Multiple sequence alignment - TraesCS4D01G366300

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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 TraesCS4D01G366300 chr4D 100.000 3650 0 0 1 3650 509853835 509850186 0.000000e+00 6741.0
1 TraesCS4D01G366300 chr4B 97.752 3069 66 3 1 3067 656880189 656883256 0.000000e+00 5282.0
2 TraesCS4D01G366300 chr4B 88.350 412 14 8 3264 3650 656883598 656884000 7.140000e-127 464.0
3 TraesCS4D01G366300 chr4B 91.617 167 9 3 3098 3263 656883357 656883519 3.670000e-55 226.0
4 TraesCS4D01G366300 chr4B 96.875 32 1 0 3203 3234 656883732 656883763 2.000000e-03 54.7
5 TraesCS4D01G366300 chr5A 95.414 3009 114 10 1 3009 698691369 698688385 0.000000e+00 4771.0
6 TraesCS4D01G366300 chr5B 90.789 1824 156 9 1 1816 711963002 711964821 0.000000e+00 2427.0
7 TraesCS4D01G366300 chr5B 88.920 1796 184 8 1 1784 711931550 711933342 0.000000e+00 2200.0
8 TraesCS4D01G366300 chr5B 87.935 1840 191 17 3 1813 711412762 711410925 0.000000e+00 2139.0
9 TraesCS4D01G366300 chr5B 89.585 1661 165 8 39 1693 711736526 711738184 0.000000e+00 2102.0
10 TraesCS4D01G366300 chr5B 83.425 911 119 15 1810 2706 711738486 711739378 0.000000e+00 817.0
11 TraesCS4D01G366300 chr5B 84.458 830 105 14 1895 2705 711406810 711405986 0.000000e+00 797.0
12 TraesCS4D01G366300 chr5B 84.279 846 96 19 1810 2641 711933527 711934349 0.000000e+00 791.0
13 TraesCS4D01G366300 chr5B 78.947 266 22 19 3341 3582 711405229 711404974 2.270000e-32 150.0
14 TraesCS4D01G366300 chr5B 78.161 261 27 13 3346 3582 711349049 711348795 4.910000e-29 139.0
15 TraesCS4D01G366300 chr5B 86.047 86 7 4 3482 3562 711741915 711742000 1.810000e-13 87.9
16 TraesCS4D01G366300 chr5B 77.124 153 10 13 3373 3500 694366777 694366929 8.460000e-07 65.8
17 TraesCS4D01G366300 chr5B 100.000 35 0 0 2755 2789 711331908 711331874 8.460000e-07 65.8
18 TraesCS4D01G366300 chr5B 83.099 71 9 2 2719 2789 711405951 711405884 1.090000e-05 62.1
19 TraesCS4D01G366300 chr5D 89.918 1835 166 8 1 1816 561924439 561926273 0.000000e+00 2346.0
20 TraesCS4D01G366300 chr5D 89.927 1787 172 5 1 1783 561897104 561898886 0.000000e+00 2296.0
21 TraesCS4D01G366300 chr5D 84.468 1822 247 21 6 1800 556539883 556538071 0.000000e+00 1764.0
22 TraesCS4D01G366300 chr5D 89.803 1216 111 9 1 1204 552859990 552858776 0.000000e+00 1546.0
23 TraesCS4D01G366300 chr5D 85.841 904 106 15 1810 2706 551882201 551883089 0.000000e+00 941.0
24 TraesCS4D01G366300 chr5D 84.598 909 121 16 1810 2706 561926488 561927389 0.000000e+00 885.0
25 TraesCS4D01G366300 chr5D 84.165 922 113 19 1810 2706 561899072 561899985 0.000000e+00 863.0
26 TraesCS4D01G366300 chr5D 83.964 555 68 10 1810 2346 561641920 561641369 2.510000e-141 512.0
27 TraesCS4D01G366300 chr5D 87.442 215 19 3 3373 3583 551883709 551883919 1.310000e-59 241.0
28 TraesCS4D01G366300 chr7B 89.888 1424 137 4 397 1816 889419 887999 0.000000e+00 1825.0
29 TraesCS4D01G366300 chr7B 86.154 910 108 12 1810 2706 1034248 1033344 0.000000e+00 966.0
30 TraesCS4D01G366300 chr7B 86.013 908 104 16 1810 2704 883316 882419 0.000000e+00 952.0
31 TraesCS4D01G366300 chr7B 86.013 908 104 16 1810 2704 887787 886890 0.000000e+00 952.0
32 TraesCS4D01G366300 chr7B 84.863 839 110 7 1813 2638 1307799 1308633 0.000000e+00 830.0
33 TraesCS4D01G366300 chr7B 85.388 657 78 11 2060 2701 1101507 1100854 0.000000e+00 665.0
34 TraesCS4D01G366300 chr7B 82.667 225 19 7 3375 3583 829210 828990 8.050000e-42 182.0
35 TraesCS4D01G366300 chr7B 78.233 317 33 18 3299 3583 1032406 1032094 1.740000e-38 171.0
36 TraesCS4D01G366300 chr7B 79.245 212 15 16 3378 3562 1352365 1352574 1.780000e-23 121.0
37 TraesCS4D01G366300 chr7B 80.368 163 11 7 2711 2859 882376 882221 1.790000e-18 104.0
38 TraesCS4D01G366300 chr7B 80.368 163 11 7 2711 2859 886847 886692 1.790000e-18 104.0
39 TraesCS4D01G366300 chr7B 100.000 47 0 0 3502 3548 1326945 1326991 1.810000e-13 87.9
40 TraesCS4D01G366300 chr7B 100.000 35 0 0 3310 3344 886081 886047 8.460000e-07 65.8
41 TraesCS4D01G366300 chr7B 77.444 133 14 7 3117 3240 1032406 1032281 8.460000e-07 65.8
42 TraesCS4D01G366300 chr7B 97.222 36 1 0 3203 3238 850827 850862 1.090000e-05 62.1
43 TraesCS4D01G366300 chr7B 100.000 29 0 0 2886 2914 1100469 1100441 2.000000e-03 54.7
44 TraesCS4D01G366300 chr2A 94.886 176 9 0 3373 3548 306138605 306138430 3.590000e-70 276.0
45 TraesCS4D01G366300 chr2B 92.614 176 13 0 3373 3548 357169679 357169504 1.680000e-63 254.0


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 TraesCS4D01G366300 chr4D 509850186 509853835 3649 True 6741.000000 6741 100.000000 1 3650 1 chr4D.!!$R1 3649
1 TraesCS4D01G366300 chr4B 656880189 656884000 3811 False 1506.675000 5282 93.648500 1 3650 4 chr4B.!!$F1 3649
2 TraesCS4D01G366300 chr5A 698688385 698691369 2984 True 4771.000000 4771 95.414000 1 3009 1 chr5A.!!$R1 3008
3 TraesCS4D01G366300 chr5B 711963002 711964821 1819 False 2427.000000 2427 90.789000 1 1816 1 chr5B.!!$F2 1815
4 TraesCS4D01G366300 chr5B 711410925 711412762 1837 True 2139.000000 2139 87.935000 3 1813 1 chr5B.!!$R3 1810
5 TraesCS4D01G366300 chr5B 711931550 711934349 2799 False 1495.500000 2200 86.599500 1 2641 2 chr5B.!!$F4 2640
6 TraesCS4D01G366300 chr5B 711736526 711742000 5474 False 1002.300000 2102 86.352333 39 3562 3 chr5B.!!$F3 3523
7 TraesCS4D01G366300 chr5B 711404974 711406810 1836 True 336.366667 797 82.168000 1895 3582 3 chr5B.!!$R4 1687
8 TraesCS4D01G366300 chr5D 556538071 556539883 1812 True 1764.000000 1764 84.468000 6 1800 1 chr5D.!!$R2 1794
9 TraesCS4D01G366300 chr5D 561924439 561927389 2950 False 1615.500000 2346 87.258000 1 2706 2 chr5D.!!$F3 2705
10 TraesCS4D01G366300 chr5D 561897104 561899985 2881 False 1579.500000 2296 87.046000 1 2706 2 chr5D.!!$F2 2705
11 TraesCS4D01G366300 chr5D 552858776 552859990 1214 True 1546.000000 1546 89.803000 1 1204 1 chr5D.!!$R1 1203
12 TraesCS4D01G366300 chr5D 551882201 551883919 1718 False 591.000000 941 86.641500 1810 3583 2 chr5D.!!$F1 1773
13 TraesCS4D01G366300 chr5D 561641369 561641920 551 True 512.000000 512 83.964000 1810 2346 1 chr5D.!!$R3 536
14 TraesCS4D01G366300 chr7B 1307799 1308633 834 False 830.000000 830 84.863000 1813 2638 1 chr7B.!!$F2 825
15 TraesCS4D01G366300 chr7B 882221 889419 7198 True 667.133333 1825 87.108333 397 3344 6 chr7B.!!$R2 2947
16 TraesCS4D01G366300 chr7B 1032094 1034248 2154 True 400.933333 966 80.610333 1810 3583 3 chr7B.!!$R3 1773
17 TraesCS4D01G366300 chr7B 1100441 1101507 1066 True 359.850000 665 92.694000 2060 2914 2 chr7B.!!$R4 854

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
976 1028 3.294038 AGCATCTGCAGGAGCTAAAAT 57.706 42.857 25.6 7.79 45.16 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2792 3283 1.700739 AGTCGGTTGGTTTGTATCCCA 59.299 47.619 0.0 0.0 0.0 4.37 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
782 834 9.850628 CAAAATTAGTTCATCTCACAATGACAT 57.149 29.630 0.00 0.00 35.44 3.06
976 1028 3.294038 AGCATCTGCAGGAGCTAAAAT 57.706 42.857 25.60 7.79 45.16 1.82
1135 1187 6.890979 AGTTGAAAAAGAATCTGAAGGAGG 57.109 37.500 0.00 0.00 0.00 4.30
1197 1252 4.691685 GCTGATATCCTTGATGCTCTTCAG 59.308 45.833 0.00 0.00 33.07 3.02
1248 1303 1.400494 GCAAATCATGGTGGTACCGTC 59.600 52.381 7.57 2.76 42.58 4.79
1283 1338 4.955811 TGTGTCTTGACATCTGGTTAGT 57.044 40.909 6.74 0.00 0.00 2.24
1555 1610 2.016318 GCATCGATTGTCCCAATGTCA 58.984 47.619 0.00 0.00 0.00 3.58
1655 1710 0.915872 TCCATGCCTCACACCTCCAT 60.916 55.000 0.00 0.00 0.00 3.41
1992 2326 0.548031 TGGCCATGGGAGAATCAGAC 59.452 55.000 15.13 0.00 36.25 3.51
2248 2609 4.104776 CAAATTATTGCCTGCAGGTTACG 58.895 43.478 32.81 8.64 37.57 3.18
2652 3027 7.650504 CCACATTTATCCGTCGAAGAATAACTA 59.349 37.037 0.00 0.00 39.69 2.24
2794 3285 3.379057 TGCACATTAATCAGCAGATGTGG 59.621 43.478 14.78 0.00 45.79 4.17
3045 4323 2.558554 GATGCTGCCTGCTGCTTTGG 62.559 60.000 19.48 1.86 43.37 3.28
3121 4474 2.039818 TGTAGTAGAGAGGGCTGTCG 57.960 55.000 0.00 0.00 0.00 4.35
3143 4503 0.179020 TCTTGTCTTGGTGGTGCAGG 60.179 55.000 0.00 0.00 0.00 4.85
3150 4510 0.037590 TTGGTGGTGCAGGATGGTAC 59.962 55.000 0.00 0.00 35.86 3.34
3167 4528 6.935208 GGATGGTACTATGAATGTAACCTTCC 59.065 42.308 0.00 8.06 33.74 3.46
3170 4531 8.246430 TGGTACTATGAATGTAACCTTCCTAG 57.754 38.462 0.00 0.00 31.22 3.02
3224 4585 7.439056 AGTTGAGTATGCTTTCCAATTTGTTTG 59.561 33.333 0.00 0.00 34.93 2.93
3239 4600 9.453325 CCAATTTGTTTGATTCTTGAAAAATGG 57.547 29.630 0.00 0.00 37.53 3.16
3257 4618 4.993029 ATGGAGTAGCAGAGAGTTACAC 57.007 45.455 0.00 0.00 36.49 2.90
3455 4980 0.683504 TCCTCTAGGACCGGAGCAAC 60.684 60.000 9.46 0.00 39.78 4.17
3500 6385 2.936498 CTGAAAGTATTGTACCCGGCTG 59.064 50.000 0.00 0.00 0.00 4.85
3594 6585 8.004087 AGGTAATGAATGATCCAAGTTCATTG 57.996 34.615 22.38 0.00 46.36 2.82
3627 6618 0.466124 GGATCCTGCAGTCCCAGTAC 59.534 60.000 13.81 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
782 834 5.948162 AGTGTACTAGGTAACCTCATTTCGA 59.052 40.000 0.00 0.00 34.61 3.71
1135 1187 1.559682 TCTGCCCCAGAGTAATTCCAC 59.440 52.381 0.00 0.00 35.39 4.02
1158 1210 1.204704 TCAGCATCTGTAGTTGGTCCG 59.795 52.381 0.00 0.00 32.61 4.79
1197 1252 2.197577 GCTCTAAGATTCGAGTGTGGC 58.802 52.381 0.00 0.00 0.00 5.01
1248 1303 1.343465 AGACACAACCAACTAGGACCG 59.657 52.381 0.00 0.00 41.22 4.79
1283 1338 9.661563 CTTCTAGAGTGAGAGTCTCTAAACTTA 57.338 37.037 20.64 9.87 41.84 2.24
1448 1503 3.487574 CGGCATCTCATAAAACTCGACTC 59.512 47.826 0.00 0.00 0.00 3.36
1527 1582 5.419239 TGGGACAATCGATGCATATGATA 57.581 39.130 6.97 0.00 31.92 2.15
1555 1610 1.554160 CTCTGAGAAGGGCATCACACT 59.446 52.381 0.00 0.00 0.00 3.55
1678 1733 3.139077 ACAACGTTTCTGAATCACCTCC 58.861 45.455 0.00 0.00 0.00 4.30
1992 2326 1.824852 GCAGGGAAAGGGTAAATGGTG 59.175 52.381 0.00 0.00 0.00 4.17
2248 2609 4.727507 TGAGCTTCTCCAATCTAGACAC 57.272 45.455 0.00 0.00 0.00 3.67
2652 3027 3.284617 GACAAGTGTTACCTTGGGTGTT 58.715 45.455 14.63 0.00 44.89 3.32
2792 3283 1.700739 AGTCGGTTGGTTTGTATCCCA 59.299 47.619 0.00 0.00 0.00 4.37
2794 3285 3.329929 AGAGTCGGTTGGTTTGTATCC 57.670 47.619 0.00 0.00 0.00 2.59
3071 4354 9.881773 ACCTACTACTACTAGAGAGTACAGTAT 57.118 37.037 0.00 0.00 37.10 2.12
3073 4356 9.131791 GTACCTACTACTACTAGAGAGTACAGT 57.868 40.741 0.00 3.83 37.10 3.55
3078 4361 9.881773 ACATAGTACCTACTACTACTAGAGAGT 57.118 37.037 0.00 1.80 40.18 3.24
3092 4445 6.013466 AGCCCTCTCTACTACATAGTACCTAC 60.013 46.154 0.00 0.00 37.73 3.18
3093 4446 6.013553 CAGCCCTCTCTACTACATAGTACCTA 60.014 46.154 0.00 0.00 37.73 3.08
3095 4448 5.005094 CAGCCCTCTCTACTACATAGTACC 58.995 50.000 0.00 0.00 37.73 3.34
3096 4449 5.623169 ACAGCCCTCTCTACTACATAGTAC 58.377 45.833 0.00 0.00 37.73 2.73
3107 4460 0.328592 AGACACGACAGCCCTCTCTA 59.671 55.000 0.00 0.00 0.00 2.43
3121 4474 0.663153 GCACCACCAAGACAAGACAC 59.337 55.000 0.00 0.00 0.00 3.67
3143 4503 7.736893 AGGAAGGTTACATTCATAGTACCATC 58.263 38.462 11.81 0.00 0.00 3.51
3176 4537 8.873830 CAACTCAATTTCACTTCACGATACTAT 58.126 33.333 0.00 0.00 0.00 2.12
3224 4585 7.335422 TCTCTGCTACTCCATTTTTCAAGAATC 59.665 37.037 0.00 0.00 0.00 2.52
3257 4618 3.615496 CCGTCCCAAAATTGTACGTAGAG 59.385 47.826 0.00 0.00 35.31 2.43
3263 4624 2.089201 CCCTCCGTCCCAAAATTGTAC 58.911 52.381 0.00 0.00 0.00 2.90
3264 4625 1.986631 TCCCTCCGTCCCAAAATTGTA 59.013 47.619 0.00 0.00 0.00 2.41
3265 4626 0.774908 TCCCTCCGTCCCAAAATTGT 59.225 50.000 0.00 0.00 0.00 2.71
3301 4740 2.917933 CACCACCAAGACAAGACAGAA 58.082 47.619 0.00 0.00 0.00 3.02
3302 4741 1.475034 GCACCACCAAGACAAGACAGA 60.475 52.381 0.00 0.00 0.00 3.41
3303 4742 0.947244 GCACCACCAAGACAAGACAG 59.053 55.000 0.00 0.00 0.00 3.51
3304 4743 0.254462 TGCACCACCAAGACAAGACA 59.746 50.000 0.00 0.00 0.00 3.41
3305 4744 1.609208 ATGCACCACCAAGACAAGAC 58.391 50.000 0.00 0.00 0.00 3.01
3351 4824 7.019774 TCTCAACTCAATTCAGTTTCACTTG 57.980 36.000 0.00 0.00 34.17 3.16
3402 4916 7.988028 AGTATCAGGCTAAATAGGTTCAAGAAC 59.012 37.037 4.39 4.39 40.45 3.01
3455 4980 0.169672 CTGCCCAAGCACAATTCTCG 59.830 55.000 0.00 0.00 46.52 4.04


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

AutoCloner maintained by Alex Coulton.