TraesCS1A01G231400 chr3B 81.300 754 90 31 598 1329 781142010 781141286 6.770000e-157 564.0
26 TraesCS1A01G231400 chr3B 96.970 33 1 0 500 532 781134090 781134058 5.040000e-04 56.5
27 TraesCS1A01G231400 chr7B 81.135 758 90 32 598 1329 508710487 508709757 3.150000e-155 558.0
28 TraesCS1A01G231400 chr7B 81.003 758 91 32 598 1329 508717101 508716371 1.470000e-153 553.0
29 TraesCS1A01G231400 chr6B 76.136 704 132 26 669 1348 436217798 436218489 1.610000e-88 337.0
30 TraesCS1A01G231400 chr6B 80.909 110 18 3 635 742 273891943 273892051 2.310000e-12 84.2
31 TraesCS1A01G231400 chr7D 78.947 494 70 20 599 1076 134512788 134512313 4.530000e-79 305.0
32 TraesCS1A01G231400 chr7D 85.882 170 15 9 128 293 115909746 115909582 4.800000e-39 172.0


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 TraesCS1A01G231400 chr1A 404387548 404391160 3612 True 6673 6673 100.000 1 3613 1 chr1A.!!$R3 3612
1 TraesCS1A01G231400 chr1A 343290638 343292786 2148 False 2961 2961 91.562 631 2780 1 chr1A.!!$F2 2149
2 TraesCS1A01G231400 chr1A 384857226 384858058 832 False 1267 1267 94.118 2781 3613 1 chr1A.!!$F3 832
3 TraesCS1A01G231400 chr1A 254226659 254227491 832 True 1262 1262 93.998 2781 3613 1 chr1A.!!$R2 832
4 TraesCS1A01G231400 chr1A 249224209 249225041 832 True 1256 1256 93.878 2781 3613 1 chr1A.!!$R1 832
5 TraesCS1A01G231400 chr1A 94071268 94072100 832 False 1251 1251 93.758 2781 3613 1 chr1A.!!$F1 832
6 TraesCS1A01G231400 chr7A 384155700 384157817 2117 True 3121 3121 93.274 660 2780 1 chr7A.!!$R3 2120
7 TraesCS1A01G231400 chr7A 384147806 384149922 2116 True 3066 3066 92.807 660 2780 1 chr7A.!!$R2 2120
8 TraesCS1A01G231400 chr7A 252543000 252545126 2126 False 2983 2983 91.998 652 2780 1 chr7A.!!$F2 2128
9 TraesCS1A01G231400 chr7A 283236327 283238454 2127 False 2961 2961 91.815 652 2780 1 chr7A.!!$F3 2128
10 TraesCS1A01G231400 chr7A 648897403 648899570 2167 True 2929 2929 91.000 596 2781 1 chr7A.!!$R4 2185
11 TraesCS1A01G231400 chr7A 176872090 176873262 1172 True 1243 1243 86.178 500 1668 1 chr7A.!!$R1 1168
12 TraesCS1A01G231400 chr6A 8353200 8355323 2123 False 3118 3118 93.162 653 2780 1 chr6A.!!$F1 2127
13 TraesCS1A01G231400 chr6A 8361021 8363146 2125 False 3031 3031 92.416 653 2781 1 chr6A.!!$F2 2128
14 TraesCS1A01G231400 chr6A 420046034 420047378 1344 True 1701 1701 89.711 1 1332 1 chr6A.!!$R3 1331
15 TraesCS1A01G231400 chr6A 210890652 210891484 832 True 1290 1290 94.598 2781 3613 1 chr6A.!!$R2 832
16 TraesCS1A01G231400 chr6A 504433414 504434246 832 False 1273 1273 94.238 2781 3613 1 chr6A.!!$F3 832
17 TraesCS1A01G231400 chr2A 59186487 59188623 2136 False 2979 2979 91.783 630 2780 1 chr2A.!!$F1 2150
18 TraesCS1A01G231400 chr2D 344668887 344671357 2470 True 2861 2861 87.709 238 2718 1 chr2D.!!$R1 2480
19 TraesCS1A01G231400 chr2D 344677208 344679726 2518 True 2835 2835 87.082 238 2780 1 chr2D.!!$R2 2542
20 TraesCS1A01G231400 chr4A 582618025 582618857 832 False 1267 1267 94.118 2781 3613 1 chr4A.!!$F1 832
21 TraesCS1A01G231400 chr4A 231142191 231143023 832 True 1251 1251 93.758 2781 3613 1 chr4A.!!$R1 832
22 TraesCS1A01G231400 chr4A 545290121 545290953 832 True 1251 1251 93.758 2781 3613 1 chr4A.!!$R2 832
23 TraesCS1A01G231400 chr3B 781141286 781142010 724 True 564 564 81.300 598 1329 1 chr3B.!!$R2 731
24 TraesCS1A01G231400 chr7B 508709757 508710487 730 True 558 558 81.135 598 1329 1 chr7B.!!$R1 731
25 TraesCS1A01G231400 chr7B 508716371 508717101 730 True 553 553 81.003 598 1329 1 chr7B.!!$R2 731
26 TraesCS1A01G231400 chr6B 436217798 436218489 691 False 337 337 76.136 669 1348 1 chr6B.!!$F2 679

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
147 149 1.374631 CGTACTGCTGCTCTTGCCA 60.375 57.895 0.00 0.00 38.71 4.92 F
1301 1388 0.981183 TACTGGGCCGTGATCACTTT 59.019 50.000 22.95 2.74 0.00 2.66 F
2088 2185 0.251832 AACAGGGCGAAGAGGAGAGA 60.252 55.000 0.00 0.00 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1525 0.249953 TCGCTCCGCCACAAAGTAAA 60.250 50.0 0.0 0.0 0.00 2.01 R
2372 2483 0.331616 TCCTGGACTCCATCGTCTGA 59.668 55.0 0.0 0.0 34.38 3.27 R
3300 3414 0.615331 GGATGTGCAGGAGGAAGTCA 59.385 55.0 0.0 0.0 0.00 3.41 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
29 30 4.537433 GCGCCCTGCCTCACCTAG 62.537 72.222 0.00 0.00 37.76 3.02
31 32 2.790791 CGCCCTGCCTCACCTAGAG 61.791 68.421 0.00 0.00 44.31 2.43
40 41 1.381327 TCACCTAGAGGCCCCTTCG 60.381 63.158 0.00 0.00 39.32 3.79
88 90 2.046892 GCCTGCAGACGTCCATGT 60.047 61.111 17.39 0.00 0.00 3.21
147 149 1.374631 CGTACTGCTGCTCTTGCCA 60.375 57.895 0.00 0.00 38.71 4.92
208 210 4.099170 GCTGCTCCTTGCGTGCTG 62.099 66.667 0.00 0.00 46.63 4.41
312 314 1.519455 CTTCGTCCATGGCCTCGAC 60.519 63.158 20.09 5.81 32.14 4.20
318 320 2.665000 CATGGCCTCGACCAGTGT 59.335 61.111 3.32 0.00 44.71 3.55
556 561 4.607293 TTGACTGCACTGTTGACTAGAT 57.393 40.909 0.00 0.00 0.00 1.98
627 642 9.226345 GTACACATAGCAATTTTCTCATTTAGC 57.774 33.333 0.00 0.00 0.00 3.09
921 941 3.059175 GCGTTAGAACACGTTTAGCTCTC 59.941 47.826 0.00 0.00 42.43 3.20
1215 1299 4.342092 TGTTACCTTTACCCGCTATCCTAC 59.658 45.833 0.00 0.00 0.00 3.18
1301 1388 0.981183 TACTGGGCCGTGATCACTTT 59.019 50.000 22.95 2.74 0.00 2.66
1437 1525 3.382832 CCCGACAGCCCTCGACTT 61.383 66.667 2.25 0.00 35.58 3.01
1605 1699 3.513912 CCATCTATGCGGGGACAGTTATA 59.486 47.826 0.00 0.00 0.00 0.98
1881 1976 4.641396 CATGACCTAGAAAAGTGTGTCCA 58.359 43.478 0.00 0.00 0.00 4.02
2043 2139 1.101049 AACACACCCTTCCAAGTGCG 61.101 55.000 0.00 0.00 37.51 5.34
2088 2185 0.251832 AACAGGGCGAAGAGGAGAGA 60.252 55.000 0.00 0.00 0.00 3.10
2217 2320 3.655972 AGCTATCCCCCTCTTATTCCA 57.344 47.619 0.00 0.00 0.00 3.53
2372 2483 1.540363 CCTATACCCGTTTGCTGCGAT 60.540 52.381 0.00 0.00 0.00 4.58
2385 2496 0.383590 CTGCGATCAGACGATGGAGT 59.616 55.000 0.00 0.00 42.95 3.85
2400 2511 1.679305 GAGTCCAGGAGCCAGACGA 60.679 63.158 0.00 0.00 35.65 4.20
2473 2584 4.129737 CCCGCTGACGACGACCAT 62.130 66.667 0.00 0.00 43.93 3.55
2534 2645 5.302059 CCTCTTTCGATCTGTATCCCAGTTA 59.698 44.000 0.00 0.00 42.19 2.24
2547 2658 1.555075 CCCAGTTAGTGCTAGCCTTCA 59.445 52.381 13.29 0.00 0.00 3.02
2551 2662 5.428253 CCAGTTAGTGCTAGCCTTCATAAA 58.572 41.667 13.29 0.00 0.00 1.40
2552 2663 6.058183 CCAGTTAGTGCTAGCCTTCATAAAT 58.942 40.000 13.29 0.88 0.00 1.40
2555 2666 6.989169 AGTTAGTGCTAGCCTTCATAAATCAG 59.011 38.462 13.29 0.00 0.00 2.90
2631 2742 4.632538 TGATCGAGCTCTTGTATTCGAA 57.367 40.909 12.85 0.00 44.11 3.71
2706 2820 8.534333 TTTGTAGAGTTGTGTTGTGATATCTC 57.466 34.615 3.98 0.63 0.00 2.75
2707 2821 7.468141 TGTAGAGTTGTGTTGTGATATCTCT 57.532 36.000 3.98 0.00 35.61 3.10
2795 2909 1.086696 CACATTGCGGTCGAGGAATT 58.913 50.000 0.00 0.00 29.57 2.17
2802 2916 1.804748 GCGGTCGAGGAATTTGAACTT 59.195 47.619 0.00 0.00 0.00 2.66
2960 3074 2.925706 TTAGCCTGCACCCCGACA 60.926 61.111 0.00 0.00 0.00 4.35
3041 3155 2.159114 AGGACAAAGCAAAACACGCAAT 60.159 40.909 0.00 0.00 0.00 3.56
3063 3177 1.069668 TCGATCTACGGATCACGAGGA 59.930 52.381 10.05 7.72 46.30 3.71
3264 3378 7.201670 GGTTTCAAACCCGTAAATATCGAATCT 60.202 37.037 8.27 0.00 46.12 2.40
3300 3414 1.561643 ATCCTGCGGTATGGATCGAT 58.438 50.000 0.00 0.00 38.60 3.59
3321 3435 1.211457 GACTTCCTCCTGCACATCCAT 59.789 52.381 0.00 0.00 0.00 3.41
3377 3491 1.163554 CTCCCACTCAAGCTCAAAGC 58.836 55.000 0.00 0.00 42.84 3.51
3423 3537 0.332293 TGCCAGCAGAATCCATTGGA 59.668 50.000 8.08 8.08 35.55 3.53
3424 3538 1.272592 TGCCAGCAGAATCCATTGGAA 60.273 47.619 9.98 0.00 34.34 3.53
3536 3650 2.512896 GCCAGAGGAATCGGCCAT 59.487 61.111 2.24 0.00 40.07 4.40
3538 3652 1.528824 CCAGAGGAATCGGCCATGT 59.471 57.895 2.24 0.00 0.00 3.21
3568 3682 4.024302 GGACACGGTTCCTAACAAAGAAAG 60.024 45.833 0.00 0.00 32.24 2.62
3597 3711 1.215382 CGACTGTCCGGATGCAGAA 59.785 57.895 24.59 0.25 36.62 3.02
3605 3719 1.402896 CCGGATGCAGAAGCCCTAGA 61.403 60.000 0.00 0.00 41.13 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 3.188786 GGCGACATGGACGTCTGC 61.189 66.667 16.46 9.74 35.85 4.26
312 314 4.081030 CTGCTTGCGCGACACTGG 62.081 66.667 12.10 1.92 39.65 4.00
529 534 3.625764 GTCAACAGTGCAGTCAAAAGGTA 59.374 43.478 0.00 0.00 0.00 3.08
556 561 3.864983 GACAGGTGGGGTCCAGGGA 62.865 68.421 0.00 0.00 32.34 4.20
710 725 9.816354 AGCAACTTTCATGTACAAAGTATTTTT 57.184 25.926 10.96 0.00 42.14 1.94
921 941 3.084039 AGTGCATAACATGACAACAGGG 58.916 45.455 0.00 0.00 31.68 4.45
1189 1270 2.189594 AGCGGGTAAAGGTAACAACC 57.810 50.000 0.00 0.00 41.41 3.77
1215 1299 6.582677 ACACTAGCATCCTATACTAAGCAG 57.417 41.667 0.00 0.00 0.00 4.24
1301 1388 3.399181 GCCCGTGATCACCTCCCA 61.399 66.667 20.03 0.00 0.00 4.37
1392 1480 2.140792 CCACCTCTACCGGGATGGG 61.141 68.421 6.32 4.76 44.64 4.00
1437 1525 0.249953 TCGCTCCGCCACAAAGTAAA 60.250 50.000 0.00 0.00 0.00 2.01
1605 1699 4.039357 CCACGACGTCGAGTGCCT 62.039 66.667 41.52 17.80 43.02 4.75
1668 1763 1.441849 CGTTACGCGGTCCAACGTA 60.442 57.895 21.38 9.49 43.35 3.57
1669 1764 2.730604 CGTTACGCGGTCCAACGT 60.731 61.111 21.38 11.32 45.85 3.99
1670 1765 4.125097 GCGTTACGCGGTCCAACG 62.125 66.667 23.76 23.76 44.55 4.10
1881 1976 1.258445 ACGCTCGATCCCCTTTGTCT 61.258 55.000 0.00 0.00 0.00 3.41
2079 2176 4.141135 TCCTAACCGATGATTCTCTCCTCT 60.141 45.833 0.00 0.00 0.00 3.69
2088 2185 6.100004 CGTAGCATAATCCTAACCGATGATT 58.900 40.000 0.00 0.00 33.54 2.57
2140 2240 1.275856 CTTGCAGCAGGAGAAGAGAGT 59.724 52.381 0.00 0.00 0.00 3.24
2141 2241 1.549620 TCTTGCAGCAGGAGAAGAGAG 59.450 52.381 2.39 0.00 0.00 3.20
2142 2242 1.637338 TCTTGCAGCAGGAGAAGAGA 58.363 50.000 2.39 0.00 0.00 3.10
2321 2427 0.537828 GGGGGAACAAAGCAACCGTA 60.538 55.000 0.00 0.00 0.00 4.02
2372 2483 0.331616 TCCTGGACTCCATCGTCTGA 59.668 55.000 0.00 0.00 34.38 3.27
2385 2496 2.117423 TGTCGTCTGGCTCCTGGA 59.883 61.111 0.00 0.00 0.00 3.86
2400 2511 3.601443 AGTAGTAGTAGTCGACGGTGT 57.399 47.619 10.46 0.00 0.00 4.16
2411 2522 6.717540 CCTCCCGAGTAGTAGTAGTAGTAGTA 59.282 46.154 0.52 0.00 0.00 1.82
2414 2525 5.303078 CACCTCCCGAGTAGTAGTAGTAGTA 59.697 48.000 0.00 0.00 0.00 1.82
2415 2526 4.100808 CACCTCCCGAGTAGTAGTAGTAGT 59.899 50.000 0.00 0.00 0.00 2.73
2416 2527 4.630111 CACCTCCCGAGTAGTAGTAGTAG 58.370 52.174 0.00 0.00 0.00 2.57
2417 2528 3.181461 GCACCTCCCGAGTAGTAGTAGTA 60.181 52.174 0.00 0.00 0.00 1.82
2473 2584 4.547671 CTGGGATCCTCCTAAACTACTCA 58.452 47.826 12.58 0.00 36.57 3.41
2509 2620 3.910989 TGGGATACAGATCGAAAGAGGA 58.089 45.455 0.00 0.00 41.83 3.71
2534 2645 5.130145 AGTCTGATTTATGAAGGCTAGCACT 59.870 40.000 18.24 8.50 0.00 4.40
2555 2666 9.472361 TGAGTACAGACATAAGTTAAACAAGTC 57.528 33.333 0.00 0.00 0.00 3.01
2706 2820 1.135915 CAAGATCAGGGACTCACGGAG 59.864 57.143 0.00 0.03 34.60 4.63
2707 2821 1.186200 CAAGATCAGGGACTCACGGA 58.814 55.000 0.00 0.00 34.60 4.69
2786 2900 3.074412 GGCTCAAGTTCAAATTCCTCGA 58.926 45.455 0.00 0.00 0.00 4.04
2928 3042 4.270084 GCAGGCTAAGTTTTTGGTTGAAAC 59.730 41.667 0.00 0.00 37.28 2.78
2960 3074 6.183360 TGCCTTGTCATTTTTATTTGAGTGGT 60.183 34.615 0.00 0.00 0.00 4.16
3264 3378 4.417506 CAGGATATGTTGTGTCGTCGTAA 58.582 43.478 0.00 0.00 0.00 3.18
3300 3414 0.615331 GGATGTGCAGGAGGAAGTCA 59.385 55.000 0.00 0.00 0.00 3.41
3377 3491 3.818787 GCCAATGCCGAGCTGGTG 61.819 66.667 0.00 0.00 41.21 4.17
3423 3537 2.291217 GGCTTCCAGATCTTCCCAACTT 60.291 50.000 0.00 0.00 0.00 2.66
3424 3538 1.283321 GGCTTCCAGATCTTCCCAACT 59.717 52.381 0.00 0.00 0.00 3.16
3536 3650 2.635915 AGGAACCGTGTCCAGAATTACA 59.364 45.455 4.58 0.00 40.48 2.41
3538 3652 4.283978 TGTTAGGAACCGTGTCCAGAATTA 59.716 41.667 4.58 0.00 40.48 1.40
3568 3682 1.846782 CGGACAGTCGACGATTTGATC 59.153 52.381 10.46 10.68 0.00 2.92


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

AutoCloner maintained by Alex Coulton.