Multiple sequence alignment - TraesCS5B01G424300

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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 TraesCS5B01G424300 chr5B 100.000 5428 0 0 1 5428 600492719 600487292 0.000000e+00 10024.0
1 TraesCS5B01G424300 chr5B 94.382 89 2 2 4160 4245 704531943 704532031 3.410000e-27 134.0
2 TraesCS5B01G424300 chr5D 93.281 3944 170 38 270 4161 487884246 487880346 0.000000e+00 5727.0
3 TraesCS5B01G424300 chr5D 91.477 2065 91 30 1 2017 487884542 487882515 0.000000e+00 2760.0
4 TraesCS5B01G424300 chr5D 90.557 826 44 9 4243 5039 487880344 487879524 0.000000e+00 1062.0
5 TraesCS5B01G424300 chr5D 86.528 193 17 2 2067 2258 487882619 487882435 2.560000e-48 204.0
6 TraesCS5B01G424300 chr5D 93.137 102 4 2 5327 5428 487877969 487877871 4.380000e-31 147.0
7 TraesCS5B01G424300 chr5A 88.585 2085 135 56 1 2026 608608348 608606308 0.000000e+00 2436.0
8 TraesCS5B01G424300 chr5A 90.517 1740 125 27 2012 3729 608606292 608604571 0.000000e+00 2263.0
9 TraesCS5B01G424300 chr5A 88.242 893 62 21 4241 5107 608604102 608603227 0.000000e+00 1027.0
10 TraesCS5B01G424300 chr5A 88.508 496 37 6 3669 4164 608604577 608604102 2.820000e-162 582.0
11 TraesCS5B01G424300 chr5A 91.262 103 5 3 4157 4255 612161563 612161461 2.640000e-28 137.0
12 TraesCS5B01G424300 chr5A 92.593 54 4 0 5243 5296 608601684 608601631 1.620000e-10 78.7
13 TraesCS5B01G424300 chr1B 93.000 100 3 3 4151 4246 549520154 549520055 5.670000e-30 143.0
14 TraesCS5B01G424300 chr1B 84.270 89 10 3 3087 3172 540727160 540727073 3.480000e-12 84.2
15 TraesCS5B01G424300 chr1B 83.721 86 8 3 3091 3172 31367181 31367098 5.830000e-10 76.8
16 TraesCS5B01G424300 chr7B 94.505 91 1 3 4160 4246 698886784 698886694 2.640000e-28 137.0
17 TraesCS5B01G424300 chr3A 95.455 88 1 2 4158 4242 696373520 696373433 2.640000e-28 137.0
18 TraesCS5B01G424300 chr3A 95.402 87 1 2 4159 4242 663575324 663575410 9.480000e-28 135.0
19 TraesCS5B01G424300 chr7D 94.444 90 2 2 4161 4247 180445011 180444922 9.480000e-28 135.0
20 TraesCS5B01G424300 chr7A 94.382 89 2 2 4161 4246 553036688 553036600 3.410000e-27 134.0
21 TraesCS5B01G424300 chr7A 94.253 87 3 1 4158 4242 553036602 553036688 1.230000e-26 132.0
22 TraesCS5B01G424300 chr1D 84.270 89 10 1 3088 3172 201494980 201495068 3.480000e-12 84.2
23 TraesCS5B01G424300 chr3D 84.270 89 7 6 3088 3172 250918803 250918718 4.510000e-11 80.5
24 TraesCS5B01G424300 chr1A 85.714 77 7 1 3100 3172 255486683 255486759 1.620000e-10 78.7
25 TraesCS5B01G424300 chrUn 83.721 86 8 3 3091 3172 134112272 134112355 5.830000e-10 76.8
26 TraesCS5B01G424300 chr6D 83.721 86 8 3 3091 3172 159233560 159233477 5.830000e-10 76.8
27 TraesCS5B01G424300 chr4A 83.721 86 8 3 3091 3172 596708552 596708635 5.830000e-10 76.8


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 TraesCS5B01G424300 chr5B 600487292 600492719 5427 True 10024.00 10024 100.000 1 5428 1 chr5B.!!$R1 5427
1 TraesCS5B01G424300 chr5D 487877871 487884542 6671 True 1980.00 5727 90.996 1 5428 5 chr5D.!!$R1 5427
2 TraesCS5B01G424300 chr5A 608601631 608608348 6717 True 1277.34 2436 89.689 1 5296 5 chr5A.!!$R2 5295

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
570 616 0.306840 TAGTATCTTCTCCGCGTGCG 59.693 55.0 4.92 7.38 39.44 5.34 F
1221 1284 0.108186 TGTAGGATGTCTGCAAGGCG 60.108 55.0 0.00 0.00 45.90 5.52 F
2738 2877 0.837272 GATGGGGATTCGTCCAGGAA 59.163 55.0 0.00 0.00 36.38 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 1569 1.003545 GGCATGCAATATATAGGCGCG 60.004 52.381 21.36 0.0 0.00 6.86 R
2811 2950 0.036952 CACTGCTTGGGTGACGAGAT 60.037 55.000 0.00 0.0 36.89 2.75 R
4667 4899 0.593518 CACTCTCAGGCATACGCTCG 60.594 60.000 0.00 0.0 38.60 5.03 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
110 111 1.154093 CATCTTTGCAGCTGTGGCG 60.154 57.895 16.64 2.26 44.37 5.69
139 140 1.115930 ACCAACCTCAGTCAGACGCT 61.116 55.000 0.00 0.00 0.00 5.07
176 177 3.304559 CACAAAATCTAGCGGAAGACTCG 59.695 47.826 0.00 0.00 0.00 4.18
215 216 1.135199 CCGTTAACAAGCGCTCCTAGA 60.135 52.381 12.06 0.00 0.00 2.43
268 270 0.326264 AGCCAGCACGAAATTCTCCT 59.674 50.000 0.00 0.00 0.00 3.69
399 427 2.528127 TTGCTCACCGGGAAGGGA 60.528 61.111 6.32 0.00 46.96 4.20
460 500 2.418910 CGGCTCTGGATCTCACGGT 61.419 63.158 0.00 0.00 0.00 4.83
570 616 0.306840 TAGTATCTTCTCCGCGTGCG 59.693 55.000 4.92 7.38 39.44 5.34
571 617 2.278596 TATCTTCTCCGCGTGCGC 60.279 61.111 9.07 0.00 38.24 6.09
661 718 0.813821 GCCCATCCTGAGAAGCAAAC 59.186 55.000 0.00 0.00 0.00 2.93
876 939 4.308458 TGCAGGTACGCCACGCTT 62.308 61.111 0.00 0.00 36.67 4.68
925 988 1.944896 TAGATCCGCCTCCACTCCCA 61.945 60.000 0.00 0.00 0.00 4.37
926 989 3.083997 ATCCGCCTCCACTCCCAC 61.084 66.667 0.00 0.00 0.00 4.61
933 996 4.348495 TCCACTCCCACCCTCCCC 62.348 72.222 0.00 0.00 0.00 4.81
1127 1190 4.176752 CGTAAGAGCCCAGCCCCC 62.177 72.222 0.00 0.00 43.02 5.40
1173 1236 0.388659 TTTTGCCTTCTGCGTGCAAT 59.611 45.000 0.00 0.00 43.78 3.56
1177 1240 1.675310 CCTTCTGCGTGCAATCCCA 60.675 57.895 0.00 0.00 0.00 4.37
1186 1249 2.353208 GCGTGCAATCCCATTTTAACCA 60.353 45.455 0.00 0.00 0.00 3.67
1190 1253 3.843027 TGCAATCCCATTTTAACCATGGT 59.157 39.130 13.00 13.00 39.86 3.55
1198 1261 4.451774 CCATTTTAACCATGGTTGCTGTTG 59.548 41.667 35.49 24.36 38.92 3.33
1221 1284 0.108186 TGTAGGATGTCTGCAAGGCG 60.108 55.000 0.00 0.00 45.90 5.52
1271 1334 8.443979 TGAATTCATGGTATGGTATGGTATGAA 58.556 33.333 3.38 0.00 37.44 2.57
1272 1335 9.466497 GAATTCATGGTATGGTATGGTATGAAT 57.534 33.333 0.00 0.00 42.36 2.57
1275 1338 9.904198 TTCATGGTATGGTATGGTATGAATATG 57.096 33.333 0.00 0.00 30.67 1.78
1276 1339 9.278011 TCATGGTATGGTATGGTATGAATATGA 57.722 33.333 0.00 0.00 0.00 2.15
1301 1364 5.188163 TGATCAATGATGCAAGGGTTCAAAT 59.812 36.000 0.00 0.00 0.00 2.32
1324 1387 5.058149 TGTTGCCATATGTGTGATTTGAC 57.942 39.130 1.24 0.00 0.00 3.18
1355 1418 3.883744 AAGTGGCGCGCTGCTTACT 62.884 57.895 32.29 22.17 45.43 2.24
1363 1426 1.700600 GCGCTGCTTACTCCTGCTTC 61.701 60.000 0.00 0.00 0.00 3.86
1366 1429 1.941668 GCTGCTTACTCCTGCTTCGTT 60.942 52.381 0.00 0.00 0.00 3.85
1499 1562 3.581755 CCTTATTCGACCGTTTGTCTGA 58.418 45.455 0.00 0.00 42.13 3.27
1506 1569 2.027625 CCGTTTGTCTGAGTCCGGC 61.028 63.158 0.00 0.00 0.00 6.13
1509 1572 4.717629 TTGTCTGAGTCCGGCGCG 62.718 66.667 0.00 0.00 0.00 6.86
1515 1578 3.667282 GAGTCCGGCGCGCCTATA 61.667 66.667 43.60 27.59 0.00 1.31
1552 1615 1.360820 GCTTCGTGGCCTTAACTCTC 58.639 55.000 3.32 0.00 0.00 3.20
1761 1824 2.553086 TGTAAAACGTTCTTCGCCACT 58.447 42.857 0.00 0.00 44.19 4.00
1818 1888 7.452880 TCTAACATGCAGAGCAGTTAATTTT 57.547 32.000 0.00 0.00 43.65 1.82
1988 2066 6.610075 ATTCAAGCAACAAAGGGTGATAAT 57.390 33.333 0.00 0.00 0.00 1.28
2090 2226 4.340381 GCTCCTCCTTTGCATTAACATCAT 59.660 41.667 0.00 0.00 0.00 2.45
2121 2257 9.686683 ACTTCATTTGCCATATCTACTTTACTT 57.313 29.630 0.00 0.00 0.00 2.24
2283 2420 8.034215 CCTGCCATTTTTCTTGTTCATATTGTA 58.966 33.333 0.00 0.00 0.00 2.41
2315 2452 7.801104 TCATATGACACCTTCAGCCTTTTATA 58.199 34.615 0.00 0.00 37.77 0.98
2356 2493 7.148289 CCAACAAGAGCATATATAAGCTGATGG 60.148 40.741 16.76 13.00 42.04 3.51
2550 2689 1.039856 ATGTGCCTGGTTGTGGTTTC 58.960 50.000 0.00 0.00 0.00 2.78
2738 2877 0.837272 GATGGGGATTCGTCCAGGAA 59.163 55.000 0.00 0.00 36.38 3.36
2797 2936 8.668353 TGATTAAAGTTGACTGCATTCAGATAC 58.332 33.333 6.85 3.33 42.95 2.24
2811 2950 6.572119 GCATTCAGATACCAAATGTTTCCACA 60.572 38.462 0.00 0.00 37.31 4.17
2822 2961 1.270625 TGTTTCCACATCTCGTCACCC 60.271 52.381 0.00 0.00 0.00 4.61
2832 2971 1.224069 CTCGTCACCCAAGCAGTGTG 61.224 60.000 0.00 0.00 36.58 3.82
2837 2976 1.037030 CACCCAAGCAGTGTGTTGGT 61.037 55.000 19.32 7.82 41.57 3.67
2874 3013 0.174162 GGTTCTGGGTGATGCATTGC 59.826 55.000 0.00 0.46 0.00 3.56
2876 3015 1.135199 GTTCTGGGTGATGCATTGCTG 60.135 52.381 10.49 0.00 0.00 4.41
3096 3236 5.523916 GTGTGAAGTGTTGTCAATGTACTCT 59.476 40.000 0.00 0.00 0.00 3.24
3103 3243 3.850122 TGTCAATGTACTCTCTCCGTG 57.150 47.619 0.00 0.00 0.00 4.94
3117 3257 8.184304 ACTCTCTCCGTGCTAAAATATAAGAT 57.816 34.615 0.00 0.00 0.00 2.40
3303 3455 9.482627 GAGGGTTAAATCATGTCATAGTTCTAG 57.517 37.037 0.00 0.00 0.00 2.43
3827 4034 3.209410 GTGAAAGAGGCATCTATGTGGG 58.791 50.000 0.00 0.00 33.45 4.61
3894 4101 4.077108 AGCACATGATTGAGTTGTGTCAT 58.923 39.130 0.00 0.00 42.11 3.06
3900 4107 8.456471 CACATGATTGAGTTGTGTCATATTCTT 58.544 33.333 0.00 0.00 36.77 2.52
3986 4193 0.882927 TTCCCAAAGCGTCACCTTCG 60.883 55.000 0.00 0.00 0.00 3.79
4010 4217 2.803133 GCAGAGCGCCTGTCAATACATA 60.803 50.000 21.68 0.00 44.71 2.29
4021 4229 8.248253 CGCCTGTCAATACATACTTGGTATATA 58.752 37.037 0.00 0.00 34.37 0.86
4051 4259 5.995897 ACAGGTGTACTAGATTTGTTGGTTC 59.004 40.000 0.00 0.00 0.00 3.62
4052 4260 5.411669 CAGGTGTACTAGATTTGTTGGTTCC 59.588 44.000 0.00 0.00 0.00 3.62
4072 4280 4.307259 TCCCCCTAGCTTTCAATACTGAT 58.693 43.478 0.00 0.00 0.00 2.90
4077 4285 3.411415 AGCTTTCAATACTGATTGCGC 57.589 42.857 0.00 0.00 42.01 6.09
4078 4286 3.012518 AGCTTTCAATACTGATTGCGCT 58.987 40.909 9.73 0.00 42.01 5.92
4083 4291 3.860641 TCAATACTGATTGCGCTGAGAA 58.139 40.909 9.73 0.00 42.01 2.87
4089 4297 0.095417 GATTGCGCTGAGAAACGACC 59.905 55.000 9.73 0.00 0.00 4.79
4127 4335 7.716612 ACTGAAACTGGTTAATTTCCTTTCAG 58.283 34.615 23.52 23.52 44.12 3.02
4132 4340 7.039313 ACTGGTTAATTTCCTTTCAGTGTTC 57.961 36.000 0.00 0.00 33.44 3.18
4139 4347 9.545105 TTAATTTCCTTTCAGTGTTCGTAGTTA 57.455 29.630 0.00 0.00 0.00 2.24
4163 4371 5.717119 AATTTCTTCCCATGCCTACTACT 57.283 39.130 0.00 0.00 0.00 2.57
4164 4372 4.755266 TTTCTTCCCATGCCTACTACTC 57.245 45.455 0.00 0.00 0.00 2.59
4165 4373 2.679082 TCTTCCCATGCCTACTACTCC 58.321 52.381 0.00 0.00 0.00 3.85
4166 4374 1.694696 CTTCCCATGCCTACTACTCCC 59.305 57.143 0.00 0.00 0.00 4.30
4167 4375 0.941963 TCCCATGCCTACTACTCCCT 59.058 55.000 0.00 0.00 0.00 4.20
4168 4376 1.133136 TCCCATGCCTACTACTCCCTC 60.133 57.143 0.00 0.00 0.00 4.30
4169 4377 1.133009 CCCATGCCTACTACTCCCTCT 60.133 57.143 0.00 0.00 0.00 3.69
4170 4378 1.967066 CCATGCCTACTACTCCCTCTG 59.033 57.143 0.00 0.00 0.00 3.35
4171 4379 2.672098 CATGCCTACTACTCCCTCTGT 58.328 52.381 0.00 0.00 0.00 3.41
4172 4380 3.436615 CCATGCCTACTACTCCCTCTGTA 60.437 52.174 0.00 0.00 0.00 2.74
4173 4381 3.294038 TGCCTACTACTCCCTCTGTAC 57.706 52.381 0.00 0.00 0.00 2.90
4174 4382 2.091994 TGCCTACTACTCCCTCTGTACC 60.092 54.545 0.00 0.00 0.00 3.34
4175 4383 2.848691 CCTACTACTCCCTCTGTACCG 58.151 57.143 0.00 0.00 0.00 4.02
4176 4384 2.437281 CCTACTACTCCCTCTGTACCGA 59.563 54.545 0.00 0.00 0.00 4.69
4177 4385 3.118112 CCTACTACTCCCTCTGTACCGAA 60.118 52.174 0.00 0.00 0.00 4.30
4178 4386 3.446442 ACTACTCCCTCTGTACCGAAA 57.554 47.619 0.00 0.00 0.00 3.46
4179 4387 3.978610 ACTACTCCCTCTGTACCGAAAT 58.021 45.455 0.00 0.00 0.00 2.17
4180 4388 5.121380 ACTACTCCCTCTGTACCGAAATA 57.879 43.478 0.00 0.00 0.00 1.40
4181 4389 5.131784 ACTACTCCCTCTGTACCGAAATAG 58.868 45.833 0.00 0.00 0.00 1.73
4182 4390 3.978610 ACTCCCTCTGTACCGAAATAGT 58.021 45.455 0.00 0.00 0.00 2.12
4183 4391 4.351127 ACTCCCTCTGTACCGAAATAGTT 58.649 43.478 0.00 0.00 0.00 2.24
4184 4392 4.159879 ACTCCCTCTGTACCGAAATAGTTG 59.840 45.833 0.00 0.00 0.00 3.16
4185 4393 4.091549 TCCCTCTGTACCGAAATAGTTGT 58.908 43.478 0.00 0.00 0.00 3.32
4186 4394 4.159135 TCCCTCTGTACCGAAATAGTTGTC 59.841 45.833 0.00 0.00 0.00 3.18
4187 4395 4.103357 CCTCTGTACCGAAATAGTTGTCG 58.897 47.826 0.00 0.00 37.01 4.35
4188 4396 3.504863 TCTGTACCGAAATAGTTGTCGC 58.495 45.455 0.00 0.00 35.93 5.19
4189 4397 3.192001 TCTGTACCGAAATAGTTGTCGCT 59.808 43.478 0.00 0.00 35.93 4.93
4190 4398 3.247442 TGTACCGAAATAGTTGTCGCTG 58.753 45.455 0.00 0.00 35.93 5.18
4191 4399 1.722011 ACCGAAATAGTTGTCGCTGG 58.278 50.000 0.00 0.00 35.93 4.85
4192 4400 1.274167 ACCGAAATAGTTGTCGCTGGA 59.726 47.619 0.00 0.00 35.93 3.86
4193 4401 1.927174 CCGAAATAGTTGTCGCTGGAG 59.073 52.381 0.00 0.00 35.93 3.86
4194 4402 2.607187 CGAAATAGTTGTCGCTGGAGT 58.393 47.619 0.00 0.00 0.00 3.85
4195 4403 3.428452 CCGAAATAGTTGTCGCTGGAGTA 60.428 47.826 0.00 0.00 35.93 2.59
4196 4404 3.791887 CGAAATAGTTGTCGCTGGAGTAG 59.208 47.826 0.00 0.00 0.00 2.57
4225 4433 2.873133 GCTACTCCAGCGACAACTAT 57.127 50.000 0.00 0.00 41.37 2.12
4226 4434 3.166489 GCTACTCCAGCGACAACTATT 57.834 47.619 0.00 0.00 41.37 1.73
4227 4435 3.522553 GCTACTCCAGCGACAACTATTT 58.477 45.455 0.00 0.00 41.37 1.40
4228 4436 3.933332 GCTACTCCAGCGACAACTATTTT 59.067 43.478 0.00 0.00 41.37 1.82
4229 4437 4.201724 GCTACTCCAGCGACAACTATTTTG 60.202 45.833 0.00 0.00 41.37 2.44
4230 4438 3.074412 ACTCCAGCGACAACTATTTTGG 58.926 45.455 0.00 0.00 0.00 3.28
4231 4439 3.074412 CTCCAGCGACAACTATTTTGGT 58.926 45.455 0.00 0.00 0.00 3.67
4232 4440 4.250464 CTCCAGCGACAACTATTTTGGTA 58.750 43.478 0.00 0.00 0.00 3.25
4233 4441 4.250464 TCCAGCGACAACTATTTTGGTAG 58.750 43.478 0.00 0.00 0.00 3.18
4234 4442 4.020928 TCCAGCGACAACTATTTTGGTAGA 60.021 41.667 0.00 0.00 0.00 2.59
4235 4443 4.330074 CCAGCGACAACTATTTTGGTAGAG 59.670 45.833 0.00 0.00 0.00 2.43
4236 4444 4.330074 CAGCGACAACTATTTTGGTAGAGG 59.670 45.833 0.00 0.00 0.00 3.69
4237 4445 3.621715 GCGACAACTATTTTGGTAGAGGG 59.378 47.826 0.00 0.00 0.00 4.30
4238 4446 4.622220 GCGACAACTATTTTGGTAGAGGGA 60.622 45.833 0.00 0.00 0.00 4.20
4239 4447 5.109903 CGACAACTATTTTGGTAGAGGGAG 58.890 45.833 0.00 0.00 0.00 4.30
4293 4501 5.227908 TGTCTTCTTCTAACCGATCACAAC 58.772 41.667 0.00 0.00 0.00 3.32
4318 4526 3.631686 TGTGAAAACTGAATGTCCTGGTG 59.368 43.478 0.00 0.00 0.00 4.17
4442 4650 5.957798 ACACCATGAACATGAATTCATCAC 58.042 37.500 18.16 12.24 44.30 3.06
4468 4676 1.810030 CGCCGTCTTACTCCAAGGC 60.810 63.158 0.00 0.00 41.03 4.35
4542 4750 2.256117 TCGTGATCTCGCTCCTATCA 57.744 50.000 12.18 0.00 0.00 2.15
4551 4759 1.522569 GCTCCTATCACAGCGGGTT 59.477 57.895 0.00 0.00 0.00 4.11
4554 4762 2.224305 GCTCCTATCACAGCGGGTTTAT 60.224 50.000 0.00 0.00 0.00 1.40
4578 4786 2.654749 TTGCGACGATCTGATTGACT 57.345 45.000 11.82 0.00 0.00 3.41
4586 4794 4.899502 ACGATCTGATTGACTGTCCTTTT 58.100 39.130 11.82 0.00 0.00 2.27
4646 4878 2.507102 CTGTACCGAGGTGCTGCG 60.507 66.667 11.44 0.00 0.00 5.18
4667 4899 3.411418 TTGAGCGATCGTCTCCGGC 62.411 63.158 25.96 7.54 33.95 6.13
4730 4964 1.527370 GGCTGTCCCTTTCGCCTAT 59.473 57.895 0.00 0.00 39.42 2.57
5019 5254 3.739810 GGTTACTTTCTCCACTGACGTTC 59.260 47.826 0.00 0.00 0.00 3.95
5049 6240 1.739067 ATAGTTGCTGAGCGTTTCCC 58.261 50.000 0.00 0.00 0.00 3.97
5050 6241 0.669318 TAGTTGCTGAGCGTTTCCCG 60.669 55.000 0.00 0.00 40.40 5.14
5054 6245 4.735132 CTGAGCGTTTCCCGGCGA 62.735 66.667 9.30 0.00 36.94 5.54
5055 6246 4.077184 TGAGCGTTTCCCGGCGAT 62.077 61.111 9.30 0.00 36.94 4.58
5056 6247 3.564027 GAGCGTTTCCCGGCGATG 61.564 66.667 9.30 0.00 36.94 3.84
5059 6250 3.202001 CGTTTCCCGGCGATGCAT 61.202 61.111 9.30 0.00 0.00 3.96
5060 6251 1.885388 CGTTTCCCGGCGATGCATA 60.885 57.895 9.30 0.00 0.00 3.14
5061 6252 1.227999 CGTTTCCCGGCGATGCATAT 61.228 55.000 9.30 0.00 0.00 1.78
5062 6253 0.238289 GTTTCCCGGCGATGCATATG 59.762 55.000 9.30 0.00 0.00 1.78
5063 6254 1.514678 TTTCCCGGCGATGCATATGC 61.515 55.000 21.09 21.09 42.50 3.14
5096 6287 1.210155 GCGTTCAGGGTCAATGCAC 59.790 57.895 0.00 0.00 36.04 4.57
5158 7800 1.656652 CGATGGCTTACTGGAACTGG 58.343 55.000 0.00 0.00 0.00 4.00
5188 7830 0.329261 TTCTGGCCTTGTCCTCCATG 59.671 55.000 3.32 0.00 0.00 3.66
5219 7862 4.907034 CGCGAGCGTCTATGCGGT 62.907 66.667 0.00 0.00 46.31 5.68
5220 7863 2.330393 GCGAGCGTCTATGCGGTA 59.670 61.111 0.00 0.00 42.89 4.02
5221 7864 1.726322 GCGAGCGTCTATGCGGTAG 60.726 63.158 0.00 0.00 42.89 3.18
5222 7865 1.082038 CGAGCGTCTATGCGGTAGG 60.082 63.158 0.00 0.00 42.89 3.18
5241 7888 4.533919 AGGTTGATCAGTCAGTCTCTTG 57.466 45.455 0.00 0.00 35.39 3.02
5273 7951 1.661112 CTTTCGCCTTGATTCGTCCTC 59.339 52.381 0.00 0.00 0.00 3.71
5295 7973 2.435938 GGCCGAACGATGCCTTGA 60.436 61.111 7.11 0.00 44.46 3.02
5296 7974 1.819632 GGCCGAACGATGCCTTGAT 60.820 57.895 7.11 0.00 44.46 2.57
5297 7975 1.376609 GGCCGAACGATGCCTTGATT 61.377 55.000 7.11 0.00 44.46 2.57
5298 7976 0.028110 GCCGAACGATGCCTTGATTC 59.972 55.000 0.00 0.00 0.00 2.52
5299 7977 0.657840 CCGAACGATGCCTTGATTCC 59.342 55.000 0.00 0.00 0.00 3.01
5300 7978 0.301687 CGAACGATGCCTTGATTCCG 59.698 55.000 0.00 0.00 0.00 4.30
5301 7979 0.028110 GAACGATGCCTTGATTCCGC 59.972 55.000 0.00 0.00 0.00 5.54
5302 7980 1.705337 AACGATGCCTTGATTCCGCG 61.705 55.000 0.00 0.00 0.00 6.46
5303 7981 2.329339 GATGCCTTGATTCCGCGC 59.671 61.111 0.00 0.00 0.00 6.86
5304 7982 2.124570 ATGCCTTGATTCCGCGCT 60.125 55.556 5.56 0.00 0.00 5.92
5305 7983 2.384391 GATGCCTTGATTCCGCGCTG 62.384 60.000 5.56 0.00 0.00 5.18
5306 7984 2.819595 GCCTTGATTCCGCGCTGA 60.820 61.111 5.56 0.00 0.00 4.26
5307 7985 2.817423 GCCTTGATTCCGCGCTGAG 61.817 63.158 5.56 0.00 0.00 3.35
5308 7986 2.705826 CTTGATTCCGCGCTGAGC 59.294 61.111 5.56 0.00 43.95 4.26
5309 7987 2.817423 CTTGATTCCGCGCTGAGCC 61.817 63.158 5.56 0.54 44.76 4.70
5311 7989 4.873129 GATTCCGCGCTGAGCCGA 62.873 66.667 15.14 0.00 44.76 5.54
5315 7993 4.914420 CCGCGCTGAGCCGACTAG 62.914 72.222 15.14 0.00 44.76 2.57
5316 7994 4.914420 CGCGCTGAGCCGACTAGG 62.914 72.222 5.56 0.00 44.76 3.02
5317 7995 4.577246 GCGCTGAGCCGACTAGGG 62.577 72.222 0.00 0.00 41.48 3.53
5318 7996 2.829003 CGCTGAGCCGACTAGGGA 60.829 66.667 0.00 0.00 41.48 4.20
5319 7997 2.196925 CGCTGAGCCGACTAGGGAT 61.197 63.158 0.00 0.00 41.48 3.85
5320 7998 1.365633 GCTGAGCCGACTAGGGATG 59.634 63.158 0.00 0.00 41.48 3.51
5321 7999 1.365633 CTGAGCCGACTAGGGATGC 59.634 63.158 0.00 0.00 41.48 3.91
5322 8000 1.381191 TGAGCCGACTAGGGATGCA 60.381 57.895 0.00 0.00 41.48 3.96
5323 8001 1.365633 GAGCCGACTAGGGATGCAG 59.634 63.158 0.00 0.00 41.48 4.41
5324 8002 1.075970 AGCCGACTAGGGATGCAGA 60.076 57.895 0.00 0.00 41.48 4.26
5325 8003 1.068250 GCCGACTAGGGATGCAGAC 59.932 63.158 0.00 0.00 41.48 3.51
5343 8021 4.829968 CAGACTGATTGATTGTCCTCTGT 58.170 43.478 0.00 0.00 0.00 3.41
5377 8055 2.827921 ACTTGGCTCCATCAAATGAACC 59.172 45.455 0.00 0.00 0.00 3.62
5388 8066 7.356680 TCCATCAAATGAACCAGGATTTCTAT 58.643 34.615 0.00 0.00 0.00 1.98
5394 8072 8.408601 CAAATGAACCAGGATTTCTATAAGTGG 58.591 37.037 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 3.049674 GTGCTGCCGCTTGCTGTA 61.050 61.111 0.70 0.00 42.00 2.74
176 177 2.866762 CGGAGAATTCCCGTCAAATCTC 59.133 50.000 20.72 2.08 40.67 2.75
197 198 2.094130 AGGTCTAGGAGCGCTTGTTAAC 60.094 50.000 13.26 8.02 35.00 2.01
215 216 2.100989 AGAATCGCCGTCTTCTTAGGT 58.899 47.619 0.09 0.00 0.00 3.08
297 325 2.815647 CGACGGAGCTTGCCTTCC 60.816 66.667 0.00 0.00 0.00 3.46
299 327 2.185310 AATCCGACGGAGCTTGCCTT 62.185 55.000 22.99 6.78 34.05 4.35
343 371 1.756950 CTTCCGTCCGATCTGGGGA 60.757 63.158 4.16 0.00 38.76 4.81
399 427 2.685380 CTCACTCCCTTCCGGCCT 60.685 66.667 0.00 0.00 0.00 5.19
440 480 2.107953 GTGAGATCCAGAGCCGCC 59.892 66.667 0.00 0.00 0.00 6.13
441 481 2.279120 CGTGAGATCCAGAGCCGC 60.279 66.667 0.00 0.00 0.00 6.53
442 482 2.415010 CCGTGAGATCCAGAGCCG 59.585 66.667 0.00 0.00 0.00 5.52
443 483 1.142748 CACCGTGAGATCCAGAGCC 59.857 63.158 0.00 0.00 0.00 4.70
444 484 0.749649 ATCACCGTGAGATCCAGAGC 59.250 55.000 7.41 0.00 0.00 4.09
445 485 2.293122 GAGATCACCGTGAGATCCAGAG 59.707 54.545 7.41 0.00 42.19 3.35
460 500 1.680989 TCCCAAGGCGACGAGATCA 60.681 57.895 0.00 0.00 0.00 2.92
649 695 1.301677 GAGCCCGGTTTGCTTCTCAG 61.302 60.000 5.12 0.00 39.69 3.35
876 939 0.178995 AAAGTCGCCGGGGGTAAAAA 60.179 50.000 19.63 0.00 0.00 1.94
936 999 2.925162 ATTACAGCGAGGGCCGAAGC 62.925 60.000 11.91 11.91 41.76 3.86
937 1000 0.462047 AATTACAGCGAGGGCCGAAG 60.462 55.000 0.00 0.00 41.76 3.79
938 1001 0.742990 CAATTACAGCGAGGGCCGAA 60.743 55.000 0.00 0.00 41.76 4.30
939 1002 1.153449 CAATTACAGCGAGGGCCGA 60.153 57.895 0.00 0.00 41.76 5.54
944 1007 3.270027 TCCAATCACAATTACAGCGAGG 58.730 45.455 0.00 0.00 0.00 4.63
1177 1240 4.102367 ACCAACAGCAACCATGGTTAAAAT 59.898 37.500 29.36 13.12 43.47 1.82
1186 1249 2.229792 CTACACACCAACAGCAACCAT 58.770 47.619 0.00 0.00 0.00 3.55
1190 1253 2.158682 ACATCCTACACACCAACAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
1198 1261 2.350522 CTTGCAGACATCCTACACACC 58.649 52.381 0.00 0.00 0.00 4.16
1221 1284 1.289380 GATGTAGGGATCGGCGACC 59.711 63.158 13.76 15.71 0.00 4.79
1271 1334 6.253758 ACCCTTGCATCATTGATCATCATAT 58.746 36.000 0.00 0.00 0.00 1.78
1272 1335 5.637127 ACCCTTGCATCATTGATCATCATA 58.363 37.500 0.00 0.00 0.00 2.15
1273 1336 4.480115 ACCCTTGCATCATTGATCATCAT 58.520 39.130 0.00 0.00 0.00 2.45
1274 1337 3.905968 ACCCTTGCATCATTGATCATCA 58.094 40.909 0.00 0.00 0.00 3.07
1275 1338 4.340097 TGAACCCTTGCATCATTGATCATC 59.660 41.667 0.00 0.00 0.00 2.92
1276 1339 4.283337 TGAACCCTTGCATCATTGATCAT 58.717 39.130 0.00 0.00 0.00 2.45
1355 1418 3.596214 GATTTAGGACAACGAAGCAGGA 58.404 45.455 0.00 0.00 0.00 3.86
1419 1482 4.579869 ACCAGCCAGTATAAAGTGAACTG 58.420 43.478 0.00 0.00 40.24 3.16
1499 1562 1.035932 ATATATAGGCGCGCCGGACT 61.036 55.000 41.70 28.24 41.95 3.85
1506 1569 1.003545 GGCATGCAATATATAGGCGCG 60.004 52.381 21.36 0.00 0.00 6.86
1509 1572 5.434352 CATCAGGCATGCAATATATAGGC 57.566 43.478 21.36 0.00 0.00 3.93
1536 1599 1.544691 GAGTGAGAGTTAAGGCCACGA 59.455 52.381 5.01 0.00 33.37 4.35
1552 1615 5.201713 TCTACAGTGGTGAAAGAAGAGTG 57.798 43.478 0.00 0.00 0.00 3.51
1597 1660 1.032114 GGTATGCCCTGGTCTTGTGC 61.032 60.000 0.00 0.00 0.00 4.57
1818 1888 6.088016 AGCAACAAAAAGCATCACATCTAA 57.912 33.333 0.00 0.00 0.00 2.10
1885 1955 9.447157 AATTCAGCTTCCATATTTAGATAGAGC 57.553 33.333 0.00 0.00 0.00 4.09
1958 2028 5.130311 ACCCTTTGTTGCTTGAATAAAAGGT 59.870 36.000 10.24 0.00 37.95 3.50
2121 2257 5.563867 CGCCCTTTATTGCTTGAGTAAAACA 60.564 40.000 0.00 0.00 0.00 2.83
2283 2420 5.453903 GCTGAAGGTGTCATATGATACAGGT 60.454 44.000 27.46 15.31 37.82 4.00
2388 2525 6.158598 GCCAAAATGCAGTTTGATCTTAGAA 58.841 36.000 34.25 0.00 40.29 2.10
2395 2532 3.069872 TGAGTGCCAAAATGCAGTTTGAT 59.930 39.130 34.25 19.67 44.70 2.57
2511 2650 8.470002 GGCACATAAGAGAAAAGGAATATTTGT 58.530 33.333 0.00 0.00 0.00 2.83
2550 2689 2.668279 GCACAGTATTCCCTGCAAAACG 60.668 50.000 0.00 0.00 35.83 3.60
2797 2936 3.501828 TGACGAGATGTGGAAACATTTGG 59.498 43.478 0.00 0.00 46.14 3.28
2811 2950 0.036952 CACTGCTTGGGTGACGAGAT 60.037 55.000 0.00 0.00 36.89 2.75
2822 2961 2.164219 AGAACAACCAACACACTGCTTG 59.836 45.455 0.00 0.00 0.00 4.01
2832 2971 3.130340 TGAAGAAAGGCAGAACAACCAAC 59.870 43.478 0.00 0.00 0.00 3.77
2837 2976 3.297134 ACCTGAAGAAAGGCAGAACAA 57.703 42.857 0.00 0.00 41.46 2.83
2874 3013 3.502211 GCCGTAAATATGATGTTCCCCAG 59.498 47.826 0.00 0.00 0.00 4.45
2876 3015 2.817844 GGCCGTAAATATGATGTTCCCC 59.182 50.000 0.00 0.00 0.00 4.81
3044 3184 9.601217 GAATGAGATAACAACAGGTGTACTTAT 57.399 33.333 0.00 0.00 40.60 1.73
3096 3236 8.958119 AAACATCTTATATTTTAGCACGGAGA 57.042 30.769 0.00 0.00 0.00 3.71
3132 3272 7.867445 AAATATCGTTTTCGCAGTTCAAATT 57.133 28.000 0.00 0.00 43.73 1.82
3133 3273 7.148820 CCAAAATATCGTTTTCGCAGTTCAAAT 60.149 33.333 0.00 0.00 43.73 2.32
3144 3284 7.373778 ACCTCTGTACCAAAATATCGTTTTC 57.626 36.000 0.00 0.00 0.00 2.29
3225 3377 7.416731 AGGCCCCGATAGTAAACTCTTATATA 58.583 38.462 0.00 0.00 0.00 0.86
3303 3455 5.292101 GTGAGCCAAGTATAACACACAGATC 59.708 44.000 0.00 0.00 0.00 2.75
3489 3641 4.450976 GAAACTCCCAAACCTGCAAATTT 58.549 39.130 0.00 0.00 0.00 1.82
3651 3805 7.710907 TCTTATTGATGTGGAAGAATCCTAACG 59.289 37.037 0.00 0.00 46.70 3.18
3698 3852 9.335891 TGTTTATTTATACGTTGATTTGTGCTG 57.664 29.630 0.00 0.00 0.00 4.41
3752 3959 3.065925 ACGGCTACTTATTACCAGTCGAC 59.934 47.826 7.70 7.70 38.34 4.20
3919 4126 4.635223 CCGAGGCAAAGATCTATCAATCA 58.365 43.478 0.00 0.00 0.00 2.57
3933 4140 1.378882 GCATGATCAAGCCGAGGCAA 61.379 55.000 17.18 1.60 44.88 4.52
3934 4141 1.820906 GCATGATCAAGCCGAGGCA 60.821 57.895 17.18 0.00 44.88 4.75
4010 4217 2.545113 CCTGTGCGCGTATATACCAAGT 60.545 50.000 8.43 0.00 0.00 3.16
4021 4229 1.211969 CTAGTACACCTGTGCGCGT 59.788 57.895 8.43 0.00 35.74 6.01
4051 4259 4.713792 ATCAGTATTGAAAGCTAGGGGG 57.286 45.455 0.00 0.00 36.78 5.40
4052 4260 4.276926 GCAATCAGTATTGAAAGCTAGGGG 59.723 45.833 2.38 0.00 44.50 4.79
4072 4280 2.307309 CGGTCGTTTCTCAGCGCAA 61.307 57.895 11.47 0.00 0.00 4.85
4077 4285 3.608506 CAGTACAATCGGTCGTTTCTCAG 59.391 47.826 0.00 0.00 0.00 3.35
4078 4286 3.253921 TCAGTACAATCGGTCGTTTCTCA 59.746 43.478 0.00 0.00 0.00 3.27
4083 4291 3.739300 CAGTTTCAGTACAATCGGTCGTT 59.261 43.478 0.00 0.00 0.00 3.85
4089 4297 5.236478 ACCAGTTTCAGTTTCAGTACAATCG 59.764 40.000 0.00 0.00 0.00 3.34
4127 4335 7.641760 TGGGAAGAAATTTTAACTACGAACAC 58.358 34.615 0.00 0.00 0.00 3.32
4132 4340 6.033966 GGCATGGGAAGAAATTTTAACTACG 58.966 40.000 0.00 0.00 0.00 3.51
4139 4347 6.494059 AGTAGTAGGCATGGGAAGAAATTTT 58.506 36.000 0.00 0.00 0.00 1.82
4163 4371 4.091549 ACAACTATTTCGGTACAGAGGGA 58.908 43.478 0.00 0.00 0.00 4.20
4164 4372 4.430908 GACAACTATTTCGGTACAGAGGG 58.569 47.826 0.00 0.00 0.00 4.30
4165 4373 4.103357 CGACAACTATTTCGGTACAGAGG 58.897 47.826 0.00 0.00 0.00 3.69
4166 4374 3.546670 GCGACAACTATTTCGGTACAGAG 59.453 47.826 0.00 0.00 35.73 3.35
4167 4375 3.192001 AGCGACAACTATTTCGGTACAGA 59.808 43.478 0.00 0.00 43.71 3.41
4168 4376 3.303495 CAGCGACAACTATTTCGGTACAG 59.697 47.826 0.00 0.00 43.70 2.74
4169 4377 3.247442 CAGCGACAACTATTTCGGTACA 58.753 45.455 0.00 0.00 43.70 2.90
4170 4378 2.601763 CCAGCGACAACTATTTCGGTAC 59.398 50.000 0.00 0.00 43.70 3.34
4171 4379 2.492881 TCCAGCGACAACTATTTCGGTA 59.507 45.455 0.00 0.00 43.70 4.02
4172 4380 1.274167 TCCAGCGACAACTATTTCGGT 59.726 47.619 0.00 0.00 46.29 4.69
4173 4381 1.927174 CTCCAGCGACAACTATTTCGG 59.073 52.381 0.00 0.00 35.73 4.30
4174 4382 2.607187 ACTCCAGCGACAACTATTTCG 58.393 47.619 0.00 0.00 38.31 3.46
4175 4383 3.552294 GCTACTCCAGCGACAACTATTTC 59.448 47.826 0.00 0.00 41.37 2.17
4176 4384 3.522553 GCTACTCCAGCGACAACTATTT 58.477 45.455 0.00 0.00 41.37 1.40
4177 4385 3.166489 GCTACTCCAGCGACAACTATT 57.834 47.619 0.00 0.00 41.37 1.73
4178 4386 2.873133 GCTACTCCAGCGACAACTAT 57.127 50.000 0.00 0.00 41.37 2.12
4207 4415 4.330074 CCAAAATAGTTGTCGCTGGAGTAG 59.670 45.833 0.00 0.00 0.00 2.57
4208 4416 4.250464 CCAAAATAGTTGTCGCTGGAGTA 58.750 43.478 0.00 0.00 0.00 2.59
4209 4417 3.074412 CCAAAATAGTTGTCGCTGGAGT 58.926 45.455 0.00 0.00 0.00 3.85
4210 4418 3.074412 ACCAAAATAGTTGTCGCTGGAG 58.926 45.455 0.00 0.00 0.00 3.86
4211 4419 3.134574 ACCAAAATAGTTGTCGCTGGA 57.865 42.857 0.00 0.00 0.00 3.86
4212 4420 4.250464 TCTACCAAAATAGTTGTCGCTGG 58.750 43.478 0.00 0.00 0.00 4.85
4213 4421 4.330074 CCTCTACCAAAATAGTTGTCGCTG 59.670 45.833 0.00 0.00 0.00 5.18
4214 4422 4.504858 CCTCTACCAAAATAGTTGTCGCT 58.495 43.478 0.00 0.00 0.00 4.93
4215 4423 3.621715 CCCTCTACCAAAATAGTTGTCGC 59.378 47.826 0.00 0.00 0.00 5.19
4216 4424 5.080969 TCCCTCTACCAAAATAGTTGTCG 57.919 43.478 0.00 0.00 0.00 4.35
4217 4425 6.051179 ACTCCCTCTACCAAAATAGTTGTC 57.949 41.667 0.00 0.00 0.00 3.18
4218 4426 7.750947 ATACTCCCTCTACCAAAATAGTTGT 57.249 36.000 0.00 0.00 0.00 3.32
4224 4432 9.448587 AGTGTTATATACTCCCTCTACCAAAAT 57.551 33.333 0.00 0.00 0.00 1.82
4225 4433 8.701895 CAGTGTTATATACTCCCTCTACCAAAA 58.298 37.037 0.00 0.00 0.00 2.44
4226 4434 8.063153 TCAGTGTTATATACTCCCTCTACCAAA 58.937 37.037 0.00 0.00 0.00 3.28
4227 4435 7.589081 TCAGTGTTATATACTCCCTCTACCAA 58.411 38.462 0.00 0.00 0.00 3.67
4228 4436 7.157947 TCAGTGTTATATACTCCCTCTACCA 57.842 40.000 0.00 0.00 0.00 3.25
4229 4437 8.474710 TTTCAGTGTTATATACTCCCTCTACC 57.525 38.462 0.00 0.00 0.00 3.18
4230 4438 9.968870 CTTTTCAGTGTTATATACTCCCTCTAC 57.031 37.037 0.00 0.00 0.00 2.59
4231 4439 9.144298 CCTTTTCAGTGTTATATACTCCCTCTA 57.856 37.037 0.00 0.00 0.00 2.43
4232 4440 7.844779 TCCTTTTCAGTGTTATATACTCCCTCT 59.155 37.037 0.00 0.00 0.00 3.69
4233 4441 7.927092 GTCCTTTTCAGTGTTATATACTCCCTC 59.073 40.741 0.00 0.00 0.00 4.30
4234 4442 7.147532 GGTCCTTTTCAGTGTTATATACTCCCT 60.148 40.741 0.00 0.00 0.00 4.20
4235 4443 6.990939 GGTCCTTTTCAGTGTTATATACTCCC 59.009 42.308 0.00 0.00 0.00 4.30
4236 4444 6.990939 GGGTCCTTTTCAGTGTTATATACTCC 59.009 42.308 0.00 0.00 0.00 3.85
4237 4445 6.700520 CGGGTCCTTTTCAGTGTTATATACTC 59.299 42.308 0.00 0.00 0.00 2.59
4238 4446 6.381994 TCGGGTCCTTTTCAGTGTTATATACT 59.618 38.462 0.00 0.00 0.00 2.12
4239 4447 6.576185 TCGGGTCCTTTTCAGTGTTATATAC 58.424 40.000 0.00 0.00 0.00 1.47
4293 4501 2.549754 AGGACATTCAGTTTTCACAGCG 59.450 45.455 0.00 0.00 0.00 5.18
4340 4548 1.667722 GCAGTGGGCTTTTGGGAAG 59.332 57.895 0.00 0.00 40.25 3.46
4468 4676 1.143073 GGTAAATCTGGGGGCTACCTG 59.857 57.143 0.84 0.71 40.03 4.00
4477 4685 4.010349 GAGTGAAACAGGGTAAATCTGGG 58.990 47.826 0.00 0.00 41.43 4.45
4542 4750 2.415357 CGCAAATGAATAAACCCGCTGT 60.415 45.455 0.00 0.00 0.00 4.40
4549 4757 5.795766 TCAGATCGTCGCAAATGAATAAAC 58.204 37.500 0.00 0.00 0.00 2.01
4551 4759 6.257630 TCAATCAGATCGTCGCAAATGAATAA 59.742 34.615 0.00 0.00 0.00 1.40
4554 4762 3.932089 TCAATCAGATCGTCGCAAATGAA 59.068 39.130 0.00 0.00 0.00 2.57
4578 4786 2.869801 CTGCACGAACACTAAAAGGACA 59.130 45.455 0.00 0.00 0.00 4.02
4586 4794 1.197036 CTCGACTCTGCACGAACACTA 59.803 52.381 0.00 0.00 38.05 2.74
4640 4872 4.393155 ATCGCTCAACCCGCAGCA 62.393 61.111 0.00 0.00 35.15 4.41
4646 4878 1.227002 GGAGACGATCGCTCAACCC 60.227 63.158 28.28 17.65 34.07 4.11
4667 4899 0.593518 CACTCTCAGGCATACGCTCG 60.594 60.000 0.00 0.00 38.60 5.03
4730 4964 3.714798 CCTACTCCTACTTGGGCCATAAA 59.285 47.826 7.26 0.00 36.20 1.40
4836 5070 1.086696 CAAACATACAGGCACCGGAG 58.913 55.000 9.46 0.00 0.00 4.63
4840 5075 4.261801 AGACATACAAACATACAGGCACC 58.738 43.478 0.00 0.00 0.00 5.01
4844 5079 4.755411 ACGGAGACATACAAACATACAGG 58.245 43.478 0.00 0.00 0.00 4.00
4893 5128 6.238402 GCTCTTTTTCTCTTTTCTACAACGGT 60.238 38.462 0.00 0.00 0.00 4.83
4909 5144 0.796927 CGACCCGGAAGCTCTTTTTC 59.203 55.000 0.73 0.00 0.00 2.29
5019 5254 3.239254 TCAGCAACTATACGAACACACG 58.761 45.455 0.00 0.00 39.31 4.49
5056 6247 4.337763 CTCGACTCAAAAACTGCATATGC 58.662 43.478 21.09 21.09 42.50 3.14
5057 6248 4.337763 GCTCGACTCAAAAACTGCATATG 58.662 43.478 0.00 0.00 0.00 1.78
5058 6249 3.062639 CGCTCGACTCAAAAACTGCATAT 59.937 43.478 0.00 0.00 0.00 1.78
5059 6250 2.411748 CGCTCGACTCAAAAACTGCATA 59.588 45.455 0.00 0.00 0.00 3.14
5060 6251 1.195448 CGCTCGACTCAAAAACTGCAT 59.805 47.619 0.00 0.00 0.00 3.96
5061 6252 0.581529 CGCTCGACTCAAAAACTGCA 59.418 50.000 0.00 0.00 0.00 4.41
5062 6253 0.582005 ACGCTCGACTCAAAAACTGC 59.418 50.000 0.00 0.00 0.00 4.40
5063 6254 2.284150 TGAACGCTCGACTCAAAAACTG 59.716 45.455 0.00 0.00 0.00 3.16
5064 6255 2.540101 CTGAACGCTCGACTCAAAAACT 59.460 45.455 0.00 0.00 0.00 2.66
5065 6256 2.348591 CCTGAACGCTCGACTCAAAAAC 60.349 50.000 0.00 0.00 0.00 2.43
5119 7761 1.735700 GCGTCACAGGAATCGATGACA 60.736 52.381 13.36 0.00 41.26 3.58
5132 7774 0.735978 CAGTAAGCCATCGCGTCACA 60.736 55.000 5.77 0.00 41.18 3.58
5137 7779 0.460284 AGTTCCAGTAAGCCATCGCG 60.460 55.000 0.00 0.00 41.18 5.87
5188 7830 2.025359 CTCGCGAGCAAAATCGGTCC 62.025 60.000 25.07 0.00 42.94 4.46
5214 7857 1.204704 CTGACTGATCAACCTACCGCA 59.795 52.381 0.00 0.00 33.30 5.69
5219 7862 4.464244 CCAAGAGACTGACTGATCAACCTA 59.536 45.833 0.00 0.00 33.30 3.08
5220 7863 3.260380 CCAAGAGACTGACTGATCAACCT 59.740 47.826 0.00 0.00 33.30 3.50
5221 7864 3.007398 ACCAAGAGACTGACTGATCAACC 59.993 47.826 0.00 0.00 33.30 3.77
5222 7865 4.241681 GACCAAGAGACTGACTGATCAAC 58.758 47.826 0.00 0.00 33.30 3.18
5241 7888 3.479269 CGAAAGCGAGCGTGGACC 61.479 66.667 0.00 0.00 40.82 4.46
5284 7962 2.173669 CGCGGAATCAAGGCATCGT 61.174 57.895 0.00 0.00 0.00 3.73
5291 7969 2.705826 GCTCAGCGCGGAATCAAG 59.294 61.111 12.27 0.19 0.00 3.02
5292 7970 2.819595 GGCTCAGCGCGGAATCAA 60.820 61.111 12.27 0.00 40.44 2.57
5294 7972 4.873129 TCGGCTCAGCGCGGAATC 62.873 66.667 12.27 6.32 43.85 2.52
5298 7976 4.914420 CTAGTCGGCTCAGCGCGG 62.914 72.222 8.83 0.00 40.44 6.46
5299 7977 4.914420 CCTAGTCGGCTCAGCGCG 62.914 72.222 0.00 0.00 40.44 6.86
5300 7978 4.577246 CCCTAGTCGGCTCAGCGC 62.577 72.222 0.00 0.00 38.13 5.92
5301 7979 2.196925 ATCCCTAGTCGGCTCAGCG 61.197 63.158 0.00 0.00 0.00 5.18
5302 7980 1.365633 CATCCCTAGTCGGCTCAGC 59.634 63.158 0.00 0.00 0.00 4.26
5303 7981 1.365633 GCATCCCTAGTCGGCTCAG 59.634 63.158 0.00 0.00 0.00 3.35
5304 7982 1.381191 TGCATCCCTAGTCGGCTCA 60.381 57.895 0.00 0.00 0.00 4.26
5305 7983 1.109920 TCTGCATCCCTAGTCGGCTC 61.110 60.000 0.00 0.00 0.00 4.70
5306 7984 1.075970 TCTGCATCCCTAGTCGGCT 60.076 57.895 0.00 0.00 0.00 5.52
5307 7985 1.068250 GTCTGCATCCCTAGTCGGC 59.932 63.158 0.00 0.00 0.00 5.54
5308 7986 0.387202 CAGTCTGCATCCCTAGTCGG 59.613 60.000 0.00 0.00 0.00 4.79
5309 7987 1.393603 TCAGTCTGCATCCCTAGTCG 58.606 55.000 0.00 0.00 0.00 4.18
5310 7988 3.386078 TCAATCAGTCTGCATCCCTAGTC 59.614 47.826 0.00 0.00 0.00 2.59
5311 7989 3.378512 TCAATCAGTCTGCATCCCTAGT 58.621 45.455 0.00 0.00 0.00 2.57
5312 7990 4.620589 ATCAATCAGTCTGCATCCCTAG 57.379 45.455 0.00 0.00 0.00 3.02
5313 7991 4.164796 ACAATCAATCAGTCTGCATCCCTA 59.835 41.667 0.00 0.00 0.00 3.53
5314 7992 3.053842 ACAATCAATCAGTCTGCATCCCT 60.054 43.478 0.00 0.00 0.00 4.20
5315 7993 3.285484 ACAATCAATCAGTCTGCATCCC 58.715 45.455 0.00 0.00 0.00 3.85
5316 7994 3.314635 GGACAATCAATCAGTCTGCATCC 59.685 47.826 0.00 0.00 32.98 3.51
5317 7995 4.197750 AGGACAATCAATCAGTCTGCATC 58.802 43.478 0.00 0.00 32.98 3.91
5318 7996 4.080469 AGAGGACAATCAATCAGTCTGCAT 60.080 41.667 0.00 0.00 32.98 3.96
5319 7997 3.262660 AGAGGACAATCAATCAGTCTGCA 59.737 43.478 0.00 0.00 32.98 4.41
5320 7998 3.622163 CAGAGGACAATCAATCAGTCTGC 59.378 47.826 0.00 0.00 32.98 4.26
5321 7999 4.630505 CACAGAGGACAATCAATCAGTCTG 59.369 45.833 0.00 0.00 35.93 3.51
5322 8000 4.323333 CCACAGAGGACAATCAATCAGTCT 60.323 45.833 0.00 0.00 41.22 3.24
5323 8001 3.937706 CCACAGAGGACAATCAATCAGTC 59.062 47.826 0.00 0.00 41.22 3.51
5324 8002 3.871463 GCCACAGAGGACAATCAATCAGT 60.871 47.826 0.00 0.00 41.22 3.41
5325 8003 2.681848 GCCACAGAGGACAATCAATCAG 59.318 50.000 0.00 0.00 41.22 2.90
5343 8021 1.553690 GCCAAGTAGGGTCAGAGCCA 61.554 60.000 21.01 4.16 38.48 4.75
5377 8055 8.511604 AAATCACACCACTTATAGAAATCCTG 57.488 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.