Multiple sequence alignment - TraesCS2D01G010000
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 | TraesCS2D01G010000 | chr2D | 100.000 | 3700 | 0 | 0 | 2466 | 6165 | 5182538 | 5178839 | 0.000000e+00 | 6833.0 |
1 | TraesCS2D01G010000 | chr2D | 100.000 | 2066 | 0 | 0 | 1 | 2066 | 5185003 | 5182938 | 0.000000e+00 | 3816.0 |
2 | TraesCS2D01G010000 | chr2A | 96.493 | 1768 | 57 | 5 | 296 | 2061 | 3608385 | 3610149 | 0.000000e+00 | 2916.0 |
3 | TraesCS2D01G010000 | chr2A | 95.044 | 1695 | 43 | 15 | 2842 | 4510 | 3619365 | 3621044 | 0.000000e+00 | 2627.0 |
4 | TraesCS2D01G010000 | chr2A | 92.027 | 1505 | 89 | 18 | 4511 | 6004 | 3621073 | 3622557 | 0.000000e+00 | 2085.0 |
5 | TraesCS2D01G010000 | chr2A | 93.019 | 1146 | 74 | 5 | 4514 | 5653 | 3715664 | 3716809 | 0.000000e+00 | 1668.0 |
6 | TraesCS2D01G010000 | chr2A | 92.323 | 977 | 58 | 10 | 2466 | 3434 | 3713812 | 3714779 | 0.000000e+00 | 1373.0 |
7 | TraesCS2D01G010000 | chr2A | 91.667 | 996 | 61 | 12 | 1 | 976 | 3711651 | 3712644 | 0.000000e+00 | 1360.0 |
8 | TraesCS2D01G010000 | chr2A | 89.242 | 818 | 57 | 11 | 3466 | 4263 | 3714772 | 3715578 | 0.000000e+00 | 994.0 |
9 | TraesCS2D01G010000 | chr2A | 91.392 | 697 | 35 | 6 | 1006 | 1701 | 3712641 | 3713313 | 0.000000e+00 | 931.0 |
10 | TraesCS2D01G010000 | chr2A | 97.486 | 358 | 7 | 2 | 2493 | 2850 | 3610374 | 3610729 | 1.470000e-170 | 610.0 |
11 | TraesCS2D01G010000 | chr2A | 91.781 | 365 | 28 | 2 | 1698 | 2062 | 3713354 | 3713716 | 1.980000e-139 | 507.0 |
12 | TraesCS2D01G010000 | chr2A | 86.710 | 459 | 42 | 8 | 5683 | 6136 | 3716804 | 3717248 | 5.550000e-135 | 492.0 |
13 | TraesCS2D01G010000 | chr2A | 96.386 | 249 | 8 | 1 | 1 | 249 | 3608140 | 3608387 | 5.750000e-110 | 409.0 |
14 | TraesCS2D01G010000 | chr2A | 96.216 | 185 | 6 | 1 | 4263 | 4447 | 66912296 | 66912113 | 1.000000e-77 | 302.0 |
15 | TraesCS2D01G010000 | chr2A | 92.593 | 189 | 12 | 2 | 4263 | 4451 | 563202202 | 563202016 | 2.830000e-68 | 270.0 |
16 | TraesCS2D01G010000 | chr2B | 92.865 | 1808 | 87 | 15 | 2466 | 4248 | 6297699 | 6295909 | 0.000000e+00 | 2586.0 |
17 | TraesCS2D01G010000 | chr2B | 91.282 | 1732 | 112 | 20 | 1 | 1701 | 62208877 | 62210600 | 0.000000e+00 | 2326.0 |
18 | TraesCS2D01G010000 | chr2B | 92.166 | 1085 | 69 | 5 | 4514 | 5596 | 6295807 | 6294737 | 0.000000e+00 | 1519.0 |
19 | TraesCS2D01G010000 | chr2B | 91.265 | 1099 | 78 | 11 | 4677 | 5770 | 62213829 | 62214914 | 0.000000e+00 | 1482.0 |
20 | TraesCS2D01G010000 | chr2B | 89.318 | 1011 | 83 | 10 | 1 | 990 | 6299783 | 6298777 | 0.000000e+00 | 1245.0 |
21 | TraesCS2D01G010000 | chr2B | 93.165 | 790 | 26 | 16 | 1280 | 2066 | 6298554 | 6297790 | 0.000000e+00 | 1134.0 |
22 | TraesCS2D01G010000 | chr2B | 89.976 | 838 | 61 | 9 | 3429 | 4247 | 62210979 | 62211812 | 0.000000e+00 | 1061.0 |
23 | TraesCS2D01G010000 | chr2B | 93.496 | 246 | 15 | 1 | 1698 | 1943 | 62210641 | 62210885 | 1.260000e-96 | 364.0 |
24 | TraesCS2D01G010000 | chr2B | 94.619 | 223 | 10 | 2 | 1020 | 1240 | 6298776 | 6298554 | 1.650000e-90 | 344.0 |
25 | TraesCS2D01G010000 | chr2B | 83.924 | 367 | 29 | 6 | 5770 | 6136 | 62333412 | 62333748 | 2.140000e-84 | 324.0 |
26 | TraesCS2D01G010000 | chr2B | 96.196 | 184 | 6 | 1 | 4263 | 4446 | 63059160 | 63058978 | 3.610000e-77 | 300.0 |
27 | TraesCS2D01G010000 | chr2B | 95.266 | 169 | 8 | 0 | 4514 | 4682 | 62211915 | 62212083 | 1.020000e-67 | 268.0 |
28 | TraesCS2D01G010000 | chr4A | 93.782 | 193 | 10 | 2 | 4260 | 4451 | 415467321 | 415467512 | 7.820000e-74 | 289.0 |
29 | TraesCS2D01G010000 | chr4A | 93.264 | 193 | 10 | 3 | 4260 | 4451 | 733663898 | 733663708 | 1.310000e-71 | 281.0 |
30 | TraesCS2D01G010000 | chr7D | 93.158 | 190 | 11 | 2 | 4260 | 4448 | 6579899 | 6580087 | 1.690000e-70 | 278.0 |
31 | TraesCS2D01G010000 | chr7A | 93.122 | 189 | 11 | 2 | 4260 | 4448 | 7666355 | 7666541 | 6.090000e-70 | 276.0 |
32 | TraesCS2D01G010000 | chr5A | 92.593 | 189 | 13 | 1 | 4263 | 4451 | 431654391 | 431654204 | 2.830000e-68 | 270.0 |
33 | TraesCS2D01G010000 | chrUn | 88.406 | 69 | 8 | 0 | 3710 | 3778 | 45118860 | 45118792 | 3.960000e-12 | 84.2 |
34 | TraesCS2D01G010000 | chr4D | 89.394 | 66 | 7 | 0 | 3710 | 3775 | 6759764 | 6759829 | 3.960000e-12 | 84.2 |
35 | TraesCS2D01G010000 | chr4D | 89.394 | 66 | 7 | 0 | 3710 | 3775 | 123305539 | 123305604 | 3.960000e-12 | 84.2 |
36 | TraesCS2D01G010000 | chr4D | 89.394 | 66 | 7 | 0 | 3710 | 3775 | 123308681 | 123308746 | 3.960000e-12 | 84.2 |
37 | TraesCS2D01G010000 | chr4D | 88.406 | 69 | 8 | 0 | 3710 | 3778 | 123459748 | 123459680 | 3.960000e-12 | 84.2 |
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 | TraesCS2D01G010000 | chr2D | 5178839 | 5185003 | 6164 | True | 5324.500000 | 6833 | 100.000000 | 1 | 6165 | 2 | chr2D.!!$R1 | 6164 |
1 | TraesCS2D01G010000 | chr2A | 3619365 | 3622557 | 3192 | False | 2356.000000 | 2627 | 93.535500 | 2842 | 6004 | 2 | chr2A.!!$F2 | 3162 |
2 | TraesCS2D01G010000 | chr2A | 3608140 | 3610729 | 2589 | False | 1311.666667 | 2916 | 96.788333 | 1 | 2850 | 3 | chr2A.!!$F1 | 2849 |
3 | TraesCS2D01G010000 | chr2A | 3711651 | 3717248 | 5597 | False | 1046.428571 | 1668 | 90.876286 | 1 | 6136 | 7 | chr2A.!!$F3 | 6135 |
4 | TraesCS2D01G010000 | chr2B | 6294737 | 6299783 | 5046 | True | 1365.600000 | 2586 | 92.426600 | 1 | 5596 | 5 | chr2B.!!$R2 | 5595 |
5 | TraesCS2D01G010000 | chr2B | 62208877 | 62214914 | 6037 | False | 1100.200000 | 2326 | 92.257000 | 1 | 5770 | 5 | chr2B.!!$F2 | 5769 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
651 | 679 | 2.364970 | CCCACATTTGTGTCATGGTTGT | 59.635 | 45.455 | 9.66 | 0.00 | 44.21 | 3.32 | F |
1489 | 1531 | 2.158608 | AGCTGAGGTTTGCCAAAGTAGT | 60.159 | 45.455 | 0.00 | 0.00 | 37.19 | 2.73 | F |
1781 | 1867 | 3.248125 | GTCAAACAAATTGCACCCATGTG | 59.752 | 43.478 | 0.00 | 0.00 | 45.65 | 3.21 | F |
2682 | 2772 | 4.891168 | TGTGTGGAGACTACTGTTCAAGTA | 59.109 | 41.667 | 0.00 | 0.00 | 40.56 | 2.24 | F |
3950 | 4109 | 0.386985 | GTGGGAGACGACGTTCTCAC | 60.387 | 60.000 | 19.87 | 19.87 | 45.12 | 3.51 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2018 | 2107 | 7.172703 | GTGCTACTTTTAGTAGGTGTTGACAAT | 59.827 | 37.037 | 13.95 | 0.00 | 46.31 | 2.71 | R |
3065 | 3160 | 0.179145 | ATACCGGACAAGCGTCTTCG | 60.179 | 55.000 | 9.46 | 0.00 | 42.21 | 3.79 | R |
3569 | 3709 | 2.236893 | TGATGGTGATGCTAGCTTGTCA | 59.763 | 45.455 | 17.23 | 14.15 | 0.00 | 3.58 | R |
4020 | 4179 | 0.036483 | TCACCCACATCATCACCACG | 60.036 | 55.000 | 0.00 | 0.00 | 0.00 | 4.94 | R |
5567 | 7524 | 0.171007 | CAAATCAAGCCCATTCGCGT | 59.829 | 50.000 | 5.77 | 0.00 | 0.00 | 6.01 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
267 | 270 | 3.876914 | GACATGTGTCACTTTCCTTGTCA | 59.123 | 43.478 | 1.15 | 0.00 | 44.18 | 3.58 |
269 | 272 | 4.276678 | ACATGTGTCACTTTCCTTGTCATG | 59.723 | 41.667 | 0.00 | 0.00 | 36.99 | 3.07 |
389 | 394 | 5.977725 | GTCAAAACTTTCCCTCTTGTAAAGC | 59.022 | 40.000 | 0.00 | 0.00 | 45.70 | 3.51 |
559 | 584 | 7.882791 | TGAAACATACTCTCTTTCTTGCCATTA | 59.117 | 33.333 | 0.00 | 0.00 | 0.00 | 1.90 |
651 | 679 | 2.364970 | CCCACATTTGTGTCATGGTTGT | 59.635 | 45.455 | 9.66 | 0.00 | 44.21 | 3.32 |
821 | 851 | 7.277174 | TCTGCATATATGTATAGTCATCCGG | 57.723 | 40.000 | 14.14 | 0.00 | 0.00 | 5.14 |
1035 | 1074 | 4.996758 | TCAAGATCTTCATCAAAACGAGCA | 59.003 | 37.500 | 4.57 | 0.00 | 0.00 | 4.26 |
1245 | 1286 | 6.164408 | TGTTGTTATGTAGTCTTGATTGCG | 57.836 | 37.500 | 0.00 | 0.00 | 0.00 | 4.85 |
1489 | 1531 | 2.158608 | AGCTGAGGTTTGCCAAAGTAGT | 60.159 | 45.455 | 0.00 | 0.00 | 37.19 | 2.73 |
1504 | 1546 | 6.151144 | GCCAAAGTAGTTCCAAGACATACAAT | 59.849 | 38.462 | 0.00 | 0.00 | 0.00 | 2.71 |
1651 | 1693 | 7.201548 | CCAATGGCTAAAATTCTTGCATTGTAC | 60.202 | 37.037 | 0.00 | 0.00 | 0.00 | 2.90 |
1701 | 1743 | 6.161381 | GTGAAAGAAAATCTGCCAACATGAT | 58.839 | 36.000 | 0.00 | 0.00 | 0.00 | 2.45 |
1781 | 1867 | 3.248125 | GTCAAACAAATTGCACCCATGTG | 59.752 | 43.478 | 0.00 | 0.00 | 45.65 | 3.21 |
2046 | 2135 | 5.070714 | TCAACACCTACTAAAAGTAGCACCA | 59.929 | 40.000 | 8.32 | 0.00 | 45.21 | 4.17 |
2682 | 2772 | 4.891168 | TGTGTGGAGACTACTGTTCAAGTA | 59.109 | 41.667 | 0.00 | 0.00 | 40.56 | 2.24 |
3065 | 3160 | 5.382618 | AGTCCAATCAAACAATGAAGAGC | 57.617 | 39.130 | 0.00 | 0.00 | 42.54 | 4.09 |
3458 | 3556 | 8.996651 | AGGAAATTCAATATACCTTGTTAGGG | 57.003 | 34.615 | 0.00 | 0.00 | 46.58 | 3.53 |
3459 | 3557 | 8.787818 | AGGAAATTCAATATACCTTGTTAGGGA | 58.212 | 33.333 | 0.00 | 0.00 | 46.58 | 4.20 |
3462 | 3560 | 9.936329 | AAATTCAATATACCTTGTTAGGGATGT | 57.064 | 29.630 | 0.00 | 0.00 | 45.30 | 3.06 |
3463 | 3561 | 8.924511 | ATTCAATATACCTTGTTAGGGATGTG | 57.075 | 34.615 | 0.00 | 0.00 | 45.30 | 3.21 |
3464 | 3562 | 7.446106 | TCAATATACCTTGTTAGGGATGTGT | 57.554 | 36.000 | 0.00 | 0.00 | 45.30 | 3.72 |
3465 | 3563 | 7.867921 | TCAATATACCTTGTTAGGGATGTGTT | 58.132 | 34.615 | 0.00 | 0.00 | 45.30 | 3.32 |
3466 | 3564 | 8.333235 | TCAATATACCTTGTTAGGGATGTGTTT | 58.667 | 33.333 | 0.00 | 0.00 | 45.30 | 2.83 |
3467 | 3565 | 8.966868 | CAATATACCTTGTTAGGGATGTGTTTT | 58.033 | 33.333 | 0.00 | 0.00 | 45.30 | 2.43 |
3468 | 3566 | 9.541884 | AATATACCTTGTTAGGGATGTGTTTTT | 57.458 | 29.630 | 0.00 | 0.00 | 45.30 | 1.94 |
3569 | 3709 | 7.667219 | ACCAAAGATAGAACATGTTGAGTCATT | 59.333 | 33.333 | 17.58 | 7.02 | 0.00 | 2.57 |
3828 | 3969 | 6.190346 | TGGTGTAGGTGTACCATAAAAACT | 57.810 | 37.500 | 3.56 | 0.00 | 41.80 | 2.66 |
3829 | 3970 | 7.313740 | TGGTGTAGGTGTACCATAAAAACTA | 57.686 | 36.000 | 3.56 | 0.00 | 41.80 | 2.24 |
3830 | 3971 | 7.388437 | TGGTGTAGGTGTACCATAAAAACTAG | 58.612 | 38.462 | 3.56 | 0.00 | 41.80 | 2.57 |
3831 | 3972 | 6.314648 | GGTGTAGGTGTACCATAAAAACTAGC | 59.685 | 42.308 | 3.56 | 0.00 | 38.89 | 3.42 |
3832 | 3973 | 6.314648 | GTGTAGGTGTACCATAAAAACTAGCC | 59.685 | 42.308 | 3.56 | 0.00 | 38.89 | 3.93 |
3833 | 3974 | 5.774102 | AGGTGTACCATAAAAACTAGCCT | 57.226 | 39.130 | 3.56 | 0.00 | 38.89 | 4.58 |
3834 | 3975 | 6.879367 | AGGTGTACCATAAAAACTAGCCTA | 57.121 | 37.500 | 3.56 | 0.00 | 38.89 | 3.93 |
3835 | 3976 | 6.885922 | AGGTGTACCATAAAAACTAGCCTAG | 58.114 | 40.000 | 3.56 | 0.00 | 38.89 | 3.02 |
3850 | 4009 | 2.965831 | AGCCTAGAGAATGGTTATGCGA | 59.034 | 45.455 | 0.00 | 0.00 | 0.00 | 5.10 |
3895 | 4054 | 9.125026 | CACCAGAGATTAAATGCTAGGTTTAAT | 57.875 | 33.333 | 4.14 | 4.14 | 41.77 | 1.40 |
3950 | 4109 | 0.386985 | GTGGGAGACGACGTTCTCAC | 60.387 | 60.000 | 19.87 | 19.87 | 45.12 | 3.51 |
3999 | 4158 | 7.401484 | TTCGTCAATCTTAAAATTTTGCACC | 57.599 | 32.000 | 13.76 | 0.00 | 0.00 | 5.01 |
4020 | 4179 | 3.496870 | CCATGGTATTCAGTAGGCCCTTC | 60.497 | 52.174 | 2.57 | 0.00 | 0.00 | 3.46 |
4179 | 4338 | 3.259374 | ACTCAGTCACTCACATTGGTAGG | 59.741 | 47.826 | 0.00 | 0.00 | 0.00 | 3.18 |
4248 | 4408 | 5.559427 | TGTCACATTTTGATATCAACGGG | 57.441 | 39.130 | 17.76 | 10.54 | 36.32 | 5.28 |
4251 | 4411 | 6.207614 | TGTCACATTTTGATATCAACGGGAAA | 59.792 | 34.615 | 17.76 | 9.52 | 36.32 | 3.13 |
4363 | 4524 | 1.373435 | CAAGTGGCGACCCTGGTTA | 59.627 | 57.895 | 0.00 | 0.00 | 0.00 | 2.85 |
4384 | 4545 | 8.511465 | GGTTAAGAGAAACCGAAAATTTAACC | 57.489 | 34.615 | 6.97 | 6.97 | 39.62 | 2.85 |
4417 | 4578 | 4.023107 | GCTTCTTTTGTTTCTGTCCCTACC | 60.023 | 45.833 | 0.00 | 0.00 | 0.00 | 3.18 |
4421 | 4582 | 4.781775 | TTTGTTTCTGTCCCTACCTTCA | 57.218 | 40.909 | 0.00 | 0.00 | 0.00 | 3.02 |
4510 | 4671 | 1.369692 | CTAGTGTGTGCCCCGAACA | 59.630 | 57.895 | 0.00 | 0.00 | 0.00 | 3.18 |
4511 | 4672 | 0.670546 | CTAGTGTGTGCCCCGAACAG | 60.671 | 60.000 | 0.00 | 0.00 | 0.00 | 3.16 |
4512 | 4673 | 1.404479 | TAGTGTGTGCCCCGAACAGT | 61.404 | 55.000 | 0.00 | 0.00 | 0.00 | 3.55 |
4571 | 4760 | 2.264813 | CATTTGCCAACATGCTGCTAC | 58.735 | 47.619 | 0.00 | 0.00 | 0.00 | 3.58 |
4632 | 4821 | 8.514594 | TCCAAGCTACATTCAGTTCTTTATTTG | 58.485 | 33.333 | 0.00 | 0.00 | 0.00 | 2.32 |
4648 | 4837 | 6.823182 | TCTTTATTTGCTGCTAAGATGCACTA | 59.177 | 34.615 | 0.00 | 0.00 | 38.12 | 2.74 |
4825 | 6768 | 1.814394 | TGCACCAAGCTGATTCATGTC | 59.186 | 47.619 | 0.00 | 0.00 | 45.94 | 3.06 |
4851 | 6794 | 9.770503 | CTCAAGAATCAATATATAGTTGCATGC | 57.229 | 33.333 | 11.82 | 11.82 | 0.00 | 4.06 |
4852 | 6795 | 9.287373 | TCAAGAATCAATATATAGTTGCATGCA | 57.713 | 29.630 | 18.46 | 18.46 | 0.00 | 3.96 |
4902 | 6845 | 4.616604 | CGATTTCTTCACATTGCACACCAT | 60.617 | 41.667 | 0.00 | 0.00 | 0.00 | 3.55 |
4903 | 6846 | 3.646611 | TTCTTCACATTGCACACCATG | 57.353 | 42.857 | 0.00 | 0.00 | 0.00 | 3.66 |
4923 | 6866 | 3.401182 | TGATTTTGCAAACATCAAGGCC | 58.599 | 40.909 | 23.13 | 0.00 | 0.00 | 5.19 |
5154 | 7102 | 0.322816 | GCAGGGAGCCAAGATGAACA | 60.323 | 55.000 | 0.00 | 0.00 | 37.23 | 3.18 |
5258 | 7206 | 8.099364 | ACTCGATGTGTTAGTCATTTCAATTT | 57.901 | 30.769 | 0.00 | 0.00 | 0.00 | 1.82 |
5479 | 7428 | 8.109705 | TGTTATTTATTGGATGCGATTGCTAT | 57.890 | 30.769 | 6.47 | 0.00 | 43.34 | 2.97 |
5567 | 7524 | 2.988688 | GCCGCGAAAAAGGATGGCA | 61.989 | 57.895 | 8.23 | 0.00 | 42.03 | 4.92 |
5569 | 7526 | 1.511887 | CGCGAAAAAGGATGGCACG | 60.512 | 57.895 | 0.00 | 0.00 | 0.00 | 5.34 |
5571 | 7528 | 1.511887 | CGAAAAAGGATGGCACGCG | 60.512 | 57.895 | 3.53 | 3.53 | 0.00 | 6.01 |
5586 | 7543 | 0.171007 | ACGCGAATGGGCTTGATTTG | 59.829 | 50.000 | 15.93 | 0.00 | 0.00 | 2.32 |
5670 | 7629 | 5.446473 | CGGTCAATCAGAAGCAATACACTTC | 60.446 | 44.000 | 0.00 | 0.00 | 43.16 | 3.01 |
5748 | 7708 | 4.081030 | CAAGTGCGCAGTGCTCCG | 62.081 | 66.667 | 20.39 | 1.47 | 46.63 | 4.63 |
5771 | 7736 | 6.150474 | CCGAAATTTCTGGTGGTACAAACTAT | 59.850 | 38.462 | 15.92 | 0.00 | 44.16 | 2.12 |
5778 | 7743 | 8.556213 | TTCTGGTGGTACAAACTATATTTCAC | 57.444 | 34.615 | 0.00 | 0.00 | 44.16 | 3.18 |
5906 | 7871 | 6.183360 | CCAATCTTTGAACAATGAATTCTGCG | 60.183 | 38.462 | 7.05 | 0.00 | 0.00 | 5.18 |
5950 | 7915 | 4.583426 | TCAAACAAACACGAGAATGTTCG | 58.417 | 39.130 | 7.98 | 0.00 | 42.01 | 3.95 |
5955 | 7920 | 5.025826 | ACAAACACGAGAATGTTCGAAAAC | 58.974 | 37.500 | 0.00 | 0.00 | 42.01 | 2.43 |
6004 | 7969 | 2.196595 | TCCTGGCTGCCAAATACTACT | 58.803 | 47.619 | 23.51 | 0.00 | 30.80 | 2.57 |
6005 | 7970 | 3.380393 | TCCTGGCTGCCAAATACTACTA | 58.620 | 45.455 | 23.51 | 0.00 | 30.80 | 1.82 |
6006 | 7971 | 3.388024 | TCCTGGCTGCCAAATACTACTAG | 59.612 | 47.826 | 23.51 | 6.54 | 30.80 | 2.57 |
6008 | 7973 | 4.372656 | CTGGCTGCCAAATACTACTAGAC | 58.627 | 47.826 | 23.51 | 0.00 | 30.80 | 2.59 |
6010 | 7975 | 4.408921 | TGGCTGCCAAATACTACTAGACAT | 59.591 | 41.667 | 21.08 | 0.00 | 0.00 | 3.06 |
6011 | 7976 | 4.991687 | GGCTGCCAAATACTACTAGACATC | 59.008 | 45.833 | 15.17 | 0.00 | 0.00 | 3.06 |
6012 | 7977 | 4.991687 | GCTGCCAAATACTACTAGACATCC | 59.008 | 45.833 | 0.00 | 0.00 | 0.00 | 3.51 |
6013 | 7978 | 5.221541 | GCTGCCAAATACTACTAGACATCCT | 60.222 | 44.000 | 0.00 | 0.00 | 0.00 | 3.24 |
6014 | 7979 | 6.686632 | GCTGCCAAATACTACTAGACATCCTT | 60.687 | 42.308 | 0.00 | 0.00 | 0.00 | 3.36 |
6015 | 7980 | 6.817184 | TGCCAAATACTACTAGACATCCTTC | 58.183 | 40.000 | 0.00 | 0.00 | 0.00 | 3.46 |
6024 | 7989 | 7.863722 | ACTACTAGACATCCTTCAGTCTTCTA | 58.136 | 38.462 | 0.00 | 0.00 | 42.12 | 2.10 |
6056 | 8021 | 3.436704 | TGTCAAAATCGAAGCATCCAGTC | 59.563 | 43.478 | 0.00 | 0.00 | 0.00 | 3.51 |
6085 | 8050 | 6.655078 | ACCTGCTGAATTTTTCTACATTGT | 57.345 | 33.333 | 0.00 | 0.00 | 0.00 | 2.71 |
6102 | 8067 | 0.603065 | TGTGTCTCATCGACCACCTG | 59.397 | 55.000 | 0.00 | 0.00 | 42.13 | 4.00 |
6129 | 8094 | 4.364415 | AAAACAAGCTACGCAAACTTCA | 57.636 | 36.364 | 0.00 | 0.00 | 0.00 | 3.02 |
6136 | 8101 | 6.090898 | ACAAGCTACGCAAACTTCAAGTATAG | 59.909 | 38.462 | 0.00 | 0.00 | 0.00 | 1.31 |
6137 | 8102 | 5.109903 | AGCTACGCAAACTTCAAGTATAGG | 58.890 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
6138 | 8103 | 5.105473 | AGCTACGCAAACTTCAAGTATAGGA | 60.105 | 40.000 | 0.00 | 0.00 | 0.00 | 2.94 |
6139 | 8104 | 5.579511 | GCTACGCAAACTTCAAGTATAGGAA | 59.420 | 40.000 | 0.00 | 0.00 | 0.00 | 3.36 |
6140 | 8105 | 6.091713 | GCTACGCAAACTTCAAGTATAGGAAA | 59.908 | 38.462 | 0.00 | 0.00 | 0.00 | 3.13 |
6141 | 8106 | 6.870971 | ACGCAAACTTCAAGTATAGGAAAA | 57.129 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
6142 | 8107 | 7.266922 | ACGCAAACTTCAAGTATAGGAAAAA | 57.733 | 32.000 | 0.00 | 0.00 | 0.00 | 1.94 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
267 | 270 | 6.263842 | TGAACTTTCATGTGAAAAGCTCTCAT | 59.736 | 34.615 | 9.24 | 0.00 | 42.72 | 2.90 |
269 | 272 | 6.017605 | TCTGAACTTTCATGTGAAAAGCTCTC | 60.018 | 38.462 | 9.24 | 0.00 | 42.72 | 3.20 |
343 | 348 | 8.034313 | TGACTAACTGAGCCATTTTAGGATAT | 57.966 | 34.615 | 0.00 | 0.00 | 0.00 | 1.63 |
365 | 370 | 5.977725 | GCTTTACAAGAGGGAAAGTTTTGAC | 59.022 | 40.000 | 1.42 | 0.00 | 33.58 | 3.18 |
1035 | 1074 | 4.281688 | CCCATCTTCATGACCAACAACTTT | 59.718 | 41.667 | 0.00 | 0.00 | 30.57 | 2.66 |
1119 | 1159 | 5.983540 | TGTTTGTTGGTGCCTAAAAGATTT | 58.016 | 33.333 | 0.00 | 0.00 | 0.00 | 2.17 |
1651 | 1693 | 9.828220 | CACATTTTTGTAATGTTTTCGTGTTAG | 57.172 | 29.630 | 0.64 | 0.00 | 38.69 | 2.34 |
1781 | 1867 | 7.928706 | ACTACTTCATAAACCATCTACATGCTC | 59.071 | 37.037 | 0.00 | 0.00 | 0.00 | 4.26 |
2018 | 2107 | 7.172703 | GTGCTACTTTTAGTAGGTGTTGACAAT | 59.827 | 37.037 | 13.95 | 0.00 | 46.31 | 2.71 |
2853 | 2943 | 8.461222 | TGGATTTATGTGCTGAATTCTAAGTTG | 58.539 | 33.333 | 7.05 | 0.00 | 0.00 | 3.16 |
3065 | 3160 | 0.179145 | ATACCGGACAAGCGTCTTCG | 60.179 | 55.000 | 9.46 | 0.00 | 42.21 | 3.79 |
3249 | 3345 | 9.868277 | AAAGTGATGTATCTTTGTTTTGACAAA | 57.132 | 25.926 | 0.00 | 0.00 | 37.90 | 2.83 |
3432 | 3530 | 9.421399 | CCCTAACAAGGTATATTGAATTTCCTT | 57.579 | 33.333 | 0.00 | 0.00 | 35.97 | 3.36 |
3433 | 3531 | 8.787818 | TCCCTAACAAGGTATATTGAATTTCCT | 58.212 | 33.333 | 0.00 | 0.00 | 34.20 | 3.36 |
3434 | 3532 | 8.990163 | TCCCTAACAAGGTATATTGAATTTCC | 57.010 | 34.615 | 0.00 | 0.00 | 34.20 | 3.13 |
3436 | 3534 | 9.936329 | ACATCCCTAACAAGGTATATTGAATTT | 57.064 | 29.630 | 0.00 | 0.00 | 34.20 | 1.82 |
3437 | 3535 | 9.354673 | CACATCCCTAACAAGGTATATTGAATT | 57.645 | 33.333 | 0.00 | 0.00 | 34.20 | 2.17 |
3438 | 3536 | 8.502738 | ACACATCCCTAACAAGGTATATTGAAT | 58.497 | 33.333 | 0.00 | 0.00 | 34.20 | 2.57 |
3439 | 3537 | 7.867921 | ACACATCCCTAACAAGGTATATTGAA | 58.132 | 34.615 | 0.00 | 0.00 | 34.20 | 2.69 |
3440 | 3538 | 7.446106 | ACACATCCCTAACAAGGTATATTGA | 57.554 | 36.000 | 0.00 | 0.00 | 34.20 | 2.57 |
3441 | 3539 | 8.519799 | AAACACATCCCTAACAAGGTATATTG | 57.480 | 34.615 | 0.00 | 0.00 | 36.22 | 1.90 |
3442 | 3540 | 9.541884 | AAAAACACATCCCTAACAAGGTATATT | 57.458 | 29.630 | 0.00 | 0.00 | 0.00 | 1.28 |
3466 | 3564 | 5.685520 | AGGTTTTGCCTCTGGTTTAAAAA | 57.314 | 34.783 | 0.00 | 0.00 | 46.96 | 1.94 |
3493 | 3631 | 7.581213 | TGTTGGTCTCAATTAGTGAAACAAT | 57.419 | 32.000 | 0.00 | 0.00 | 35.42 | 2.71 |
3569 | 3709 | 2.236893 | TGATGGTGATGCTAGCTTGTCA | 59.763 | 45.455 | 17.23 | 14.15 | 0.00 | 3.58 |
3828 | 3969 | 4.149598 | TCGCATAACCATTCTCTAGGCTA | 58.850 | 43.478 | 0.00 | 0.00 | 0.00 | 3.93 |
3829 | 3970 | 2.965831 | TCGCATAACCATTCTCTAGGCT | 59.034 | 45.455 | 0.00 | 0.00 | 0.00 | 4.58 |
3830 | 3971 | 3.243907 | ACTCGCATAACCATTCTCTAGGC | 60.244 | 47.826 | 0.00 | 0.00 | 0.00 | 3.93 |
3831 | 3972 | 4.302455 | CACTCGCATAACCATTCTCTAGG | 58.698 | 47.826 | 0.00 | 0.00 | 0.00 | 3.02 |
3832 | 3973 | 4.202161 | ACCACTCGCATAACCATTCTCTAG | 60.202 | 45.833 | 0.00 | 0.00 | 0.00 | 2.43 |
3833 | 3974 | 3.704566 | ACCACTCGCATAACCATTCTCTA | 59.295 | 43.478 | 0.00 | 0.00 | 0.00 | 2.43 |
3834 | 3975 | 2.501723 | ACCACTCGCATAACCATTCTCT | 59.498 | 45.455 | 0.00 | 0.00 | 0.00 | 3.10 |
3835 | 3976 | 2.906354 | ACCACTCGCATAACCATTCTC | 58.094 | 47.619 | 0.00 | 0.00 | 0.00 | 2.87 |
3883 | 4042 | 4.286032 | AGACACTGGACATTAAACCTAGCA | 59.714 | 41.667 | 0.00 | 0.00 | 0.00 | 3.49 |
3884 | 4043 | 4.833390 | AGACACTGGACATTAAACCTAGC | 58.167 | 43.478 | 0.00 | 0.00 | 0.00 | 3.42 |
3895 | 4054 | 3.005472 | CCTCTTTAACGAGACACTGGACA | 59.995 | 47.826 | 10.40 | 0.00 | 32.74 | 4.02 |
3950 | 4109 | 2.159043 | ACCACAGACGCCTCATTATCTG | 60.159 | 50.000 | 0.00 | 0.00 | 43.47 | 2.90 |
3999 | 4158 | 3.744660 | GAAGGGCCTACTGAATACCATG | 58.255 | 50.000 | 6.41 | 0.00 | 0.00 | 3.66 |
4020 | 4179 | 0.036483 | TCACCCACATCATCACCACG | 60.036 | 55.000 | 0.00 | 0.00 | 0.00 | 4.94 |
4179 | 4338 | 1.002792 | GAGAAGCCAAACCAACACGTC | 60.003 | 52.381 | 0.00 | 0.00 | 0.00 | 4.34 |
4341 | 4502 | 3.168528 | AGGGTCGCCACTTGTGGT | 61.169 | 61.111 | 19.47 | 0.00 | 0.00 | 4.16 |
4363 | 4524 | 6.700081 | GCTTGGTTAAATTTTCGGTTTCTCTT | 59.300 | 34.615 | 0.00 | 0.00 | 0.00 | 2.85 |
4417 | 4578 | 7.927048 | TGAAGCATGTGATATCATCTTTGAAG | 58.073 | 34.615 | 9.02 | 0.00 | 34.96 | 3.02 |
4421 | 4582 | 9.582431 | CTTTTTGAAGCATGTGATATCATCTTT | 57.418 | 29.630 | 9.02 | 0.16 | 0.00 | 2.52 |
4510 | 4671 | 8.035984 | GCTAGATACAAAAGGACTAGTTTGACT | 58.964 | 37.037 | 11.14 | 9.33 | 37.98 | 3.41 |
4511 | 4672 | 7.009357 | CGCTAGATACAAAAGGACTAGTTTGAC | 59.991 | 40.741 | 11.14 | 3.87 | 37.98 | 3.18 |
4512 | 4673 | 7.033791 | CGCTAGATACAAAAGGACTAGTTTGA | 58.966 | 38.462 | 11.14 | 0.00 | 37.98 | 2.69 |
4632 | 4821 | 7.224362 | CCATTAGATATAGTGCATCTTAGCAGC | 59.776 | 40.741 | 0.00 | 0.00 | 46.69 | 5.25 |
4648 | 4837 | 7.465116 | AGCCAATAGAACAAGCCATTAGATAT | 58.535 | 34.615 | 0.00 | 0.00 | 0.00 | 1.63 |
4779 | 6721 | 6.731467 | AGACCCCAATGAATTATGTACAGTT | 58.269 | 36.000 | 0.33 | 0.00 | 0.00 | 3.16 |
4825 | 6768 | 9.770503 | GCATGCAACTATATATTGATTCTTGAG | 57.229 | 33.333 | 14.21 | 0.00 | 0.00 | 3.02 |
4851 | 6794 | 7.017055 | GCAAAAATAATTAACAAAGCAGGCTG | 58.983 | 34.615 | 10.94 | 10.94 | 0.00 | 4.85 |
4852 | 6795 | 6.149308 | GGCAAAAATAATTAACAAAGCAGGCT | 59.851 | 34.615 | 0.00 | 0.00 | 0.00 | 4.58 |
4902 | 6845 | 3.071312 | AGGCCTTGATGTTTGCAAAATCA | 59.929 | 39.130 | 22.25 | 22.25 | 0.00 | 2.57 |
4903 | 6846 | 3.667360 | AGGCCTTGATGTTTGCAAAATC | 58.333 | 40.909 | 14.67 | 17.62 | 0.00 | 2.17 |
5154 | 7102 | 1.084370 | GCCAGCTGATTACTCGCGTT | 61.084 | 55.000 | 17.39 | 0.00 | 0.00 | 4.84 |
5258 | 7206 | 6.413783 | TGGACTTGTAGTGTCACTTATTGA | 57.586 | 37.500 | 11.54 | 0.00 | 36.26 | 2.57 |
5479 | 7428 | 6.442952 | AGCGCATAAACATACTTCAAAAACA | 58.557 | 32.000 | 11.47 | 0.00 | 0.00 | 2.83 |
5519 | 7474 | 8.778358 | GTTCATGACCTTCTCAAATATATGGAC | 58.222 | 37.037 | 0.00 | 0.00 | 30.60 | 4.02 |
5567 | 7524 | 0.171007 | CAAATCAAGCCCATTCGCGT | 59.829 | 50.000 | 5.77 | 0.00 | 0.00 | 6.01 |
5569 | 7526 | 0.817013 | TCCAAATCAAGCCCATTCGC | 59.183 | 50.000 | 0.00 | 0.00 | 0.00 | 4.70 |
5571 | 7528 | 3.515104 | TCCTTTCCAAATCAAGCCCATTC | 59.485 | 43.478 | 0.00 | 0.00 | 0.00 | 2.67 |
5599 | 7556 | 4.715527 | AGAGTATAAACGGTGTGGAGTC | 57.284 | 45.455 | 0.00 | 0.00 | 0.00 | 3.36 |
5601 | 7558 | 6.446781 | TTCTAGAGTATAAACGGTGTGGAG | 57.553 | 41.667 | 0.00 | 0.00 | 0.00 | 3.86 |
5602 | 7559 | 6.839124 | TTTCTAGAGTATAAACGGTGTGGA | 57.161 | 37.500 | 0.00 | 0.00 | 0.00 | 4.02 |
5670 | 7629 | 0.320946 | CTTTGGCCTTGCATGGTTGG | 60.321 | 55.000 | 19.05 | 3.55 | 0.00 | 3.77 |
5712 | 7671 | 7.147976 | GCACTTGGATCAGTGTTTTTATTTCT | 58.852 | 34.615 | 13.14 | 0.00 | 45.31 | 2.52 |
5716 | 7675 | 4.615912 | GCGCACTTGGATCAGTGTTTTTAT | 60.616 | 41.667 | 0.30 | 0.00 | 45.31 | 1.40 |
5717 | 7676 | 3.304391 | GCGCACTTGGATCAGTGTTTTTA | 60.304 | 43.478 | 0.30 | 0.00 | 45.31 | 1.52 |
5786 | 7751 | 7.995289 | TCGTTAGAAATTTGGCATATGACAAT | 58.005 | 30.769 | 24.42 | 10.25 | 43.55 | 2.71 |
5849 | 7814 | 7.453126 | CCCTACTTCTCCATATATCTGAACTGT | 59.547 | 40.741 | 0.00 | 0.00 | 0.00 | 3.55 |
5906 | 7871 | 6.494842 | TGAACTTGTCAGTGCTTGTTAATTC | 58.505 | 36.000 | 0.00 | 0.00 | 31.60 | 2.17 |
5950 | 7915 | 6.357240 | GCTGTCGTTCTAGTGATTTTGTTTTC | 59.643 | 38.462 | 0.00 | 0.00 | 0.00 | 2.29 |
5955 | 7920 | 6.893958 | ATAGCTGTCGTTCTAGTGATTTTG | 57.106 | 37.500 | 0.00 | 0.00 | 0.00 | 2.44 |
6004 | 7969 | 6.722328 | TGTCTAGAAGACTGAAGGATGTCTA | 58.278 | 40.000 | 8.42 | 0.00 | 45.27 | 2.59 |
6005 | 7970 | 5.575157 | TGTCTAGAAGACTGAAGGATGTCT | 58.425 | 41.667 | 8.42 | 0.00 | 45.27 | 3.41 |
6006 | 7971 | 5.906113 | TGTCTAGAAGACTGAAGGATGTC | 57.094 | 43.478 | 8.42 | 0.00 | 45.27 | 3.06 |
6008 | 7973 | 5.598005 | AGGATGTCTAGAAGACTGAAGGATG | 59.402 | 44.000 | 8.42 | 0.00 | 45.27 | 3.51 |
6010 | 7975 | 5.199982 | AGGATGTCTAGAAGACTGAAGGA | 57.800 | 43.478 | 8.42 | 0.00 | 45.27 | 3.36 |
6011 | 7976 | 5.930837 | AAGGATGTCTAGAAGACTGAAGG | 57.069 | 43.478 | 8.42 | 0.00 | 45.27 | 3.46 |
6012 | 7977 | 6.696411 | ACAAAGGATGTCTAGAAGACTGAAG | 58.304 | 40.000 | 8.42 | 0.00 | 45.27 | 3.02 |
6013 | 7978 | 6.672266 | ACAAAGGATGTCTAGAAGACTGAA | 57.328 | 37.500 | 8.42 | 0.00 | 45.27 | 3.02 |
6064 | 8029 | 7.365741 | AGACACAATGTAGAAAAATTCAGCAG | 58.634 | 34.615 | 0.00 | 0.00 | 0.00 | 4.24 |
6065 | 8030 | 7.013178 | TGAGACACAATGTAGAAAAATTCAGCA | 59.987 | 33.333 | 0.00 | 0.00 | 0.00 | 4.41 |
6066 | 8031 | 7.362662 | TGAGACACAATGTAGAAAAATTCAGC | 58.637 | 34.615 | 0.00 | 0.00 | 0.00 | 4.26 |
6067 | 8032 | 9.552114 | GATGAGACACAATGTAGAAAAATTCAG | 57.448 | 33.333 | 0.00 | 0.00 | 0.00 | 3.02 |
6068 | 8033 | 8.229811 | CGATGAGACACAATGTAGAAAAATTCA | 58.770 | 33.333 | 0.00 | 0.00 | 0.00 | 2.57 |
6070 | 8035 | 8.322906 | TCGATGAGACACAATGTAGAAAAATT | 57.677 | 30.769 | 0.00 | 0.00 | 0.00 | 1.82 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.