Multiple sequence alignment - TraesCS5B01G339900

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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 TraesCS5B01G339900 chr5B 100.000 5971 0 0 1 5971 524328056 524334026 0.000000e+00 11027.0
1 TraesCS5B01G339900 chr5B 89.380 2241 153 36 1607 3838 498537049 498539213 0.000000e+00 2741.0
2 TraesCS5B01G339900 chr5B 88.830 1692 113 30 1054 2690 498273584 498275254 0.000000e+00 2008.0
3 TraesCS5B01G339900 chr5B 87.232 1676 110 34 1054 2673 498796064 498797691 0.000000e+00 1814.0
4 TraesCS5B01G339900 chr5B 90.616 1332 76 15 2751 4077 498797695 498798982 0.000000e+00 1722.0
5 TraesCS5B01G339900 chr5B 87.716 1156 97 25 1054 2176 498282351 498283494 0.000000e+00 1306.0
6 TraesCS5B01G339900 chr5B 88.067 1014 77 17 1202 2176 498715246 498716254 0.000000e+00 1162.0
7 TraesCS5B01G339900 chr5B 91.268 355 29 2 3717 4071 498720719 498721071 3.240000e-132 483.0
8 TraesCS5B01G339900 chr5B 90.533 169 9 6 746 912 524328238 524328401 3.620000e-52 217.0
9 TraesCS5B01G339900 chr5B 90.476 168 11 5 183 346 524328801 524328967 3.620000e-52 217.0
10 TraesCS5B01G339900 chr5D 93.773 3051 111 31 1054 4077 431914043 431911045 0.000000e+00 4508.0
11 TraesCS5B01G339900 chr5D 89.995 2119 116 39 1774 3882 413607307 413609339 0.000000e+00 2651.0
12 TraesCS5B01G339900 chr5D 88.912 1930 127 37 1487 3403 413476812 413478667 0.000000e+00 2298.0
13 TraesCS5B01G339900 chr5D 89.052 1635 104 27 1106 2690 413453953 413455562 0.000000e+00 1958.0
14 TraesCS5B01G339900 chr5D 93.460 1208 58 7 4110 5310 433499586 433500779 0.000000e+00 1773.0
15 TraesCS5B01G339900 chr5D 87.353 1020 77 18 1054 2028 413576976 413577988 0.000000e+00 1122.0
16 TraesCS5B01G339900 chr5D 92.655 354 16 8 1 347 431916000 431915650 8.930000e-138 501.0
17 TraesCS5B01G339900 chr5D 87.281 456 33 9 1054 1486 413606809 413607262 1.160000e-136 497.0
18 TraesCS5B01G339900 chr5D 93.569 311 14 6 752 1056 431915812 431915502 5.450000e-125 459.0
19 TraesCS5B01G339900 chr5D 100.000 31 0 0 4073 4103 433499571 433499541 2.320000e-04 58.4
20 TraesCS5B01G339900 chr5A 96.098 2665 85 8 1054 3706 547044481 547041824 0.000000e+00 4327.0
21 TraesCS5B01G339900 chr5A 87.201 3094 224 55 1054 4077 525752001 525754992 0.000000e+00 3362.0
22 TraesCS5B01G339900 chr5A 87.810 2699 205 49 1426 4077 525841261 525843882 0.000000e+00 3048.0
23 TraesCS5B01G339900 chr5A 91.170 1846 122 17 2238 4077 526288455 526290265 0.000000e+00 2468.0
24 TraesCS5B01G339900 chr5A 90.319 1880 128 25 1535 3403 525715637 525717473 0.000000e+00 2414.0
25 TraesCS5B01G339900 chr5A 89.744 1248 100 13 2837 4077 525935025 525936251 0.000000e+00 1570.0
26 TraesCS5B01G339900 chr5A 83.941 1152 91 29 1054 2159 526287365 526288468 0.000000e+00 1016.0
27 TraesCS5B01G339900 chr5A 93.245 681 40 5 3401 4077 525717630 525718308 0.000000e+00 998.0
28 TraesCS5B01G339900 chr5A 93.761 593 29 3 4108 4694 547035534 547034944 0.000000e+00 883.0
29 TraesCS5B01G339900 chr5A 93.983 482 25 3 4830 5310 547034926 547034448 0.000000e+00 726.0
30 TraesCS5B01G339900 chr5A 85.115 524 34 15 1054 1536 525933028 525933548 4.160000e-136 496.0
31 TraesCS5B01G339900 chr5A 88.312 308 21 7 756 1056 547046213 547045914 7.360000e-94 355.0
32 TraesCS5B01G339900 chr5A 86.667 285 25 9 62 339 547046340 547046062 2.700000e-78 303.0
33 TraesCS5B01G339900 chr4B 92.598 662 48 1 5310 5971 175645471 175644811 0.000000e+00 950.0
34 TraesCS5B01G339900 chr4B 92.261 659 50 1 5313 5971 438692574 438691917 0.000000e+00 933.0
35 TraesCS5B01G339900 chr4B 91.958 659 53 0 5313 5971 566527500 566526842 0.000000e+00 924.0
36 TraesCS5B01G339900 chr3B 92.145 662 52 0 5310 5971 436649546 436650207 0.000000e+00 935.0
37 TraesCS5B01G339900 chr3B 92.261 659 48 1 5313 5971 239549626 239548971 0.000000e+00 931.0
38 TraesCS5B01G339900 chr3B 91.742 666 48 4 5310 5971 259409192 259408530 0.000000e+00 918.0
39 TraesCS5B01G339900 chr7B 91.994 662 53 0 5310 5971 524512341 524511680 0.000000e+00 929.0
40 TraesCS5B01G339900 chr2B 91.994 662 49 2 5310 5971 318452603 318453260 0.000000e+00 926.0
41 TraesCS5B01G339900 chr2B 91.933 657 53 0 5313 5969 734139476 734138820 0.000000e+00 920.0
42 TraesCS5B01G339900 chr2B 90.488 410 33 6 347 753 386288898 386289304 2.450000e-148 536.0
43 TraesCS5B01G339900 chr1A 82.328 928 94 29 4400 5310 382741376 382742250 0.000000e+00 741.0


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 TraesCS5B01G339900 chr5B 524328056 524334026 5970 False 11027.000000 11027 100.000000 1 5971 1 chr5B.!!$F6 5970
1 TraesCS5B01G339900 chr5B 498537049 498539213 2164 False 2741.000000 2741 89.380000 1607 3838 1 chr5B.!!$F3 2231
2 TraesCS5B01G339900 chr5B 498273584 498275254 1670 False 2008.000000 2008 88.830000 1054 2690 1 chr5B.!!$F1 1636
3 TraesCS5B01G339900 chr5B 498796064 498798982 2918 False 1768.000000 1814 88.924000 1054 4077 2 chr5B.!!$F7 3023
4 TraesCS5B01G339900 chr5B 498282351 498283494 1143 False 1306.000000 1306 87.716000 1054 2176 1 chr5B.!!$F2 1122
5 TraesCS5B01G339900 chr5B 498715246 498716254 1008 False 1162.000000 1162 88.067000 1202 2176 1 chr5B.!!$F4 974
6 TraesCS5B01G339900 chr5B 524328238 524328967 729 False 217.000000 217 90.504500 183 912 2 chr5B.!!$F8 729
7 TraesCS5B01G339900 chr5D 413476812 413478667 1855 False 2298.000000 2298 88.912000 1487 3403 1 chr5D.!!$F2 1916
8 TraesCS5B01G339900 chr5D 413453953 413455562 1609 False 1958.000000 1958 89.052000 1106 2690 1 chr5D.!!$F1 1584
9 TraesCS5B01G339900 chr5D 431911045 431916000 4955 True 1822.666667 4508 93.332333 1 4077 3 chr5D.!!$R2 4076
10 TraesCS5B01G339900 chr5D 433499586 433500779 1193 False 1773.000000 1773 93.460000 4110 5310 1 chr5D.!!$F4 1200
11 TraesCS5B01G339900 chr5D 413606809 413609339 2530 False 1574.000000 2651 88.638000 1054 3882 2 chr5D.!!$F5 2828
12 TraesCS5B01G339900 chr5D 413576976 413577988 1012 False 1122.000000 1122 87.353000 1054 2028 1 chr5D.!!$F3 974
13 TraesCS5B01G339900 chr5A 525752001 525754992 2991 False 3362.000000 3362 87.201000 1054 4077 1 chr5A.!!$F1 3023
14 TraesCS5B01G339900 chr5A 525841261 525843882 2621 False 3048.000000 3048 87.810000 1426 4077 1 chr5A.!!$F2 2651
15 TraesCS5B01G339900 chr5A 526287365 526290265 2900 False 1742.000000 2468 87.555500 1054 4077 2 chr5A.!!$F5 3023
16 TraesCS5B01G339900 chr5A 525715637 525718308 2671 False 1706.000000 2414 91.782000 1535 4077 2 chr5A.!!$F3 2542
17 TraesCS5B01G339900 chr5A 547041824 547046340 4516 True 1661.666667 4327 90.359000 62 3706 3 chr5A.!!$R2 3644
18 TraesCS5B01G339900 chr5A 525933028 525936251 3223 False 1033.000000 1570 87.429500 1054 4077 2 chr5A.!!$F4 3023
19 TraesCS5B01G339900 chr5A 547034448 547035534 1086 True 804.500000 883 93.872000 4108 5310 2 chr5A.!!$R1 1202
20 TraesCS5B01G339900 chr4B 175644811 175645471 660 True 950.000000 950 92.598000 5310 5971 1 chr4B.!!$R1 661
21 TraesCS5B01G339900 chr4B 438691917 438692574 657 True 933.000000 933 92.261000 5313 5971 1 chr4B.!!$R2 658
22 TraesCS5B01G339900 chr4B 566526842 566527500 658 True 924.000000 924 91.958000 5313 5971 1 chr4B.!!$R3 658
23 TraesCS5B01G339900 chr3B 436649546 436650207 661 False 935.000000 935 92.145000 5310 5971 1 chr3B.!!$F1 661
24 TraesCS5B01G339900 chr3B 239548971 239549626 655 True 931.000000 931 92.261000 5313 5971 1 chr3B.!!$R1 658
25 TraesCS5B01G339900 chr3B 259408530 259409192 662 True 918.000000 918 91.742000 5310 5971 1 chr3B.!!$R2 661
26 TraesCS5B01G339900 chr7B 524511680 524512341 661 True 929.000000 929 91.994000 5310 5971 1 chr7B.!!$R1 661
27 TraesCS5B01G339900 chr2B 318452603 318453260 657 False 926.000000 926 91.994000 5310 5971 1 chr2B.!!$F1 661
28 TraesCS5B01G339900 chr2B 734138820 734139476 656 True 920.000000 920 91.933000 5313 5969 1 chr2B.!!$R1 656
29 TraesCS5B01G339900 chr1A 382741376 382742250 874 False 741.000000 741 82.328000 4400 5310 1 chr1A.!!$F1 910

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
77 78 4.095036 GCCTCACTTTAGTTGCAATCCTAC 59.905 45.833 0.59 0.0 0.00 3.18 F
1422 3087 1.806542 CCACATGTAACTGTCTGTGCC 59.193 52.381 0.00 0.0 38.10 5.01 F
3341 5559 0.249826 AACAAGCAAATTGGCCCACG 60.250 50.000 0.00 0.0 43.68 4.94 F
4080 6469 0.034337 AAGGCCGCTCGTTGTAGAAA 59.966 50.000 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 3677 1.369091 GCATACAAGCGGTCCCACTG 61.369 60.0 0.00 0.00 0.00 3.66 R
3352 5570 1.452110 TCAGCACACCAAATGGATCG 58.548 50.0 6.42 0.00 38.94 3.69 R
4392 6787 1.270971 CATGGCAAAATAGTGCACGC 58.729 50.0 12.01 7.43 46.81 5.34 R
5497 7910 0.116342 TGCCTCTGGGTCAGGAACTA 59.884 55.0 0.00 0.00 33.13 2.24 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
40 41 4.344104 CCAACCCATGAGACCTTGTAAAT 58.656 43.478 0.00 0.00 0.00 1.40
52 53 8.822805 TGAGACCTTGTAAATCTACCTTGTTAT 58.177 33.333 0.00 0.00 0.00 1.89
77 78 4.095036 GCCTCACTTTAGTTGCAATCCTAC 59.905 45.833 0.59 0.00 0.00 3.18
1128 2704 3.751175 TCTTTTTCTGGGTATTCTGTGCG 59.249 43.478 0.00 0.00 0.00 5.34
1138 2714 5.057149 GGGTATTCTGTGCGTGATTAGAAT 58.943 41.667 0.00 0.00 41.36 2.40
1141 2717 6.425114 GGTATTCTGTGCGTGATTAGAATCAT 59.575 38.462 8.14 0.00 46.17 2.45
1280 2898 4.582869 AGTGAAATACAGAGCTTGATGCA 58.417 39.130 0.00 0.00 45.94 3.96
1422 3087 1.806542 CCACATGTAACTGTCTGTGCC 59.193 52.381 0.00 0.00 38.10 5.01
1488 3182 3.633525 CACCTTGCATGTGGCTTATACAT 59.366 43.478 8.60 0.00 45.15 2.29
1497 3191 4.769688 TGTGGCTTATACATCAGAAGTGG 58.230 43.478 0.00 0.00 0.00 4.00
1669 3677 0.673644 ATGTGGCAGTGTTACCGAGC 60.674 55.000 0.00 0.00 0.00 5.03
1705 3713 5.428253 TGTATGCTCAGAAGGTCCAATTAC 58.572 41.667 0.00 0.00 0.00 1.89
1765 3773 0.535780 TGGGCTGAGTGCTGAAACTG 60.536 55.000 0.00 0.00 42.39 3.16
1827 3839 7.259161 AGAGTGTAATAGTTCTTGATTCGGAC 58.741 38.462 0.00 0.00 0.00 4.79
1846 3858 3.436704 GGACGATGAAGATGAAAGCACAA 59.563 43.478 0.00 0.00 0.00 3.33
1939 4022 0.835543 AGAACAGGCTGGTGCTCTCT 60.836 55.000 20.34 1.65 39.59 3.10
1953 4036 1.903183 GCTCTCTTGAGGGTGGTAACT 59.097 52.381 0.00 0.00 40.53 2.24
2004 4113 1.691196 TGCCTGTTGGAGACCAAAAG 58.309 50.000 12.31 12.31 45.73 2.27
2019 4128 4.932146 ACCAAAAGAGTCAAATTGTTCCG 58.068 39.130 0.00 0.00 0.00 4.30
2243 4385 9.070179 TGTACTGACAAACTAGTAGTATCAACA 57.930 33.333 2.50 7.62 30.68 3.33
2599 4753 6.175712 TGTTGAAATTGTGCCAAGAAAAAC 57.824 33.333 0.00 0.00 0.00 2.43
2673 4865 0.698238 CAATCCTGTGGGGGAAGACA 59.302 55.000 0.00 0.00 39.02 3.41
3131 5337 7.625817 GCCTGCAATCATGATATACAGATTCAC 60.626 40.741 23.85 10.92 30.25 3.18
3255 5472 8.864087 AGATATGTGATGATGCTTCTGTAACTA 58.136 33.333 0.88 0.00 0.00 2.24
3284 5501 7.283580 AGGCCGTTTAGCAACATATGTATTTTA 59.716 33.333 9.21 0.00 32.54 1.52
3315 5533 9.810545 TTTTGGAAGTTCTTACCAAGTATTTTG 57.189 29.630 2.25 0.00 43.15 2.44
3341 5559 0.249826 AACAAGCAAATTGGCCCACG 60.250 50.000 0.00 0.00 43.68 4.94
3546 5935 2.588314 CTCATGCCGCAGAGCCTC 60.588 66.667 0.00 0.00 0.00 4.70
3573 5962 5.390567 GCTAGACTTCGTGGGTTGTTATTTG 60.391 44.000 0.00 0.00 0.00 2.32
3604 5993 6.009589 TCCTGTATTTCCAGCATGAAGAAAA 58.990 36.000 0.00 0.00 39.69 2.29
3921 6310 2.089980 AGCAAATGAGACCACATCAGC 58.910 47.619 0.00 0.00 33.40 4.26
4040 6429 9.618890 ATGCTCATTAGTTTTATTCAGAGCTTA 57.381 29.630 11.67 0.00 45.41 3.09
4067 6456 0.760945 AGTATCCCTCTGGAAGGCCG 60.761 60.000 0.00 0.00 45.98 6.13
4077 6466 1.810030 GGAAGGCCGCTCGTTGTAG 60.810 63.158 0.00 0.00 0.00 2.74
4078 6467 1.214589 GAAGGCCGCTCGTTGTAGA 59.785 57.895 0.00 0.00 0.00 2.59
4079 6468 0.389426 GAAGGCCGCTCGTTGTAGAA 60.389 55.000 0.00 0.00 0.00 2.10
4080 6469 0.034337 AAGGCCGCTCGTTGTAGAAA 59.966 50.000 0.00 0.00 0.00 2.52
4081 6470 0.034337 AGGCCGCTCGTTGTAGAAAA 59.966 50.000 0.00 0.00 0.00 2.29
4082 6471 0.869730 GGCCGCTCGTTGTAGAAAAA 59.130 50.000 0.00 0.00 0.00 1.94
4083 6472 1.399343 GGCCGCTCGTTGTAGAAAAAC 60.399 52.381 0.00 0.00 0.00 2.43
4084 6473 1.399343 GCCGCTCGTTGTAGAAAAACC 60.399 52.381 0.00 0.00 0.00 3.27
4085 6474 1.868498 CCGCTCGTTGTAGAAAAACCA 59.132 47.619 0.00 0.00 0.00 3.67
4086 6475 2.096417 CCGCTCGTTGTAGAAAAACCAG 60.096 50.000 0.00 0.00 0.00 4.00
4087 6476 2.798283 CGCTCGTTGTAGAAAAACCAGA 59.202 45.455 0.00 0.00 0.00 3.86
4088 6477 3.432252 CGCTCGTTGTAGAAAAACCAGAT 59.568 43.478 0.00 0.00 0.00 2.90
4089 6478 4.624024 CGCTCGTTGTAGAAAAACCAGATA 59.376 41.667 0.00 0.00 0.00 1.98
4090 6479 5.220228 CGCTCGTTGTAGAAAAACCAGATAG 60.220 44.000 0.00 0.00 0.00 2.08
4091 6480 5.867716 GCTCGTTGTAGAAAAACCAGATAGA 59.132 40.000 0.00 0.00 0.00 1.98
4092 6481 6.367969 GCTCGTTGTAGAAAAACCAGATAGAA 59.632 38.462 0.00 0.00 0.00 2.10
4093 6482 7.621633 GCTCGTTGTAGAAAAACCAGATAGAAC 60.622 40.741 0.00 0.00 0.00 3.01
4094 6483 7.211573 TCGTTGTAGAAAAACCAGATAGAACA 58.788 34.615 0.00 0.00 0.00 3.18
4095 6484 7.876068 TCGTTGTAGAAAAACCAGATAGAACAT 59.124 33.333 0.00 0.00 0.00 2.71
4096 6485 9.146984 CGTTGTAGAAAAACCAGATAGAACATA 57.853 33.333 0.00 0.00 0.00 2.29
4101 6490 8.499403 AGAAAAACCAGATAGAACATAAGAGC 57.501 34.615 0.00 0.00 0.00 4.09
4102 6491 8.325046 AGAAAAACCAGATAGAACATAAGAGCT 58.675 33.333 0.00 0.00 0.00 4.09
4103 6492 8.870075 AAAAACCAGATAGAACATAAGAGCTT 57.130 30.769 0.00 0.00 0.00 3.74
4104 6493 8.870075 AAAACCAGATAGAACATAAGAGCTTT 57.130 30.769 0.00 0.00 0.00 3.51
4105 6494 8.870075 AAACCAGATAGAACATAAGAGCTTTT 57.130 30.769 0.00 0.00 0.00 2.27
4106 6495 8.499403 AACCAGATAGAACATAAGAGCTTTTC 57.501 34.615 0.00 0.00 0.00 2.29
4115 6504 9.692325 AGAACATAAGAGCTTTTCTAAATGGAT 57.308 29.630 0.00 0.00 35.35 3.41
4176 6571 8.561738 TGAACCCTATTCTTCAAGACATAAAC 57.438 34.615 0.00 0.00 0.00 2.01
4221 6616 7.540474 TTGTCACTTCTAATCTGTCTTAGGT 57.460 36.000 0.00 0.00 31.02 3.08
4232 6627 3.072476 TCTGTCTTAGGTTGGGTTTGGAG 59.928 47.826 0.00 0.00 0.00 3.86
4293 6688 8.750416 CATGAACTTCTATCATAGTCAAACGAG 58.250 37.037 0.00 0.00 35.80 4.18
4332 6727 2.839228 AGTGATTACTCCCTGCCTTCT 58.161 47.619 0.00 0.00 28.79 2.85
4394 6789 9.088512 GGATATTCAAGTATGTAAATCTAGGCG 57.911 37.037 0.00 0.00 0.00 5.52
4409 6804 0.893270 AGGCGTGCACTATTTTGCCA 60.893 50.000 26.29 0.00 44.83 4.92
4582 6977 7.066525 GCTTAATAAGTTGTGGCATTACCTACA 59.933 37.037 1.68 0.00 40.22 2.74
4583 6978 9.120538 CTTAATAAGTTGTGGCATTACCTACAT 57.879 33.333 0.00 0.00 40.22 2.29
4762 7165 2.027192 TCCCTGGAGATTTTGTTCCTCG 60.027 50.000 0.00 0.00 34.48 4.63
4775 7178 6.988622 TTTGTTCCTCGTTTTCTCAGTTTA 57.011 33.333 0.00 0.00 0.00 2.01
4782 7185 6.600427 TCCTCGTTTTCTCAGTTTACCTTTTT 59.400 34.615 0.00 0.00 0.00 1.94
4830 7234 8.561738 TGTAACCATTTGGATCTACTTTCTTC 57.438 34.615 3.01 0.00 38.94 2.87
4831 7235 8.383175 TGTAACCATTTGGATCTACTTTCTTCT 58.617 33.333 3.01 0.00 38.94 2.85
4832 7236 9.232473 GTAACCATTTGGATCTACTTTCTTCTT 57.768 33.333 3.01 0.00 38.94 2.52
4833 7237 7.929941 ACCATTTGGATCTACTTTCTTCTTC 57.070 36.000 3.01 0.00 38.94 2.87
4834 7238 7.694093 ACCATTTGGATCTACTTTCTTCTTCT 58.306 34.615 3.01 0.00 38.94 2.85
4835 7239 8.166726 ACCATTTGGATCTACTTTCTTCTTCTT 58.833 33.333 3.01 0.00 38.94 2.52
4836 7240 8.457261 CCATTTGGATCTACTTTCTTCTTCTTG 58.543 37.037 0.00 0.00 37.39 3.02
4903 7307 6.282199 TCTAGTCTCTGTGAATTTACCACC 57.718 41.667 0.00 0.00 33.80 4.61
4983 7387 4.214971 TGATACGATAGAAAGTAGCCCGAC 59.785 45.833 0.00 0.00 41.38 4.79
5269 7681 1.061033 AGGAGGGTATTCAGGCCAGAT 60.061 52.381 5.01 0.00 0.00 2.90
5335 7747 4.887655 TCGAGAGGTTGATACTATTGCTGA 59.112 41.667 0.00 0.00 0.00 4.26
5475 7888 4.782019 TTGCATAACCCATCAGTGAAAC 57.218 40.909 0.00 0.00 0.00 2.78
5559 7972 5.255397 TGTTATCCCTGATTGGACTGTTT 57.745 39.130 0.00 0.00 37.20 2.83
5567 7980 5.878116 CCCTGATTGGACTGTTTCGTATTTA 59.122 40.000 0.00 0.00 38.35 1.40
5691 8104 3.093057 TGCAGTGTTACAAGGGTGTTTT 58.907 40.909 0.00 0.00 39.30 2.43
5707 8120 5.278604 GGTGTTTTAACAATGCGTTTCTCT 58.721 37.500 0.00 0.00 41.21 3.10
5740 8153 5.678871 GCCGTGAAATTTTAAGGGAGATTCC 60.679 44.000 15.01 0.00 35.23 3.01
5796 8213 3.498777 GTCTCTCGTTGCTAAGGCTTTTT 59.501 43.478 4.45 0.00 39.59 1.94
5815 8232 3.971245 TTGTCATGGGTTTTATTGGCC 57.029 42.857 0.00 0.00 0.00 5.36
5820 8237 0.036448 TGGGTTTTATTGGCCGACGA 59.964 50.000 0.00 0.00 0.00 4.20
5882 8299 4.976116 GGTTGTCAGAAATTTTCAAGACGG 59.024 41.667 20.28 3.84 38.80 4.79
5884 8301 4.204012 TGTCAGAAATTTTCAAGACGGGT 58.796 39.130 20.28 0.00 38.80 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.355818 GGTCTCATGGGTTGGGAACTAC 60.356 54.545 0.00 0.00 39.67 2.73
13 14 0.698818 GGTCTCATGGGTTGGGAACT 59.301 55.000 0.00 0.00 39.67 3.01
25 26 7.259088 ACAAGGTAGATTTACAAGGTCTCAT 57.741 36.000 0.00 0.00 0.00 2.90
40 41 6.869206 AAAGTGAGGCTATAACAAGGTAGA 57.131 37.500 0.00 0.00 0.00 2.59
52 53 4.019321 AGGATTGCAACTAAAGTGAGGCTA 60.019 41.667 0.00 0.00 0.00 3.93
98 99 7.893302 ACCTAAAATTCCCAATCATACACAAGA 59.107 33.333 0.00 0.00 0.00 3.02
100 101 8.429237 AACCTAAAATTCCCAATCATACACAA 57.571 30.769 0.00 0.00 0.00 3.33
132 133 2.172293 CCCCTCTCCATCTCCTTCTTTG 59.828 54.545 0.00 0.00 0.00 2.77
133 134 2.046447 TCCCCTCTCCATCTCCTTCTTT 59.954 50.000 0.00 0.00 0.00 2.52
135 136 1.324014 TCCCCTCTCCATCTCCTTCT 58.676 55.000 0.00 0.00 0.00 2.85
136 137 2.414250 ATCCCCTCTCCATCTCCTTC 57.586 55.000 0.00 0.00 0.00 3.46
144 147 1.908637 TTGCCCCTATCCCCTCTCCA 61.909 60.000 0.00 0.00 0.00 3.86
1138 2714 9.567776 TCCAAAACTCAAATACTGTTCTTATGA 57.432 29.630 0.00 0.00 0.00 2.15
1165 2741 9.451002 TTGAAATATCACCTACGGTAAATTCAA 57.549 29.630 0.00 0.00 34.61 2.69
1260 2878 5.963176 TTTGCATCAAGCTCTGTATTTCA 57.037 34.783 0.00 0.00 45.94 2.69
1422 3087 4.733887 CGTACAAGGCAATCGTAAGTAGAG 59.266 45.833 0.00 0.00 39.48 2.43
1669 3677 1.369091 GCATACAAGCGGTCCCACTG 61.369 60.000 0.00 0.00 0.00 3.66
1705 3713 2.734079 GCAGAGTCGAAAGGAAAGTCAG 59.266 50.000 0.00 0.00 0.00 3.51
1827 3839 4.727162 GCTCTTGTGCTTTCATCTTCATCG 60.727 45.833 0.00 0.00 0.00 3.84
1846 3858 1.665679 CGTCAGTTGTTTGTGTGCTCT 59.334 47.619 0.00 0.00 0.00 4.09
1939 4022 2.696775 TCCTTCAGTTACCACCCTCAA 58.303 47.619 0.00 0.00 0.00 3.02
2004 4113 6.103997 TGGACTATACGGAACAATTTGACTC 58.896 40.000 2.79 0.00 0.00 3.36
2019 4128 6.872020 TCACTAAAGTTGCACTTGGACTATAC 59.128 38.462 0.00 0.00 38.66 1.47
2243 4385 2.211250 ACTGATGAGGCAGTGCAAAT 57.789 45.000 18.61 6.79 46.72 2.32
2334 4479 5.109903 GGTACTTGTGAACTAAGATGCGAT 58.890 41.667 0.00 0.00 0.00 4.58
2673 4865 1.558756 CTCATCTTCCTCCACAGGCTT 59.441 52.381 0.00 0.00 40.12 4.35
2956 5162 9.095065 GGAAAATAAAGTACGCAGATTTCTCTA 57.905 33.333 12.74 0.00 0.00 2.43
2996 5202 7.980662 TCATTATGCCAAACAACATAAATCCAG 59.019 33.333 0.00 0.00 40.92 3.86
3131 5337 2.420642 CATACATGGCCCAGATCTTCG 58.579 52.381 0.00 0.00 0.00 3.79
3255 5472 2.128771 ATGTTGCTAAACGGCCTCAT 57.871 45.000 0.00 0.00 39.30 2.90
3315 5533 3.058983 GGCCAATTTGCTTGTTGCTAAAC 60.059 43.478 0.00 0.00 43.37 2.01
3352 5570 1.452110 TCAGCACACCAAATGGATCG 58.548 50.000 6.42 0.00 38.94 3.69
3556 5945 2.946785 ACCCAAATAACAACCCACGAA 58.053 42.857 0.00 0.00 0.00 3.85
3573 5962 4.532834 TGCTGGAAATACAGGAATAACCC 58.467 43.478 0.00 0.00 35.80 4.11
3604 5993 7.926555 ACAACTACATGCGCTATACTAGAAAAT 59.073 33.333 9.73 0.00 0.00 1.82
3707 6096 8.827599 CATACGTTTAAACTTTCAAGTCATTCG 58.172 33.333 16.01 0.72 38.57 3.34
3719 6108 7.424227 TCGTTCCAATCATACGTTTAAACTT 57.576 32.000 16.01 9.53 36.70 2.66
3921 6310 1.610522 CAGAAAGTGGAAACCTGCCAG 59.389 52.381 0.00 0.00 35.77 4.85
4040 6429 2.852449 TCCAGAGGGATACTTTGCCAAT 59.148 45.455 0.00 0.00 38.64 3.16
4067 6456 5.867716 TCTATCTGGTTTTTCTACAACGAGC 59.132 40.000 0.00 0.00 31.83 5.03
4077 6466 8.499403 AGCTCTTATGTTCTATCTGGTTTTTC 57.501 34.615 0.00 0.00 0.00 2.29
4078 6467 8.870075 AAGCTCTTATGTTCTATCTGGTTTTT 57.130 30.769 0.00 0.00 0.00 1.94
4079 6468 8.870075 AAAGCTCTTATGTTCTATCTGGTTTT 57.130 30.769 0.00 0.00 0.00 2.43
4080 6469 8.870075 AAAAGCTCTTATGTTCTATCTGGTTT 57.130 30.769 0.00 0.00 0.00 3.27
4081 6470 8.325046 AGAAAAGCTCTTATGTTCTATCTGGTT 58.675 33.333 0.00 0.00 0.00 3.67
4082 6471 7.856415 AGAAAAGCTCTTATGTTCTATCTGGT 58.144 34.615 0.00 0.00 0.00 4.00
4083 6472 9.823647 TTAGAAAAGCTCTTATGTTCTATCTGG 57.176 33.333 0.00 0.00 35.41 3.86
4089 6478 9.692325 ATCCATTTAGAAAAGCTCTTATGTTCT 57.308 29.630 0.00 0.00 35.41 3.01
4090 6479 9.943163 GATCCATTTAGAAAAGCTCTTATGTTC 57.057 33.333 0.00 0.00 35.41 3.18
4091 6480 9.466497 TGATCCATTTAGAAAAGCTCTTATGTT 57.534 29.630 0.00 0.00 35.41 2.71
4092 6481 9.638176 ATGATCCATTTAGAAAAGCTCTTATGT 57.362 29.630 0.00 0.00 35.41 2.29
4093 6482 9.894783 CATGATCCATTTAGAAAAGCTCTTATG 57.105 33.333 0.00 0.00 35.41 1.90
4094 6483 9.857656 TCATGATCCATTTAGAAAAGCTCTTAT 57.142 29.630 0.00 0.00 35.41 1.73
4095 6484 9.857656 ATCATGATCCATTTAGAAAAGCTCTTA 57.142 29.630 1.18 0.00 35.41 2.10
4096 6485 8.763984 ATCATGATCCATTTAGAAAAGCTCTT 57.236 30.769 1.18 0.00 35.41 2.85
4099 6488 9.803507 TCATATCATGATCCATTTAGAAAAGCT 57.196 29.630 12.53 0.00 33.59 3.74
4104 6493 8.963725 GCCATTCATATCATGATCCATTTAGAA 58.036 33.333 12.53 7.48 39.39 2.10
4105 6494 8.333984 AGCCATTCATATCATGATCCATTTAGA 58.666 33.333 12.53 0.00 39.39 2.10
4106 6495 8.521170 AGCCATTCATATCATGATCCATTTAG 57.479 34.615 12.53 0.00 39.39 1.85
4176 6571 6.458210 ACAATCAAGGAAGGCAAAAATGTAG 58.542 36.000 0.00 0.00 0.00 2.74
4232 6627 4.077822 CCATCTAAATCAATGAGAGGGCC 58.922 47.826 0.00 0.00 34.67 5.80
4332 6727 7.913297 GCATACATTTTAGAACTATTTTCCGCA 59.087 33.333 0.00 0.00 0.00 5.69
4377 6772 4.099573 AGTGCACGCCTAGATTTACATACT 59.900 41.667 12.01 0.00 0.00 2.12
4392 6787 1.270971 CATGGCAAAATAGTGCACGC 58.729 50.000 12.01 7.43 46.81 5.34
4394 6789 2.493278 AGGACATGGCAAAATAGTGCAC 59.507 45.455 9.40 9.40 46.81 4.57
4409 6804 4.927267 TCAAACTGGGAATGTAGGACAT 57.073 40.909 0.00 0.00 41.31 3.06
4540 6935 5.927281 ATTAAGCTACAGGGAGAAACGTA 57.073 39.130 0.00 0.00 0.00 3.57
4582 6977 6.721318 ACAGTTGATGTGGGTGAAAGTATAT 58.279 36.000 0.00 0.00 41.91 0.86
4583 6978 6.121776 ACAGTTGATGTGGGTGAAAGTATA 57.878 37.500 0.00 0.00 41.91 1.47
4826 7230 8.397906 CAAGATACAACAACAACAAGAAGAAGA 58.602 33.333 0.00 0.00 0.00 2.87
4828 7232 6.972328 GCAAGATACAACAACAACAAGAAGAA 59.028 34.615 0.00 0.00 0.00 2.52
4829 7233 6.459573 GGCAAGATACAACAACAACAAGAAGA 60.460 38.462 0.00 0.00 0.00 2.87
4830 7234 5.687285 GGCAAGATACAACAACAACAAGAAG 59.313 40.000 0.00 0.00 0.00 2.85
4831 7235 5.451242 GGGCAAGATACAACAACAACAAGAA 60.451 40.000 0.00 0.00 0.00 2.52
4832 7236 4.037446 GGGCAAGATACAACAACAACAAGA 59.963 41.667 0.00 0.00 0.00 3.02
4833 7237 4.037923 AGGGCAAGATACAACAACAACAAG 59.962 41.667 0.00 0.00 0.00 3.16
4834 7238 3.957497 AGGGCAAGATACAACAACAACAA 59.043 39.130 0.00 0.00 0.00 2.83
4835 7239 3.561143 AGGGCAAGATACAACAACAACA 58.439 40.909 0.00 0.00 0.00 3.33
4836 7240 3.568007 TGAGGGCAAGATACAACAACAAC 59.432 43.478 0.00 0.00 0.00 3.32
4903 7307 1.370414 CAGTGCAGAAAAACCGGCG 60.370 57.895 0.00 0.00 0.00 6.46
5039 7449 6.591834 GCAGTAGTTCTAATCAGTCATTGTGT 59.408 38.462 0.00 0.00 0.00 3.72
5044 7454 7.279536 CACAATGCAGTAGTTCTAATCAGTCAT 59.720 37.037 0.00 0.00 0.00 3.06
5335 7747 6.962182 TCCACTTGATATCCTTTGAAGTGAT 58.038 36.000 24.11 0.00 44.08 3.06
5414 7826 2.505167 GGGGACCGGCTTACGCTAT 61.505 63.158 0.00 0.00 40.86 2.97
5445 7858 7.436080 CACTGATGGGTTATGCAAAATATCAAC 59.564 37.037 0.00 0.00 0.00 3.18
5475 7888 1.799933 AAGTCCTCCTCCATAGGCAG 58.200 55.000 0.00 0.00 43.31 4.85
5497 7910 0.116342 TGCCTCTGGGTCAGGAACTA 59.884 55.000 0.00 0.00 33.13 2.24
5559 7972 4.338964 TCGGGTCATGTAAGCTAAATACGA 59.661 41.667 0.00 0.00 0.00 3.43
5567 7980 1.522569 GCCTCGGGTCATGTAAGCT 59.477 57.895 0.00 0.00 0.00 3.74
5691 8104 4.637276 TCCTCAAGAGAAACGCATTGTTA 58.363 39.130 0.00 0.00 40.84 2.41
5707 8120 0.404040 AATTTCACGGCCCTCCTCAA 59.596 50.000 0.00 0.00 0.00 3.02
5740 8153 2.208431 GATGACCGCAATCTCCTTCAG 58.792 52.381 0.00 0.00 0.00 3.02
5796 8213 1.821753 CGGCCAATAAAACCCATGACA 59.178 47.619 2.24 0.00 0.00 3.58
5882 8299 1.926511 CTTGAGCCGGCACATGAACC 61.927 60.000 31.54 7.15 0.00 3.62
5884 8301 0.250684 TTCTTGAGCCGGCACATGAA 60.251 50.000 35.04 35.04 31.98 2.57


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

AutoCloner maintained by Alex Coulton.