Multiple sequence alignment - TraesCS1A01G010700
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 | TraesCS1A01G010700 | chr1A | 100.000 | 2211 | 0 | 0 | 1 | 2211 | 6475852 | 6473642 | 0.000000e+00 | 4084.0 |
1 | TraesCS1A01G010700 | chr1A | 100.000 | 1618 | 0 | 0 | 2580 | 4197 | 6473273 | 6471656 | 0.000000e+00 | 2988.0 |
2 | TraesCS1A01G010700 | chr1A | 92.857 | 182 | 11 | 1 | 3746 | 3925 | 480758913 | 480758732 | 3.220000e-66 | 263.0 |
3 | TraesCS1A01G010700 | chr1A | 90.476 | 168 | 16 | 0 | 4030 | 4197 | 589866355 | 589866188 | 5.460000e-54 | 222.0 |
4 | TraesCS1A01G010700 | chr1A | 100.000 | 32 | 0 | 0 | 3909 | 3940 | 6472196 | 6472165 | 4.530000e-05 | 60.2 |
5 | TraesCS1A01G010700 | chr3A | 98.690 | 2213 | 21 | 6 | 1 | 2211 | 177677260 | 177679466 | 0.000000e+00 | 3919.0 |
6 | TraesCS1A01G010700 | chr3A | 98.971 | 1166 | 12 | 0 | 2580 | 3745 | 177679531 | 177680696 | 0.000000e+00 | 2087.0 |
7 | TraesCS1A01G010700 | chr3A | 91.700 | 1000 | 49 | 11 | 2758 | 3745 | 31807462 | 31806485 | 0.000000e+00 | 1356.0 |
8 | TraesCS1A01G010700 | chr3A | 99.654 | 289 | 0 | 1 | 3909 | 4197 | 177680701 | 177680988 | 1.030000e-145 | 527.0 |
9 | TraesCS1A01G010700 | chr3A | 96.194 | 289 | 11 | 0 | 3909 | 4197 | 31806404 | 31806116 | 1.370000e-129 | 473.0 |
10 | TraesCS1A01G010700 | chr3A | 97.826 | 46 | 0 | 1 | 3644 | 3688 | 177680687 | 177680732 | 1.250000e-10 | 78.7 |
11 | TraesCS1A01G010700 | chr3A | 100.000 | 32 | 0 | 0 | 3909 | 3940 | 31806573 | 31806542 | 4.530000e-05 | 60.2 |
12 | TraesCS1A01G010700 | chr7B | 92.486 | 519 | 31 | 4 | 1622 | 2139 | 616827857 | 616827346 | 0.000000e+00 | 736.0 |
13 | TraesCS1A01G010700 | chr7B | 94.748 | 457 | 24 | 0 | 1167 | 1623 | 616828373 | 616827917 | 0.000000e+00 | 712.0 |
14 | TraesCS1A01G010700 | chr7B | 91.466 | 457 | 34 | 2 | 1167 | 1623 | 616756473 | 616756022 | 1.280000e-174 | 623.0 |
15 | TraesCS1A01G010700 | chr7B | 88.835 | 412 | 30 | 6 | 742 | 1147 | 616828758 | 616828357 | 3.770000e-135 | 492.0 |
16 | TraesCS1A01G010700 | chr7B | 87.136 | 412 | 36 | 9 | 742 | 1147 | 616756857 | 616756457 | 6.400000e-123 | 451.0 |
17 | TraesCS1A01G010700 | chr7B | 87.111 | 225 | 27 | 2 | 1426 | 1648 | 616755884 | 616755660 | 1.940000e-63 | 254.0 |
18 | TraesCS1A01G010700 | chr7B | 87.395 | 119 | 15 | 0 | 2640 | 2758 | 616755571 | 616755453 | 2.040000e-28 | 137.0 |
19 | TraesCS1A01G010700 | chr7B | 83.158 | 95 | 10 | 4 | 7 | 101 | 68839716 | 68839804 | 9.670000e-12 | 82.4 |
20 | TraesCS1A01G010700 | chr7A | 87.195 | 492 | 48 | 8 | 1167 | 1648 | 652008857 | 652008371 | 2.850000e-151 | 545.0 |
21 | TraesCS1A01G010700 | chr7A | 84.906 | 424 | 39 | 11 | 730 | 1147 | 652009245 | 652008841 | 5.050000e-109 | 405.0 |
22 | TraesCS1A01G010700 | chr7A | 81.768 | 181 | 16 | 6 | 2587 | 2758 | 652008373 | 652008201 | 7.320000e-28 | 135.0 |
23 | TraesCS1A01G010700 | chr6D | 92.857 | 238 | 14 | 3 | 3483 | 3720 | 50183500 | 50183266 | 4.020000e-90 | 342.0 |
24 | TraesCS1A01G010700 | chr6D | 90.050 | 201 | 18 | 2 | 3711 | 3910 | 235137377 | 235137178 | 4.160000e-65 | 259.0 |
25 | TraesCS1A01G010700 | chr6D | 93.976 | 166 | 10 | 0 | 3746 | 3911 | 109240318 | 109240483 | 6.970000e-63 | 252.0 |
26 | TraesCS1A01G010700 | chr6D | 79.331 | 329 | 49 | 13 | 828 | 1147 | 269761965 | 269761647 | 3.290000e-51 | 213.0 |
27 | TraesCS1A01G010700 | chr6D | 90.604 | 149 | 14 | 0 | 3907 | 4055 | 50183269 | 50183121 | 9.200000e-47 | 198.0 |
28 | TraesCS1A01G010700 | chr6D | 87.121 | 132 | 16 | 1 | 2806 | 2937 | 373340476 | 373340346 | 9.400000e-32 | 148.0 |
29 | TraesCS1A01G010700 | chr6D | 88.889 | 108 | 12 | 0 | 3868 | 3975 | 46442034 | 46442141 | 2.630000e-27 | 134.0 |
30 | TraesCS1A01G010700 | chr6D | 88.636 | 88 | 10 | 0 | 4109 | 4196 | 50183124 | 50183037 | 1.600000e-19 | 108.0 |
31 | TraesCS1A01G010700 | chr6D | 93.333 | 45 | 3 | 0 | 3644 | 3688 | 50183280 | 50183236 | 2.710000e-07 | 67.6 |
32 | TraesCS1A01G010700 | chr6A | 91.983 | 237 | 17 | 1 | 3483 | 3717 | 64904828 | 64905064 | 8.700000e-87 | 331.0 |
33 | TraesCS1A01G010700 | chr6A | 88.938 | 226 | 18 | 2 | 3470 | 3688 | 64664907 | 64665132 | 5.350000e-69 | 272.0 |
34 | TraesCS1A01G010700 | chr6A | 93.220 | 177 | 12 | 0 | 3746 | 3922 | 204007918 | 204007742 | 1.160000e-65 | 261.0 |
35 | TraesCS1A01G010700 | chr6A | 94.675 | 169 | 8 | 1 | 3746 | 3914 | 550716827 | 550716660 | 1.160000e-65 | 261.0 |
36 | TraesCS1A01G010700 | chr6A | 78.723 | 329 | 50 | 14 | 828 | 1147 | 384089322 | 384089005 | 7.120000e-48 | 202.0 |
37 | TraesCS1A01G010700 | chr6A | 90.909 | 88 | 8 | 0 | 4109 | 4196 | 64905211 | 64905298 | 7.370000e-23 | 119.0 |
38 | TraesCS1A01G010700 | chr6B | 92.825 | 223 | 15 | 1 | 3491 | 3713 | 121429024 | 121429245 | 5.230000e-84 | 322.0 |
39 | TraesCS1A01G010700 | chr6B | 78.313 | 332 | 47 | 16 | 828 | 1147 | 422359550 | 422359232 | 1.540000e-44 | 191.0 |
40 | TraesCS1A01G010700 | chr6B | 88.889 | 108 | 12 | 0 | 3868 | 3975 | 115524054 | 115524161 | 2.630000e-27 | 134.0 |
41 | TraesCS1A01G010700 | chr6B | 87.963 | 108 | 13 | 0 | 3868 | 3975 | 114976429 | 114976536 | 1.220000e-25 | 128.0 |
42 | TraesCS1A01G010700 | chr6B | 84.211 | 95 | 9 | 4 | 7 | 101 | 67127399 | 67127311 | 2.080000e-13 | 87.9 |
43 | TraesCS1A01G010700 | chr6B | 83.908 | 87 | 10 | 3 | 15 | 101 | 67319951 | 67319869 | 3.480000e-11 | 80.5 |
44 | TraesCS1A01G010700 | chr6B | 90.000 | 50 | 2 | 1 | 3632 | 3681 | 114869085 | 114869131 | 1.260000e-05 | 62.1 |
45 | TraesCS1A01G010700 | chr5A | 97.059 | 170 | 5 | 0 | 3741 | 3910 | 558684595 | 558684764 | 1.910000e-73 | 287.0 |
46 | TraesCS1A01G010700 | chr4D | 94.767 | 172 | 8 | 1 | 3743 | 3913 | 28983049 | 28982878 | 2.490000e-67 | 267.0 |
47 | TraesCS1A01G010700 | chr7D | 94.220 | 173 | 10 | 0 | 3739 | 3911 | 530406729 | 530406901 | 8.950000e-67 | 265.0 |
48 | TraesCS1A01G010700 | chr7D | 90.957 | 188 | 15 | 2 | 3724 | 3911 | 37292835 | 37293020 | 6.970000e-63 | 252.0 |
49 | TraesCS1A01G010700 | chr7D | 93.750 | 128 | 6 | 1 | 3470 | 3595 | 412179486 | 412179613 | 1.540000e-44 | 191.0 |
50 | TraesCS1A01G010700 | chr4B | 79.433 | 141 | 19 | 5 | 2972 | 3105 | 42141609 | 42141746 | 1.610000e-14 | 91.6 |
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 | TraesCS1A01G010700 | chr1A | 6471656 | 6475852 | 4196 | True | 2377.400000 | 4084 | 100.000000 | 1 | 4197 | 3 | chr1A.!!$R3 | 4196 |
1 | TraesCS1A01G010700 | chr3A | 177677260 | 177680988 | 3728 | False | 1652.925000 | 3919 | 98.785250 | 1 | 4197 | 4 | chr3A.!!$F1 | 4196 |
2 | TraesCS1A01G010700 | chr3A | 31806116 | 31807462 | 1346 | True | 629.733333 | 1356 | 95.964667 | 2758 | 4197 | 3 | chr3A.!!$R1 | 1439 |
3 | TraesCS1A01G010700 | chr7B | 616827346 | 616828758 | 1412 | True | 646.666667 | 736 | 92.023000 | 742 | 2139 | 3 | chr7B.!!$R2 | 1397 |
4 | TraesCS1A01G010700 | chr7B | 616755453 | 616756857 | 1404 | True | 366.250000 | 623 | 88.277000 | 742 | 2758 | 4 | chr7B.!!$R1 | 2016 |
5 | TraesCS1A01G010700 | chr7A | 652008201 | 652009245 | 1044 | True | 361.666667 | 545 | 84.623000 | 730 | 2758 | 3 | chr7A.!!$R1 | 2028 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
84 | 85 | 0.338814 | TCCCTCTCCCTTGTCTACCC | 59.661 | 60.0 | 0.0 | 0.0 | 0.0 | 3.69 | F |
85 | 86 | 1.043673 | CCCTCTCCCTTGTCTACCCG | 61.044 | 65.0 | 0.0 | 0.0 | 0.0 | 5.28 | F |
86 | 87 | 1.677637 | CCTCTCCCTTGTCTACCCGC | 61.678 | 65.0 | 0.0 | 0.0 | 0.0 | 6.13 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1081 | 1102 | 3.837213 | AACAGTGCTGCAATGTCATAC | 57.163 | 42.857 | 32.04 | 5.37 | 41.85 | 2.39 | R |
2150 | 2242 | 1.765230 | ACGTGTTAAAAAGCCCCACA | 58.235 | 45.000 | 0.00 | 0.00 | 0.00 | 4.17 | R |
3255 | 3492 | 1.469595 | CGACGCGTTGGGGATAAACTA | 60.470 | 52.381 | 19.10 | 0.00 | 0.00 | 2.24 | 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 |
---|---|---|---|---|---|---|---|---|---|
83 | 84 | 1.288335 | TCTCCCTCTCCCTTGTCTACC | 59.712 | 57.143 | 0.00 | 0.00 | 0.00 | 3.18 |
84 | 85 | 0.338814 | TCCCTCTCCCTTGTCTACCC | 59.661 | 60.000 | 0.00 | 0.00 | 0.00 | 3.69 |
85 | 86 | 1.043673 | CCCTCTCCCTTGTCTACCCG | 61.044 | 65.000 | 0.00 | 0.00 | 0.00 | 5.28 |
86 | 87 | 1.677637 | CCTCTCCCTTGTCTACCCGC | 61.678 | 65.000 | 0.00 | 0.00 | 0.00 | 6.13 |
87 | 88 | 1.677637 | CTCTCCCTTGTCTACCCGCC | 61.678 | 65.000 | 0.00 | 0.00 | 0.00 | 6.13 |
88 | 89 | 3.072468 | TCCCTTGTCTACCCGCCG | 61.072 | 66.667 | 0.00 | 0.00 | 0.00 | 6.46 |
130 | 131 | 3.636231 | CCTCCCCAACCGCTGACA | 61.636 | 66.667 | 0.00 | 0.00 | 0.00 | 3.58 |
141 | 142 | 2.971598 | CGCTGACATTCCCACCCCT | 61.972 | 63.158 | 0.00 | 0.00 | 0.00 | 4.79 |
463 | 464 | 1.783250 | AAGCAGCACCAACCCTAGCT | 61.783 | 55.000 | 0.00 | 0.00 | 37.95 | 3.32 |
553 | 554 | 3.775316 | TCTCTGGTTTTCTACATCCCCTC | 59.225 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
578 | 579 | 9.078990 | TCTCGCTTTATATATCTTCTCTGGAAA | 57.921 | 33.333 | 0.00 | 0.00 | 0.00 | 3.13 |
913 | 928 | 5.193679 | GCTGGGAGGTTACAAGATGTTTAT | 58.806 | 41.667 | 0.00 | 0.00 | 0.00 | 1.40 |
914 | 929 | 5.066505 | GCTGGGAGGTTACAAGATGTTTATG | 59.933 | 44.000 | 0.00 | 0.00 | 0.00 | 1.90 |
915 | 930 | 6.134535 | TGGGAGGTTACAAGATGTTTATGT | 57.865 | 37.500 | 0.00 | 0.00 | 0.00 | 2.29 |
916 | 931 | 7.260387 | TGGGAGGTTACAAGATGTTTATGTA | 57.740 | 36.000 | 0.00 | 0.00 | 0.00 | 2.29 |
917 | 932 | 7.691213 | TGGGAGGTTACAAGATGTTTATGTAA | 58.309 | 34.615 | 0.00 | 0.00 | 37.24 | 2.41 |
1060 | 1081 | 8.806429 | TTGTGCATCTTTCTATCCTGAAATTA | 57.194 | 30.769 | 0.00 | 0.00 | 35.68 | 1.40 |
1081 | 1102 | 8.470040 | AATTATGCTGAAGTGCAAGTAATTTG | 57.530 | 30.769 | 0.00 | 0.00 | 46.61 | 2.32 |
2150 | 2242 | 2.960819 | ACTCACGAGCGCTAATTTCTT | 58.039 | 42.857 | 11.50 | 0.00 | 0.00 | 2.52 |
2191 | 2283 | 6.423001 | ACGTAAATTATCGCTATCACCCTTTC | 59.577 | 38.462 | 0.00 | 0.00 | 0.00 | 2.62 |
3255 | 3492 | 1.002069 | TGGCTGGGTTGAGGATGATT | 58.998 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
3260 | 3497 | 4.273318 | GCTGGGTTGAGGATGATTAGTTT | 58.727 | 43.478 | 0.00 | 0.00 | 0.00 | 2.66 |
3292 | 3529 | 2.813908 | GCCGTGTGTCCATCCGAC | 60.814 | 66.667 | 0.00 | 0.00 | 42.33 | 4.79 |
3418 | 3655 | 3.325870 | TGTACCTTCATGCTCTTTGACG | 58.674 | 45.455 | 0.00 | 0.00 | 0.00 | 4.35 |
3754 | 4037 | 9.251440 | TGTATGTATGTATGTATTACTCCCTCC | 57.749 | 37.037 | 0.00 | 0.00 | 0.00 | 4.30 |
3755 | 4038 | 6.829229 | TGTATGTATGTATTACTCCCTCCG | 57.171 | 41.667 | 0.00 | 0.00 | 0.00 | 4.63 |
3756 | 4039 | 6.309357 | TGTATGTATGTATTACTCCCTCCGT | 58.691 | 40.000 | 0.00 | 0.00 | 0.00 | 4.69 |
3757 | 4040 | 6.779049 | TGTATGTATGTATTACTCCCTCCGTT | 59.221 | 38.462 | 0.00 | 0.00 | 0.00 | 4.44 |
3758 | 4041 | 5.779529 | TGTATGTATTACTCCCTCCGTTC | 57.220 | 43.478 | 0.00 | 0.00 | 0.00 | 3.95 |
3759 | 4042 | 4.586001 | TGTATGTATTACTCCCTCCGTTCC | 59.414 | 45.833 | 0.00 | 0.00 | 0.00 | 3.62 |
3761 | 4044 | 4.524802 | TGTATTACTCCCTCCGTTCCTA | 57.475 | 45.455 | 0.00 | 0.00 | 0.00 | 2.94 |
3762 | 4045 | 4.870636 | TGTATTACTCCCTCCGTTCCTAA | 58.129 | 43.478 | 0.00 | 0.00 | 0.00 | 2.69 |
3765 | 4048 | 7.068702 | TGTATTACTCCCTCCGTTCCTAAATA | 58.931 | 38.462 | 0.00 | 0.00 | 0.00 | 1.40 |
3768 | 4051 | 8.731591 | ATTACTCCCTCCGTTCCTAAATATAA | 57.268 | 34.615 | 0.00 | 0.00 | 0.00 | 0.98 |
3771 | 4054 | 6.267242 | ACTCCCTCCGTTCCTAAATATAAGTC | 59.733 | 42.308 | 0.00 | 0.00 | 0.00 | 3.01 |
3773 | 4056 | 6.842807 | TCCCTCCGTTCCTAAATATAAGTCTT | 59.157 | 38.462 | 0.00 | 0.00 | 0.00 | 3.01 |
3775 | 4058 | 7.656542 | CCCTCCGTTCCTAAATATAAGTCTTTC | 59.343 | 40.741 | 0.00 | 0.00 | 0.00 | 2.62 |
3793 | 4076 | 9.921637 | AAGTCTTTCTAGAGATTCTAACAAGTG | 57.078 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
3794 | 4077 | 9.303116 | AGTCTTTCTAGAGATTCTAACAAGTGA | 57.697 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
3795 | 4078 | 9.349145 | GTCTTTCTAGAGATTCTAACAAGTGAC | 57.651 | 37.037 | 0.00 | 0.00 | 0.00 | 3.67 |
3796 | 4079 | 9.303116 | TCTTTCTAGAGATTCTAACAAGTGACT | 57.697 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
3799 | 4082 | 9.516546 | TTCTAGAGATTCTAACAAGTGACTACA | 57.483 | 33.333 | 0.00 | 0.00 | 0.00 | 2.74 |
3800 | 4083 | 9.688091 | TCTAGAGATTCTAACAAGTGACTACAT | 57.312 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
3803 | 4086 | 9.244292 | AGAGATTCTAACAAGTGACTACATACA | 57.756 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
3859 | 4142 | 7.860918 | ATGTCTATATACATCCGTATGTCGT | 57.139 | 36.000 | 0.00 | 0.00 | 42.92 | 4.34 |
3860 | 4143 | 7.677454 | TGTCTATATACATCCGTATGTCGTT | 57.323 | 36.000 | 0.00 | 0.00 | 42.92 | 3.85 |
3861 | 4144 | 7.524065 | TGTCTATATACATCCGTATGTCGTTG | 58.476 | 38.462 | 0.00 | 0.00 | 42.92 | 4.10 |
3862 | 4145 | 7.173735 | TGTCTATATACATCCGTATGTCGTTGT | 59.826 | 37.037 | 0.00 | 0.00 | 42.92 | 3.32 |
3863 | 4146 | 7.691463 | GTCTATATACATCCGTATGTCGTTGTC | 59.309 | 40.741 | 0.00 | 0.00 | 42.92 | 3.18 |
3864 | 4147 | 2.288961 | ACATCCGTATGTCGTTGTCC | 57.711 | 50.000 | 0.00 | 0.00 | 42.92 | 4.02 |
3865 | 4148 | 1.546923 | ACATCCGTATGTCGTTGTCCA | 59.453 | 47.619 | 0.00 | 0.00 | 42.92 | 4.02 |
3866 | 4149 | 2.167693 | ACATCCGTATGTCGTTGTCCAT | 59.832 | 45.455 | 0.00 | 0.00 | 42.92 | 3.41 |
3867 | 4150 | 3.194861 | CATCCGTATGTCGTTGTCCATT | 58.805 | 45.455 | 0.00 | 0.00 | 37.94 | 3.16 |
3868 | 4151 | 3.322211 | TCCGTATGTCGTTGTCCATTT | 57.678 | 42.857 | 0.00 | 0.00 | 37.94 | 2.32 |
3869 | 4152 | 2.997303 | TCCGTATGTCGTTGTCCATTTG | 59.003 | 45.455 | 0.00 | 0.00 | 37.94 | 2.32 |
3870 | 4153 | 2.997303 | CCGTATGTCGTTGTCCATTTGA | 59.003 | 45.455 | 0.00 | 0.00 | 37.94 | 2.69 |
3871 | 4154 | 3.433957 | CCGTATGTCGTTGTCCATTTGAA | 59.566 | 43.478 | 0.00 | 0.00 | 37.94 | 2.69 |
3872 | 4155 | 4.083749 | CCGTATGTCGTTGTCCATTTGAAA | 60.084 | 41.667 | 0.00 | 0.00 | 37.94 | 2.69 |
3873 | 4156 | 5.391523 | CCGTATGTCGTTGTCCATTTGAAAT | 60.392 | 40.000 | 0.00 | 0.00 | 37.94 | 2.17 |
3874 | 4157 | 5.507876 | CGTATGTCGTTGTCCATTTGAAATG | 59.492 | 40.000 | 10.84 | 10.84 | 34.52 | 2.32 |
3875 | 4158 | 4.909696 | TGTCGTTGTCCATTTGAAATGT | 57.090 | 36.364 | 15.93 | 0.00 | 0.00 | 2.71 |
3876 | 4159 | 4.854399 | TGTCGTTGTCCATTTGAAATGTC | 58.146 | 39.130 | 15.93 | 9.53 | 0.00 | 3.06 |
3877 | 4160 | 4.578516 | TGTCGTTGTCCATTTGAAATGTCT | 59.421 | 37.500 | 15.93 | 0.00 | 0.00 | 3.41 |
3878 | 4161 | 5.760743 | TGTCGTTGTCCATTTGAAATGTCTA | 59.239 | 36.000 | 15.93 | 4.32 | 0.00 | 2.59 |
3879 | 4162 | 6.261158 | TGTCGTTGTCCATTTGAAATGTCTAA | 59.739 | 34.615 | 15.93 | 5.71 | 0.00 | 2.10 |
3880 | 4163 | 7.136119 | GTCGTTGTCCATTTGAAATGTCTAAA | 58.864 | 34.615 | 15.93 | 3.49 | 0.00 | 1.85 |
3881 | 4164 | 7.646130 | GTCGTTGTCCATTTGAAATGTCTAAAA | 59.354 | 33.333 | 15.93 | 1.40 | 0.00 | 1.52 |
3882 | 4165 | 8.191446 | TCGTTGTCCATTTGAAATGTCTAAAAA | 58.809 | 29.630 | 15.93 | 0.00 | 0.00 | 1.94 |
3883 | 4166 | 8.479280 | CGTTGTCCATTTGAAATGTCTAAAAAG | 58.521 | 33.333 | 15.93 | 2.94 | 0.00 | 2.27 |
3884 | 4167 | 9.528018 | GTTGTCCATTTGAAATGTCTAAAAAGA | 57.472 | 29.630 | 15.93 | 1.84 | 0.00 | 2.52 |
3885 | 4168 | 9.528018 | TTGTCCATTTGAAATGTCTAAAAAGAC | 57.472 | 29.630 | 15.93 | 12.86 | 39.15 | 3.01 |
3886 | 4169 | 8.912988 | TGTCCATTTGAAATGTCTAAAAAGACT | 58.087 | 29.630 | 15.93 | 0.00 | 39.41 | 3.24 |
3887 | 4170 | 9.750125 | GTCCATTTGAAATGTCTAAAAAGACTT | 57.250 | 29.630 | 15.93 | 0.00 | 39.41 | 3.01 |
3905 | 4188 | 9.868160 | AAAAGACTTATATTTAGGAATGGAGGG | 57.132 | 33.333 | 0.00 | 0.00 | 0.00 | 4.30 |
3906 | 4189 | 8.814448 | AAGACTTATATTTAGGAATGGAGGGA | 57.186 | 34.615 | 0.00 | 0.00 | 0.00 | 4.20 |
3907 | 4190 | 8.442660 | AGACTTATATTTAGGAATGGAGGGAG | 57.557 | 38.462 | 0.00 | 0.00 | 0.00 | 4.30 |
4028 | 4312 | 4.788617 | AGGACCCATTAGTACATTCAGGTT | 59.211 | 41.667 | 0.00 | 0.00 | 0.00 | 3.50 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
41 | 42 | 0.833287 | AATCGAGGGATGGTGACTGG | 59.167 | 55.000 | 0.00 | 0.00 | 31.83 | 4.00 |
106 | 107 | 2.926242 | GGTTGGGGAGGTCGTGGA | 60.926 | 66.667 | 0.00 | 0.00 | 0.00 | 4.02 |
130 | 131 | 2.206223 | GAGAAGGTAAGGGGTGGGAAT | 58.794 | 52.381 | 0.00 | 0.00 | 0.00 | 3.01 |
141 | 142 | 1.628846 | GGTGAGGCAAGGAGAAGGTAA | 59.371 | 52.381 | 0.00 | 0.00 | 0.00 | 2.85 |
207 | 208 | 2.222953 | CTGAACGGTAAACAGCGCCG | 62.223 | 60.000 | 2.29 | 0.00 | 0.00 | 6.46 |
463 | 464 | 1.071542 | TGGGTCGTCATTGAAGCAAGA | 59.928 | 47.619 | 0.00 | 0.00 | 0.00 | 3.02 |
553 | 554 | 9.868277 | ATTTCCAGAGAAGATATATAAAGCGAG | 57.132 | 33.333 | 0.00 | 0.00 | 32.35 | 5.03 |
587 | 588 | 8.703378 | AGAAAGAGAGAGTCAATTTCCAAAAT | 57.297 | 30.769 | 0.00 | 0.00 | 31.69 | 1.82 |
677 | 680 | 7.168219 | ACAACCAACTGAGATTCTAATAGCAA | 58.832 | 34.615 | 0.00 | 0.00 | 0.00 | 3.91 |
913 | 928 | 5.515886 | CCCCCTTTTCAGTCCTTACATTACA | 60.516 | 44.000 | 0.00 | 0.00 | 0.00 | 2.41 |
914 | 929 | 4.948004 | CCCCCTTTTCAGTCCTTACATTAC | 59.052 | 45.833 | 0.00 | 0.00 | 0.00 | 1.89 |
915 | 930 | 4.604490 | ACCCCCTTTTCAGTCCTTACATTA | 59.396 | 41.667 | 0.00 | 0.00 | 0.00 | 1.90 |
916 | 931 | 3.401342 | ACCCCCTTTTCAGTCCTTACATT | 59.599 | 43.478 | 0.00 | 0.00 | 0.00 | 2.71 |
917 | 932 | 2.993863 | ACCCCCTTTTCAGTCCTTACAT | 59.006 | 45.455 | 0.00 | 0.00 | 0.00 | 2.29 |
1060 | 1081 | 5.458041 | ACAAATTACTTGCACTTCAGCAT | 57.542 | 34.783 | 0.00 | 0.00 | 45.19 | 3.79 |
1081 | 1102 | 3.837213 | AACAGTGCTGCAATGTCATAC | 57.163 | 42.857 | 32.04 | 5.37 | 41.85 | 2.39 |
2150 | 2242 | 1.765230 | ACGTGTTAAAAAGCCCCACA | 58.235 | 45.000 | 0.00 | 0.00 | 0.00 | 4.17 |
3255 | 3492 | 1.469595 | CGACGCGTTGGGGATAAACTA | 60.470 | 52.381 | 19.10 | 0.00 | 0.00 | 2.24 |
3260 | 3497 | 4.517815 | GGCGACGCGTTGGGGATA | 62.518 | 66.667 | 27.02 | 0.00 | 0.00 | 2.59 |
3292 | 3529 | 2.473816 | TGTTGACAGCTCTCTTGTTCG | 58.526 | 47.619 | 0.00 | 0.00 | 0.00 | 3.95 |
3745 | 4028 | 7.300658 | ACTTATATTTAGGAACGGAGGGAGTA | 58.699 | 38.462 | 0.00 | 0.00 | 0.00 | 2.59 |
3746 | 4029 | 6.141790 | ACTTATATTTAGGAACGGAGGGAGT | 58.858 | 40.000 | 0.00 | 0.00 | 0.00 | 3.85 |
3747 | 4030 | 6.494146 | AGACTTATATTTAGGAACGGAGGGAG | 59.506 | 42.308 | 0.00 | 0.00 | 0.00 | 4.30 |
3748 | 4031 | 6.379579 | AGACTTATATTTAGGAACGGAGGGA | 58.620 | 40.000 | 0.00 | 0.00 | 0.00 | 4.20 |
3749 | 4032 | 6.667558 | AGACTTATATTTAGGAACGGAGGG | 57.332 | 41.667 | 0.00 | 0.00 | 0.00 | 4.30 |
3750 | 4033 | 8.422566 | AGAAAGACTTATATTTAGGAACGGAGG | 58.577 | 37.037 | 0.00 | 0.00 | 0.00 | 4.30 |
3768 | 4051 | 9.303116 | TCACTTGTTAGAATCTCTAGAAAGACT | 57.697 | 33.333 | 0.00 | 0.00 | 32.30 | 3.24 |
3773 | 4056 | 9.516546 | TGTAGTCACTTGTTAGAATCTCTAGAA | 57.483 | 33.333 | 0.00 | 0.00 | 29.56 | 2.10 |
3777 | 4060 | 9.244292 | TGTATGTAGTCACTTGTTAGAATCTCT | 57.756 | 33.333 | 0.00 | 0.00 | 0.00 | 3.10 |
3801 | 4084 | 9.950496 | AGTGTAGATTCACTCATTTTTCTATGT | 57.050 | 29.630 | 0.00 | 0.00 | 44.07 | 2.29 |
3833 | 4116 | 9.557061 | ACGACATACGGATGTATATAGACATAT | 57.443 | 33.333 | 14.70 | 5.08 | 46.64 | 1.78 |
3834 | 4117 | 8.953368 | ACGACATACGGATGTATATAGACATA | 57.047 | 34.615 | 14.70 | 0.00 | 46.64 | 2.29 |
3835 | 4118 | 7.860918 | ACGACATACGGATGTATATAGACAT | 57.139 | 36.000 | 14.70 | 12.70 | 46.64 | 3.06 |
3836 | 4119 | 7.173735 | ACAACGACATACGGATGTATATAGACA | 59.826 | 37.037 | 14.70 | 2.07 | 46.64 | 3.41 |
3837 | 4120 | 7.524912 | ACAACGACATACGGATGTATATAGAC | 58.475 | 38.462 | 14.70 | 0.00 | 46.64 | 2.59 |
3838 | 4121 | 7.148356 | GGACAACGACATACGGATGTATATAGA | 60.148 | 40.741 | 14.70 | 0.00 | 46.64 | 1.98 |
3839 | 4122 | 6.965500 | GGACAACGACATACGGATGTATATAG | 59.035 | 42.308 | 14.70 | 5.74 | 46.64 | 1.31 |
3840 | 4123 | 6.430616 | TGGACAACGACATACGGATGTATATA | 59.569 | 38.462 | 14.70 | 0.00 | 46.64 | 0.86 |
3841 | 4124 | 5.242171 | TGGACAACGACATACGGATGTATAT | 59.758 | 40.000 | 14.70 | 0.00 | 46.64 | 0.86 |
3842 | 4125 | 4.579753 | TGGACAACGACATACGGATGTATA | 59.420 | 41.667 | 14.70 | 0.00 | 46.64 | 1.47 |
3843 | 4126 | 3.382227 | TGGACAACGACATACGGATGTAT | 59.618 | 43.478 | 14.70 | 1.66 | 46.64 | 2.29 |
3844 | 4127 | 2.754002 | TGGACAACGACATACGGATGTA | 59.246 | 45.455 | 14.70 | 0.00 | 46.64 | 2.29 |
3851 | 4134 | 6.378582 | ACATTTCAAATGGACAACGACATAC | 58.621 | 36.000 | 14.70 | 0.00 | 0.00 | 2.39 |
3852 | 4135 | 6.429692 | AGACATTTCAAATGGACAACGACATA | 59.570 | 34.615 | 14.70 | 0.00 | 0.00 | 2.29 |
3853 | 4136 | 5.241506 | AGACATTTCAAATGGACAACGACAT | 59.758 | 36.000 | 14.70 | 0.00 | 0.00 | 3.06 |
3854 | 4137 | 4.578516 | AGACATTTCAAATGGACAACGACA | 59.421 | 37.500 | 14.70 | 0.00 | 0.00 | 4.35 |
3855 | 4138 | 5.108385 | AGACATTTCAAATGGACAACGAC | 57.892 | 39.130 | 14.70 | 0.00 | 0.00 | 4.34 |
3856 | 4139 | 6.869315 | TTAGACATTTCAAATGGACAACGA | 57.131 | 33.333 | 14.70 | 0.00 | 0.00 | 3.85 |
3857 | 4140 | 7.922505 | TTTTAGACATTTCAAATGGACAACG | 57.077 | 32.000 | 14.70 | 0.00 | 0.00 | 4.10 |
3858 | 4141 | 9.528018 | TCTTTTTAGACATTTCAAATGGACAAC | 57.472 | 29.630 | 14.70 | 1.26 | 0.00 | 3.32 |
3859 | 4142 | 9.528018 | GTCTTTTTAGACATTTCAAATGGACAA | 57.472 | 29.630 | 14.70 | 2.31 | 38.59 | 3.18 |
3860 | 4143 | 8.912988 | AGTCTTTTTAGACATTTCAAATGGACA | 58.087 | 29.630 | 14.70 | 0.00 | 41.02 | 4.02 |
3861 | 4144 | 9.750125 | AAGTCTTTTTAGACATTTCAAATGGAC | 57.250 | 29.630 | 14.70 | 8.92 | 41.02 | 4.02 |
3879 | 4162 | 9.868160 | CCCTCCATTCCTAAATATAAGTCTTTT | 57.132 | 33.333 | 0.00 | 0.00 | 0.00 | 2.27 |
3880 | 4163 | 9.237706 | TCCCTCCATTCCTAAATATAAGTCTTT | 57.762 | 33.333 | 0.00 | 0.00 | 0.00 | 2.52 |
3881 | 4164 | 8.814448 | TCCCTCCATTCCTAAATATAAGTCTT | 57.186 | 34.615 | 0.00 | 0.00 | 0.00 | 3.01 |
3882 | 4165 | 8.019652 | ACTCCCTCCATTCCTAAATATAAGTCT | 58.980 | 37.037 | 0.00 | 0.00 | 0.00 | 3.24 |
3883 | 4166 | 8.208575 | ACTCCCTCCATTCCTAAATATAAGTC | 57.791 | 38.462 | 0.00 | 0.00 | 0.00 | 3.01 |
3884 | 4167 | 9.102453 | GTACTCCCTCCATTCCTAAATATAAGT | 57.898 | 37.037 | 0.00 | 0.00 | 0.00 | 2.24 |
3885 | 4168 | 9.327731 | AGTACTCCCTCCATTCCTAAATATAAG | 57.672 | 37.037 | 0.00 | 0.00 | 0.00 | 1.73 |
3886 | 4169 | 9.684702 | AAGTACTCCCTCCATTCCTAAATATAA | 57.315 | 33.333 | 0.00 | 0.00 | 0.00 | 0.98 |
3887 | 4170 | 9.101325 | CAAGTACTCCCTCCATTCCTAAATATA | 57.899 | 37.037 | 0.00 | 0.00 | 0.00 | 0.86 |
3888 | 4171 | 7.017651 | CCAAGTACTCCCTCCATTCCTAAATAT | 59.982 | 40.741 | 0.00 | 0.00 | 0.00 | 1.28 |
3889 | 4172 | 6.329197 | CCAAGTACTCCCTCCATTCCTAAATA | 59.671 | 42.308 | 0.00 | 0.00 | 0.00 | 1.40 |
3890 | 4173 | 5.132816 | CCAAGTACTCCCTCCATTCCTAAAT | 59.867 | 44.000 | 0.00 | 0.00 | 0.00 | 1.40 |
3891 | 4174 | 4.473559 | CCAAGTACTCCCTCCATTCCTAAA | 59.526 | 45.833 | 0.00 | 0.00 | 0.00 | 1.85 |
3892 | 4175 | 4.037927 | CCAAGTACTCCCTCCATTCCTAA | 58.962 | 47.826 | 0.00 | 0.00 | 0.00 | 2.69 |
3893 | 4176 | 3.013648 | ACCAAGTACTCCCTCCATTCCTA | 59.986 | 47.826 | 0.00 | 0.00 | 0.00 | 2.94 |
3894 | 4177 | 2.225908 | ACCAAGTACTCCCTCCATTCCT | 60.226 | 50.000 | 0.00 | 0.00 | 0.00 | 3.36 |
3895 | 4178 | 2.197465 | ACCAAGTACTCCCTCCATTCC | 58.803 | 52.381 | 0.00 | 0.00 | 0.00 | 3.01 |
3896 | 4179 | 4.031611 | ACTACCAAGTACTCCCTCCATTC | 58.968 | 47.826 | 0.00 | 0.00 | 32.84 | 2.67 |
3897 | 4180 | 3.775316 | CACTACCAAGTACTCCCTCCATT | 59.225 | 47.826 | 0.00 | 0.00 | 33.48 | 3.16 |
3898 | 4181 | 3.375699 | CACTACCAAGTACTCCCTCCAT | 58.624 | 50.000 | 0.00 | 0.00 | 33.48 | 3.41 |
3899 | 4182 | 2.559026 | CCACTACCAAGTACTCCCTCCA | 60.559 | 54.545 | 0.00 | 0.00 | 33.48 | 3.86 |
3900 | 4183 | 2.108970 | CCACTACCAAGTACTCCCTCC | 58.891 | 57.143 | 0.00 | 0.00 | 33.48 | 4.30 |
3901 | 4184 | 2.817665 | ACCACTACCAAGTACTCCCTC | 58.182 | 52.381 | 0.00 | 0.00 | 33.48 | 4.30 |
3902 | 4185 | 3.271153 | AACCACTACCAAGTACTCCCT | 57.729 | 47.619 | 0.00 | 0.00 | 33.48 | 4.20 |
3903 | 4186 | 4.529769 | AGTAAACCACTACCAAGTACTCCC | 59.470 | 45.833 | 0.00 | 0.00 | 34.98 | 4.30 |
3904 | 4187 | 5.479724 | AGAGTAAACCACTACCAAGTACTCC | 59.520 | 44.000 | 0.00 | 0.00 | 37.16 | 3.85 |
3905 | 4188 | 6.388278 | CAGAGTAAACCACTACCAAGTACTC | 58.612 | 44.000 | 0.00 | 0.00 | 37.72 | 2.59 |
3906 | 4189 | 5.279356 | GCAGAGTAAACCACTACCAAGTACT | 60.279 | 44.000 | 0.00 | 0.00 | 37.72 | 2.73 |
3907 | 4190 | 4.928020 | GCAGAGTAAACCACTACCAAGTAC | 59.072 | 45.833 | 0.00 | 0.00 | 37.72 | 2.73 |
4028 | 4312 | 2.392662 | CTCTAGTCCTCTTGCCATCCA | 58.607 | 52.381 | 0.00 | 0.00 | 0.00 | 3.41 |
![](/static/images/cyverse_long.png)
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.