Multiple sequence alignment - TraesCS5B01G033400

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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 TraesCS5B01G033400 chr5B 100.000 4298 0 0 1 4298 36693047 36697344 0.000000e+00 7938.0
1 TraesCS5B01G033400 chr5B 100.000 1177 0 0 1 1177 36659523 36660699 0.000000e+00 2174.0
2 TraesCS5B01G033400 chr5B 100.000 678 0 0 2996 3673 36816003 36815326 0.000000e+00 1253.0
3 TraesCS5B01G033400 chr5B 97.011 736 19 2 2259 2994 36775524 36774792 0.000000e+00 1234.0
4 TraesCS5B01G033400 chr5B 83.504 879 98 26 2079 2947 185534773 185535614 0.000000e+00 776.0
5 TraesCS5B01G033400 chr5B 83.461 786 69 33 855 1612 185523859 185524611 0.000000e+00 675.0
6 TraesCS5B01G033400 chr5B 91.086 359 19 7 898 1243 36776642 36776284 1.400000e-129 473.0
7 TraesCS5B01G033400 chr5B 91.086 359 19 7 898 1243 36817672 36817314 1.400000e-129 473.0
8 TraesCS5B01G033400 chr5B 91.520 342 10 10 1 340 36776963 36776639 1.820000e-123 453.0
9 TraesCS5B01G033400 chr5B 91.520 342 10 10 1 340 36817993 36817669 1.820000e-123 453.0
10 TraesCS5B01G033400 chr5B 87.277 393 49 1 2489 2880 185510831 185511223 8.480000e-122 448.0
11 TraesCS5B01G033400 chr5B 96.063 254 6 4 4047 4298 36773267 36773016 1.110000e-110 411.0
12 TraesCS5B01G033400 chr5B 98.515 202 3 0 1856 2057 36775958 36775757 1.470000e-94 357.0
13 TraesCS5B01G033400 chr5B 98.515 202 3 0 1856 2057 36816988 36816787 1.470000e-94 357.0
14 TraesCS5B01G033400 chr5B 92.308 221 12 3 1294 1510 36776281 36776062 4.170000e-80 309.0
15 TraesCS5B01G033400 chr5B 92.308 221 12 3 1294 1510 36817311 36817092 4.170000e-80 309.0
16 TraesCS5B01G033400 chr5B 78.080 552 74 26 3101 3633 185535753 185536276 5.400000e-79 305.0
17 TraesCS5B01G033400 chr5B 100.000 142 0 0 3889 4030 36774188 36774047 3.300000e-66 263.0
18 TraesCS5B01G033400 chr5B 88.785 214 21 1 1856 2066 185508802 185509015 4.260000e-65 259.0
19 TraesCS5B01G033400 chr5B 90.050 201 15 2 3101 3300 185511271 185511467 5.520000e-64 255.0
20 TraesCS5B01G033400 chr5B 92.614 176 9 2 1910 2082 185534557 185534731 2.570000e-62 250.0
21 TraesCS5B01G033400 chr5B 96.748 123 3 1 4177 4298 36814044 36813922 2.030000e-48 204.0
22 TraesCS5B01G033400 chr5D 95.806 1955 52 13 2079 4030 42010763 42012690 0.000000e+00 3129.0
23 TraesCS5B01G033400 chr5D 89.191 1767 102 36 2079 3795 42056989 42055262 0.000000e+00 2122.0
24 TraesCS5B01G033400 chr5D 88.095 1596 110 36 519 2082 42058562 42057015 0.000000e+00 1821.0
25 TraesCS5B01G033400 chr5D 88.184 804 52 19 730 1510 42009242 42010025 0.000000e+00 918.0
26 TraesCS5B01G033400 chr5D 87.277 393 49 1 2489 2880 136946137 136946529 8.480000e-122 448.0
27 TraesCS5B01G033400 chr5D 86.769 325 18 12 161 483 42058861 42058560 5.320000e-89 339.0
28 TraesCS5B01G033400 chr5D 93.363 226 6 2 1857 2082 42010509 42010725 4.140000e-85 326.0
29 TraesCS5B01G033400 chr5D 96.774 186 4 2 4110 4294 42013515 42013699 4.170000e-80 309.0
30 TraesCS5B01G033400 chr5D 88.584 219 21 2 1856 2070 136945411 136945629 3.300000e-66 263.0
31 TraesCS5B01G033400 chr5D 90.452 199 14 2 3103 3300 136946579 136946773 1.530000e-64 257.0
32 TraesCS5B01G033400 chr5D 90.805 174 16 0 1334 1507 136944686 136944859 2.580000e-57 233.0
33 TraesCS5B01G033400 chr5D 90.345 145 4 6 162 304 42009088 42009224 9.490000e-42 182.0
34 TraesCS5B01G033400 chr5D 90.400 125 7 2 6 125 42008882 42009006 4.450000e-35 159.0
35 TraesCS5B01G033400 chrUn 99.848 1312 2 0 1 1312 337271084 337272395 0.000000e+00 2412.0
36 TraesCS5B01G033400 chrUn 99.130 1035 1 1 2996 4030 340277393 340278419 0.000000e+00 1855.0
37 TraesCS5B01G033400 chrUn 99.034 1035 1 2 2996 4030 340335921 340336946 0.000000e+00 1847.0
38 TraesCS5B01G033400 chrUn 97.011 736 19 2 2259 2994 65844090 65844822 0.000000e+00 1234.0
39 TraesCS5B01G033400 chrUn 93.175 337 12 7 1856 2191 65843764 65844090 6.460000e-133 484.0
40 TraesCS5B01G033400 chrUn 91.086 359 19 7 898 1243 65843080 65843438 1.400000e-129 473.0
41 TraesCS5B01G033400 chrUn 91.520 342 10 10 1 340 65842759 65843083 1.820000e-123 453.0
42 TraesCS5B01G033400 chrUn 96.800 250 6 2 4047 4295 65848428 65848676 2.390000e-112 416.0
43 TraesCS5B01G033400 chrUn 96.800 250 6 2 4047 4295 340279199 340279447 2.390000e-112 416.0
44 TraesCS5B01G033400 chrUn 96.800 250 6 2 4047 4295 340337726 340337974 2.390000e-112 416.0
45 TraesCS5B01G033400 chrUn 92.308 221 12 3 1294 1510 65843441 65843660 4.170000e-80 309.0
46 TraesCS5B01G033400 chr5A 88.679 1590 87 53 2259 3807 30400718 30402255 0.000000e+00 1853.0
47 TraesCS5B01G033400 chr5A 88.600 886 61 19 651 1518 30399372 30400235 0.000000e+00 1040.0
48 TraesCS5B01G033400 chr5A 84.708 667 59 21 855 1510 168131588 168130954 1.010000e-175 627.0
49 TraesCS5B01G033400 chr5A 85.545 505 25 13 1719 2191 30400230 30400718 6.460000e-133 484.0
50 TraesCS5B01G033400 chr5A 87.786 393 47 1 2489 2880 168236764 168236372 3.920000e-125 459.0
51 TraesCS5B01G033400 chr5A 86.970 330 30 5 2079 2407 168130276 168129959 4.090000e-95 359.0
52 TraesCS5B01G033400 chr5A 93.478 230 11 2 1856 2082 168130547 168130319 5.320000e-89 339.0
53 TraesCS5B01G033400 chr5A 87.209 258 23 7 4047 4295 30403337 30403593 7.030000e-73 285.0
54 TraesCS5B01G033400 chr5A 85.465 172 10 7 172 335 30398856 30399020 9.560000e-37 165.0
55 TraesCS5B01G033400 chr5A 79.874 159 19 6 3837 3992 108781644 108781792 2.110000e-18 104.0
56 TraesCS5B01G033400 chr5A 94.030 67 3 1 3922 3988 30402477 30402542 2.730000e-17 100.0
57 TraesCS5B01G033400 chr4A 80.128 156 24 2 3837 3992 597202489 597202637 4.540000e-20 110.0
58 TraesCS5B01G033400 chr4A 77.987 159 22 6 3837 3992 382842375 382842227 2.130000e-13 87.9
59 TraesCS5B01G033400 chr7D 79.114 158 22 5 3837 3992 406811276 406811424 9.840000e-17 99.0
60 TraesCS5B01G033400 chr6A 78.571 154 26 2 3837 3990 258149149 258149003 1.270000e-15 95.3
61 TraesCS5B01G033400 chr3D 78.205 156 25 3 3837 3992 528342746 528342600 1.650000e-14 91.6
62 TraesCS5B01G033400 chr6D 97.222 36 1 0 2228 2263 436476572 436476537 1.290000e-05 62.1
63 TraesCS5B01G033400 chr2D 97.222 36 1 0 2228 2263 316147132 316147167 1.290000e-05 62.1
64 TraesCS5B01G033400 chr2D 94.444 36 2 0 2228 2263 616930716 616930751 6.000000e-04 56.5


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 TraesCS5B01G033400 chr5B 36693047 36697344 4297 False 7938.000000 7938 100.000000 1 4298 1 chr5B.!!$F2 4297
1 TraesCS5B01G033400 chr5B 36659523 36660699 1176 False 2174.000000 2174 100.000000 1 1177 1 chr5B.!!$F1 1176
2 TraesCS5B01G033400 chr5B 185523859 185524611 752 False 675.000000 675 83.461000 855 1612 1 chr5B.!!$F3 757
3 TraesCS5B01G033400 chr5B 36813922 36817993 4071 True 508.166667 1253 95.029500 1 4298 6 chr5B.!!$R2 4297
4 TraesCS5B01G033400 chr5B 36773016 36776963 3947 True 500.000000 1234 95.214714 1 4298 7 chr5B.!!$R1 4297
5 TraesCS5B01G033400 chr5B 185534557 185536276 1719 False 443.666667 776 84.732667 1910 3633 3 chr5B.!!$F5 1723
6 TraesCS5B01G033400 chr5B 185508802 185511467 2665 False 320.666667 448 88.704000 1856 3300 3 chr5B.!!$F4 1444
7 TraesCS5B01G033400 chr5D 42055262 42058861 3599 True 1427.333333 2122 88.018333 161 3795 3 chr5D.!!$R1 3634
8 TraesCS5B01G033400 chr5D 42008882 42013699 4817 False 837.166667 3129 92.478667 6 4294 6 chr5D.!!$F1 4288
9 TraesCS5B01G033400 chr5D 136944686 136946773 2087 False 300.250000 448 89.279500 1334 3300 4 chr5D.!!$F2 1966
10 TraesCS5B01G033400 chrUn 337271084 337272395 1311 False 2412.000000 2412 99.848000 1 1312 1 chrUn.!!$F1 1311
11 TraesCS5B01G033400 chrUn 340277393 340279447 2054 False 1135.500000 1855 97.965000 2996 4295 2 chrUn.!!$F3 1299
12 TraesCS5B01G033400 chrUn 340335921 340337974 2053 False 1131.500000 1847 97.917000 2996 4295 2 chrUn.!!$F4 1299
13 TraesCS5B01G033400 chrUn 65842759 65848676 5917 False 561.500000 1234 93.650000 1 4295 6 chrUn.!!$F2 4294
14 TraesCS5B01G033400 chr5A 30398856 30403593 4737 False 654.500000 1853 88.254667 172 4295 6 chr5A.!!$F2 4123
15 TraesCS5B01G033400 chr5A 168129959 168131588 1629 True 441.666667 627 88.385333 855 2407 3 chr5A.!!$R2 1552

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
1177 1389 1.021390 GGTCCTCATTGCACTCACCG 61.021 60.0 0.0 0.0 0.0 4.94 F
1625 1932 2.026262 GCATCACAGGAGGGGTCTTTTA 60.026 50.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2949 2.039405 CCTGCTTCAGCTCTGGTGC 61.039 63.158 0.00 3.16 42.66 5.01 R
3880 6004 5.872963 ACCCTTACTAACAAGGTGTTAAGG 58.127 41.667 11.67 11.67 41.70 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
1177 1389 1.021390 GGTCCTCATTGCACTCACCG 61.021 60.000 0.00 0.00 0.00 4.94
1332 1544 2.545946 GACAGACACTTGTTCCTTCAGC 59.454 50.000 0.00 0.00 0.00 4.26
1338 1550 3.141398 CACTTGTTCCTTCAGCTTGCTA 58.859 45.455 0.00 0.00 0.00 3.49
1581 1847 4.707105 CATGTGATGTACAGCCCATTCTA 58.293 43.478 6.33 0.00 43.80 2.10
1584 1850 4.100035 TGTGATGTACAGCCCATTCTAGAG 59.900 45.833 8.95 0.00 33.42 2.43
1608 1878 8.572855 AGCATAATCCTCCTTTATTAAGCATC 57.427 34.615 0.00 0.00 35.68 3.91
1625 1932 2.026262 GCATCACAGGAGGGGTCTTTTA 60.026 50.000 0.00 0.00 0.00 1.52
1653 1960 3.764237 ACACCGGTTATCTGACAGTTT 57.236 42.857 2.97 0.00 0.00 2.66
1682 2044 5.357878 TGCTTCAAGAAAGTGTCTGTCAATT 59.642 36.000 0.00 0.00 36.40 2.32
1791 2265 3.378959 GTTAACTAAACCGATGCACCG 57.621 47.619 0.00 0.00 31.38 4.94
1854 2374 2.604969 TCCACTCATTTTTAACGCGC 57.395 45.000 5.73 0.00 0.00 6.86
2087 2685 2.989840 CAGTCACACCGAGTCAATCTTC 59.010 50.000 0.00 0.00 0.00 2.87
2168 2769 5.472301 ACAGGAAAAATGGAGGTATGGAT 57.528 39.130 0.00 0.00 0.00 3.41
2284 2929 4.202070 GCACTAGAGGTGGACATAGAGAAC 60.202 50.000 0.00 0.00 45.44 3.01
2293 2938 2.197577 GACATAGAGAACGGAGCTTGC 58.802 52.381 0.00 0.00 0.00 4.01
2304 2949 2.046507 AGCTTGCGCAGAAGAGGG 60.047 61.111 11.31 0.00 39.10 4.30
2326 2971 0.676151 CCAGAGCTGAAGCAGGAACC 60.676 60.000 4.90 0.00 45.16 3.62
3880 6004 2.035066 AGCAAGTGGTTGTGATTGAAGC 59.965 45.455 0.00 0.00 35.92 3.86
3881 6005 2.863704 GCAAGTGGTTGTGATTGAAGCC 60.864 50.000 0.00 0.00 35.92 4.35
3882 6006 2.624838 CAAGTGGTTGTGATTGAAGCCT 59.375 45.455 0.00 0.00 0.00 4.58
3883 6007 2.949447 AGTGGTTGTGATTGAAGCCTT 58.051 42.857 0.00 0.00 0.00 4.35
3884 6008 4.098914 AGTGGTTGTGATTGAAGCCTTA 57.901 40.909 0.00 0.00 0.00 2.69
3885 6009 4.469657 AGTGGTTGTGATTGAAGCCTTAA 58.530 39.130 0.00 0.00 0.00 1.85
3886 6010 4.278419 AGTGGTTGTGATTGAAGCCTTAAC 59.722 41.667 0.00 0.00 0.00 2.01
3887 6011 4.037446 GTGGTTGTGATTGAAGCCTTAACA 59.963 41.667 0.00 0.00 0.00 2.41
4030 6289 1.748879 CGCCCCCATGTCGTTGAAT 60.749 57.895 0.00 0.00 0.00 2.57
4032 6291 0.455815 GCCCCCATGTCGTTGAATTC 59.544 55.000 0.00 0.00 0.00 2.17
4033 6292 1.102978 CCCCCATGTCGTTGAATTCC 58.897 55.000 2.27 0.00 0.00 3.01
4034 6293 1.615651 CCCCCATGTCGTTGAATTCCA 60.616 52.381 2.27 0.00 0.00 3.53
4035 6294 2.378038 CCCCATGTCGTTGAATTCCAT 58.622 47.619 2.27 0.00 0.00 3.41
4036 6295 2.358898 CCCCATGTCGTTGAATTCCATC 59.641 50.000 2.27 0.00 0.00 3.51
4037 6296 2.032054 CCCATGTCGTTGAATTCCATCG 59.968 50.000 2.27 5.45 38.84 3.84
4038 6297 2.032054 CCATGTCGTTGAATTCCATCGG 59.968 50.000 2.27 0.67 38.24 4.18
4039 6298 1.083489 TGTCGTTGAATTCCATCGGC 58.917 50.000 2.27 7.26 41.49 5.54
4040 6299 0.026285 GTCGTTGAATTCCATCGGCG 59.974 55.000 0.00 0.00 38.24 6.46
4041 6300 1.297598 CGTTGAATTCCATCGGCGC 60.298 57.895 0.00 0.00 35.08 6.53
4044 6303 3.287520 GAATTCCATCGGCGCCCC 61.288 66.667 23.46 0.00 0.00 5.80
4045 6304 4.894896 AATTCCATCGGCGCCCCC 62.895 66.667 23.46 0.00 0.00 5.40
4094 8700 8.777578 TTATCTAGGCTATCCAGTGTAGAAAA 57.222 34.615 0.00 0.00 33.74 2.29
4140 8746 5.690865 TCTGTAAGACAAAAACCAGGTGAT 58.309 37.500 0.00 0.00 38.67 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1177 1389 4.748144 CTCCCCAAGCTGGCCCAC 62.748 72.222 0.00 0.00 35.79 4.61
1534 1778 9.223099 TGCATCATCAGAAACATATATAACCAG 57.777 33.333 0.00 0.00 0.00 4.00
1581 1847 7.749666 TGCTTAATAAAGGAGGATTATGCTCT 58.250 34.615 13.18 0.00 38.52 4.09
1584 1850 8.239998 GTGATGCTTAATAAAGGAGGATTATGC 58.760 37.037 0.00 0.00 36.41 3.14
1608 1878 2.491675 GGTAAAAGACCCCTCCTGTG 57.508 55.000 0.00 0.00 43.25 3.66
1625 1932 2.171870 CAGATAACCGGTGTTATGGGGT 59.828 50.000 8.52 0.00 45.47 4.95
1629 1936 4.755411 ACTGTCAGATAACCGGTGTTATG 58.245 43.478 8.52 6.59 45.47 1.90
1637 1944 5.408604 AGCAACTAAAACTGTCAGATAACCG 59.591 40.000 6.91 0.00 0.00 4.44
1653 1960 5.880332 ACAGACACTTTCTTGAAGCAACTAA 59.120 36.000 0.00 0.00 39.04 2.24
1724 2113 7.147567 TGTCAGCTGTACCCATATCTTCAAATA 60.148 37.037 14.67 0.00 0.00 1.40
1738 2127 6.985188 TCTTTTTCATATGTCAGCTGTACC 57.015 37.500 14.67 3.75 0.00 3.34
1791 2265 2.716217 AGCAGAGCCAACAGGTAATTC 58.284 47.619 0.00 0.00 0.00 2.17
2067 2599 2.351835 CGAAGATTGACTCGGTGTGACT 60.352 50.000 0.00 0.00 0.00 3.41
2168 2769 4.704540 CCATGTATACCTTGTTTGCTTGGA 59.295 41.667 0.00 0.00 31.07 3.53
2293 2938 2.435586 CTGGTGCCCTCTTCTGCG 60.436 66.667 0.00 0.00 0.00 5.18
2304 2949 2.039405 CCTGCTTCAGCTCTGGTGC 61.039 63.158 0.00 3.16 42.66 5.01
2326 2971 3.426859 CGAGCTCAATTAGGTATTCTGCG 59.573 47.826 15.40 0.00 35.60 5.18
2424 3071 8.579850 TGCAAAAATCCAGTACTATCTGATTT 57.420 30.769 12.47 12.47 37.61 2.17
3880 6004 5.872963 ACCCTTACTAACAAGGTGTTAAGG 58.127 41.667 11.67 11.67 41.70 2.69
3881 6005 8.943002 CATTACCCTTACTAACAAGGTGTTAAG 58.057 37.037 2.73 0.13 41.70 1.85
3882 6006 8.439172 ACATTACCCTTACTAACAAGGTGTTAA 58.561 33.333 2.73 0.00 41.70 2.01
3883 6007 7.879160 CACATTACCCTTACTAACAAGGTGTTA 59.121 37.037 1.22 1.22 43.14 2.41
3884 6008 6.713450 CACATTACCCTTACTAACAAGGTGTT 59.287 38.462 0.00 0.00 43.14 3.32
3885 6009 6.043474 TCACATTACCCTTACTAACAAGGTGT 59.957 38.462 1.50 2.30 43.14 4.16
3886 6010 6.469410 TCACATTACCCTTACTAACAAGGTG 58.531 40.000 1.50 0.00 43.14 4.00
3887 6011 6.691255 TCACATTACCCTTACTAACAAGGT 57.309 37.500 1.50 0.00 43.14 3.50
4036 6295 4.499633 AAAGGTATGGGGGCGCCG 62.500 66.667 22.54 0.00 0.00 6.46
4037 6296 2.833121 CAAAGGTATGGGGGCGCC 60.833 66.667 21.18 21.18 0.00 6.53
4038 6297 2.119029 GTCAAAGGTATGGGGGCGC 61.119 63.158 0.00 0.00 0.00 6.53
4039 6298 1.029947 GTGTCAAAGGTATGGGGGCG 61.030 60.000 0.00 0.00 0.00 6.13
4040 6299 0.331616 AGTGTCAAAGGTATGGGGGC 59.668 55.000 0.00 0.00 0.00 5.80
4041 6300 1.406887 CGAGTGTCAAAGGTATGGGGG 60.407 57.143 0.00 0.00 0.00 5.40
4044 6303 5.682943 TTTTTCGAGTGTCAAAGGTATGG 57.317 39.130 0.00 0.00 0.00 2.74
4094 8700 2.042464 ACACATGTCGCTCCATAGGAT 58.958 47.619 0.00 0.00 0.00 3.24
4140 8746 5.876357 ACCTTTGTAGGCTTTGATAAGACA 58.124 37.500 0.00 0.00 46.22 3.41


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

AutoCloner maintained by Alex Coulton.