Multiple sequence alignment - TraesCS5D01G142000

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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 TraesCS5D01G142000 chr5D 100.000 4783 0 0 1 4783 228053239 228058021 0.000000e+00 8833.0
1 TraesCS5D01G142000 chr5D 97.436 39 1 0 1445 1483 228054644 228054682 3.090000e-07 67.6
2 TraesCS5D01G142000 chr5D 97.436 39 1 0 1406 1444 228054683 228054721 3.090000e-07 67.6
3 TraesCS5D01G142000 chr5A 94.952 4061 110 28 565 4557 306184706 306188739 0.000000e+00 6276.0
4 TraesCS5D01G142000 chr5A 93.833 227 14 0 4557 4783 306190155 306190381 4.580000e-90 342.0
5 TraesCS5D01G142000 chr5A 91.342 231 12 5 4554 4783 306192698 306192921 4.650000e-80 309.0
6 TraesCS5D01G142000 chr5A 97.436 39 1 0 1406 1444 306185599 306185637 3.090000e-07 67.6
7 TraesCS5D01G142000 chr5B 97.237 2425 63 2 1445 3868 251503290 251505711 0.000000e+00 4104.0
8 TraesCS5D01G142000 chr5B 97.076 855 24 1 590 1444 251502475 251503328 0.000000e+00 1439.0
9 TraesCS5D01G142000 chr5B 90.668 943 38 16 3853 4783 251505752 251506656 0.000000e+00 1208.0
10 TraesCS5D01G142000 chr5B 88.000 325 28 5 1 324 251501799 251502113 1.630000e-99 374.0
11 TraesCS5D01G142000 chr3A 92.857 42 1 1 4402 4443 461794356 461794317 5.170000e-05 60.2


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 TraesCS5D01G142000 chr5D 228053239 228058021 4782 False 2989.40 8833 98.290667 1 4783 3 chr5D.!!$F1 4782
1 TraesCS5D01G142000 chr5A 306184706 306188739 4033 False 3171.80 6276 96.194000 565 4557 2 chr5A.!!$F1 3992
2 TraesCS5D01G142000 chr5A 306190155 306192921 2766 False 325.50 342 92.587500 4554 4783 2 chr5A.!!$F2 229
3 TraesCS5D01G142000 chr5B 251501799 251506656 4857 False 1781.25 4104 93.245250 1 4783 4 chr5B.!!$F1 4782

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
466 511 0.606604 AGTTGGACGCATCGGTAACT 59.393 50.000 0.00 0.0 0.00 2.24 F
530 575 0.738762 CTCACCACATCTGCCACTCG 60.739 60.000 0.00 0.0 0.00 4.18 F
698 801 1.344942 CGAGCCTCGGTCGTTTTCTG 61.345 60.000 6.13 0.0 46.41 3.02 F
1286 1401 1.665679 AGCATGTACATCGGAAAAGCG 59.334 47.619 5.07 0.0 0.00 4.68 F
1775 1891 2.368329 GCCCCCATCCCTAGTGGT 60.368 66.667 0.00 0.0 34.87 4.16 F
2990 3109 1.064906 CAGGTGCTGACCATCAAGGAT 60.065 52.381 0.00 0.0 45.98 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1401 0.883833 CACCTGCTCCAAATCCACAC 59.116 55.000 0.00 0.00 0.00 3.82 R
1519 1634 2.180017 CTTGGAATGTGCAGCGGC 59.820 61.111 0.31 0.31 41.68 6.53 R
2196 2315 2.624838 ACCAACTGCAATTGAGGAACTG 59.375 45.455 9.94 0.00 41.55 3.16 R
2990 3109 1.792367 CAACGCGTGAATCTGAACAGA 59.208 47.619 14.98 6.98 42.37 3.41 R
3572 3694 0.172352 GCTCTTCAGCAGCGAGTAGT 59.828 55.000 0.00 0.00 46.06 2.73 R
4304 4526 0.031111 ATTCTCCACGGATCTCCCCA 60.031 55.000 0.00 0.00 0.00 4.96 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
45 46 3.849911 TCTTCACTAGCAACTCATTCCG 58.150 45.455 0.00 0.00 0.00 4.30
52 53 1.004745 AGCAACTCATTCCGTCCCATT 59.995 47.619 0.00 0.00 0.00 3.16
57 58 4.608948 ACTCATTCCGTCCCATTATCTC 57.391 45.455 0.00 0.00 0.00 2.75
65 66 2.291465 CGTCCCATTATCTCGTTACCGA 59.709 50.000 0.00 0.00 41.73 4.69
81 82 1.137825 CGACTCTGCCTCGAACTCC 59.862 63.158 0.00 0.00 32.65 3.85
91 92 2.352960 GCCTCGAACTCCATTGACAATC 59.647 50.000 0.00 0.00 0.00 2.67
92 93 3.599343 CCTCGAACTCCATTGACAATCA 58.401 45.455 0.00 0.00 0.00 2.57
102 103 3.616821 CCATTGACAATCAGCATTGCAAG 59.383 43.478 11.91 3.03 43.03 4.01
103 104 4.490743 CATTGACAATCAGCATTGCAAGA 58.509 39.130 11.91 8.77 43.03 3.02
104 105 4.587584 TTGACAATCAGCATTGCAAGAA 57.412 36.364 11.91 0.00 43.03 2.52
105 106 4.587584 TGACAATCAGCATTGCAAGAAA 57.412 36.364 11.91 0.00 43.03 2.52
106 107 5.142061 TGACAATCAGCATTGCAAGAAAT 57.858 34.783 11.91 0.00 43.03 2.17
107 108 5.165676 TGACAATCAGCATTGCAAGAAATC 58.834 37.500 11.91 8.10 43.03 2.17
108 109 5.142061 ACAATCAGCATTGCAAGAAATCA 57.858 34.783 11.91 0.00 43.03 2.57
109 110 5.730550 ACAATCAGCATTGCAAGAAATCAT 58.269 33.333 11.91 0.00 43.03 2.45
110 111 6.170506 ACAATCAGCATTGCAAGAAATCATT 58.829 32.000 11.91 0.00 43.03 2.57
111 112 6.312918 ACAATCAGCATTGCAAGAAATCATTC 59.687 34.615 11.91 0.00 43.03 2.67
152 153 7.016661 AGGTCTAATCCCTTGAGGTACAATATG 59.983 40.741 0.00 0.00 37.88 1.78
157 158 6.174720 TCCCTTGAGGTACAATATGATGTC 57.825 41.667 0.00 0.00 37.88 3.06
178 180 5.829391 TGTCTTAACAATGGATCCATGATGG 59.171 40.000 27.97 18.64 36.68 3.51
200 202 3.681897 GGAGCATCTCAATATGGTAAGCG 59.318 47.826 0.00 0.00 37.69 4.68
204 206 6.467677 AGCATCTCAATATGGTAAGCGTTAT 58.532 36.000 0.00 0.00 35.88 1.89
217 219 7.354257 TGGTAAGCGTTATTAAAGTTTGTCAC 58.646 34.615 0.00 0.00 0.00 3.67
219 221 5.025986 AGCGTTATTAAAGTTTGTCACGG 57.974 39.130 0.00 0.00 0.00 4.94
221 223 5.077424 GCGTTATTAAAGTTTGTCACGGAG 58.923 41.667 0.00 0.00 0.00 4.63
241 243 7.275123 CACGGAGAATATGTGATGATGTGATAG 59.725 40.741 0.00 0.00 35.66 2.08
242 244 7.177392 ACGGAGAATATGTGATGATGTGATAGA 59.823 37.037 0.00 0.00 0.00 1.98
270 272 4.690184 TGTCGAGCGAGAACACTATTAA 57.310 40.909 0.00 0.00 0.00 1.40
276 278 5.275927 CGAGCGAGAACACTATTAACATGTG 60.276 44.000 0.00 0.00 37.67 3.21
292 294 2.254546 TGTGTGCAACTAAGACCCTG 57.745 50.000 0.00 0.00 38.04 4.45
296 298 2.948979 TGTGCAACTAAGACCCTGTTTG 59.051 45.455 0.00 0.00 38.04 2.93
297 299 2.949644 GTGCAACTAAGACCCTGTTTGT 59.050 45.455 0.00 0.00 0.00 2.83
312 314 3.339141 TGTTTGTTTGGGGTTTTGCTTC 58.661 40.909 0.00 0.00 0.00 3.86
324 326 3.430790 GGTTTTGCTTCAGCTTTTCCACT 60.431 43.478 0.00 0.00 42.66 4.00
326 328 5.348164 GTTTTGCTTCAGCTTTTCCACTTA 58.652 37.500 0.00 0.00 42.66 2.24
327 329 5.590530 TTTGCTTCAGCTTTTCCACTTAA 57.409 34.783 0.00 0.00 42.66 1.85
329 331 5.590530 TGCTTCAGCTTTTCCACTTAAAA 57.409 34.783 0.00 0.00 42.66 1.52
331 333 6.042143 TGCTTCAGCTTTTCCACTTAAAAAG 58.958 36.000 0.00 4.41 43.44 2.27
336 338 4.955811 CTTTTCCACTTAAAAAGCCCCT 57.044 40.909 0.00 0.00 37.03 4.79
338 340 6.605471 CTTTTCCACTTAAAAAGCCCCTAT 57.395 37.500 0.00 0.00 37.03 2.57
339 341 7.004555 CTTTTCCACTTAAAAAGCCCCTATT 57.995 36.000 0.00 0.00 37.03 1.73
340 342 8.129496 CTTTTCCACTTAAAAAGCCCCTATTA 57.871 34.615 0.00 0.00 37.03 0.98
341 343 7.712204 TTTCCACTTAAAAAGCCCCTATTAG 57.288 36.000 0.00 0.00 0.00 1.73
342 344 5.762279 TCCACTTAAAAAGCCCCTATTAGG 58.238 41.667 2.43 2.43 34.30 2.69
354 394 3.555966 CCCTATTAGGAGCTTTTGTGGG 58.444 50.000 11.52 0.00 37.67 4.61
355 395 3.053619 CCCTATTAGGAGCTTTTGTGGGT 60.054 47.826 11.52 0.00 37.67 4.51
356 396 4.569865 CCCTATTAGGAGCTTTTGTGGGTT 60.570 45.833 11.52 0.00 37.67 4.11
357 397 5.016831 CCTATTAGGAGCTTTTGTGGGTTT 58.983 41.667 3.41 0.00 37.67 3.27
358 398 5.480422 CCTATTAGGAGCTTTTGTGGGTTTT 59.520 40.000 3.41 0.00 37.67 2.43
395 435 3.384789 GGAAAAGTTGGAAAGGCTGAAGT 59.615 43.478 0.00 0.00 0.00 3.01
412 452 4.425520 TGAAGTAAAAGCCCAAACAAACG 58.574 39.130 0.00 0.00 0.00 3.60
413 453 4.158025 TGAAGTAAAAGCCCAAACAAACGA 59.842 37.500 0.00 0.00 0.00 3.85
417 457 1.744320 AAGCCCAAACAAACGAGGCC 61.744 55.000 0.00 0.00 45.00 5.19
436 481 3.520569 GCCTTGCACAAGTCTTTCAAAA 58.479 40.909 9.41 0.00 36.72 2.44
440 485 6.424812 GCCTTGCACAAGTCTTTCAAAAATAT 59.575 34.615 9.41 0.00 36.72 1.28
461 506 2.004583 TTAAGAGTTGGACGCATCGG 57.995 50.000 0.00 0.00 0.00 4.18
466 511 0.606604 AGTTGGACGCATCGGTAACT 59.393 50.000 0.00 0.00 0.00 2.24
468 513 1.922545 GTTGGACGCATCGGTAACTAC 59.077 52.381 0.00 0.00 0.00 2.73
479 524 5.726963 GCATCGGTAACTACAAGCTTTAAGC 60.727 44.000 9.18 9.18 42.84 3.09
522 567 1.911357 TGAGGATTGCTCACCACATCT 59.089 47.619 3.46 0.00 0.00 2.90
528 573 1.002868 GCTCACCACATCTGCCACT 60.003 57.895 0.00 0.00 0.00 4.00
530 575 0.738762 CTCACCACATCTGCCACTCG 60.739 60.000 0.00 0.00 0.00 4.18
698 801 1.344942 CGAGCCTCGGTCGTTTTCTG 61.345 60.000 6.13 0.00 46.41 3.02
1077 1192 4.073425 TCCTTTGCCTTTATTCCCCATT 57.927 40.909 0.00 0.00 0.00 3.16
1286 1401 1.665679 AGCATGTACATCGGAAAAGCG 59.334 47.619 5.07 0.00 0.00 4.68
1535 1650 3.372730 GGCCGCTGCACATTCCAA 61.373 61.111 1.55 0.00 40.13 3.53
1690 1805 5.997746 TGCATATGAAACCAGGAATACTAGC 59.002 40.000 6.97 0.00 0.00 3.42
1775 1891 2.368329 GCCCCCATCCCTAGTGGT 60.368 66.667 0.00 0.00 34.87 4.16
1783 1899 4.079443 CCCCATCCCTAGTGGTTTGAATTA 60.079 45.833 0.00 0.00 34.87 1.40
2486 2605 9.944663 CACAATAATGTTAATTTAGGCGTGTAT 57.055 29.630 0.00 0.00 37.82 2.29
2990 3109 1.064906 CAGGTGCTGACCATCAAGGAT 60.065 52.381 0.00 0.00 45.98 3.24
3515 3634 3.423539 ACTGAAAGAGGCAGGAGATGCT 61.424 50.000 0.00 0.00 46.89 3.79
3572 3694 5.239306 CCTCGATATTGAAAAGGCTTATGCA 59.761 40.000 0.00 0.00 41.91 3.96
3625 3747 1.152777 CAGACACTTGTGGGGGCAA 60.153 57.895 5.72 0.00 0.00 4.52
3841 3963 2.363683 TGCGTGCATGATATGTTTCCA 58.636 42.857 10.93 0.00 0.00 3.53
3916 4094 8.960064 AGGATTCATGGGTTCTTAATATACCTT 58.040 33.333 0.00 0.00 32.46 3.50
3973 4151 5.709631 TGCACTACCATAAACATCATGTTGT 59.290 36.000 3.07 3.49 40.14 3.32
4009 4188 2.618045 GGCTGGTGTGGTGTAAGCTATT 60.618 50.000 0.00 0.00 34.29 1.73
4010 4189 2.420022 GCTGGTGTGGTGTAAGCTATTG 59.580 50.000 0.00 0.00 33.76 1.90
4053 4232 6.940298 CAGGTTTCCCTTTTCTAATACTGACA 59.060 38.462 0.00 0.00 39.89 3.58
4126 4311 8.830201 ATAGCTGTCTGATTCATCATAAGTTC 57.170 34.615 0.00 0.00 36.02 3.01
4128 4313 7.281098 AGCTGTCTGATTCATCATAAGTTCAT 58.719 34.615 0.00 0.00 36.02 2.57
4129 4314 8.427276 AGCTGTCTGATTCATCATAAGTTCATA 58.573 33.333 0.00 0.00 36.02 2.15
4130 4315 9.049523 GCTGTCTGATTCATCATAAGTTCATAA 57.950 33.333 0.00 0.00 36.02 1.90
4132 4317 9.889128 TGTCTGATTCATCATAAGTTCATAACA 57.111 29.630 0.00 0.00 36.02 2.41
4284 4506 1.963515 ACACAAAATGAAGCTGGGGAC 59.036 47.619 0.00 0.00 0.00 4.46
4350 4572 7.916450 GCTTACAAAATGTACCAAAACAGTGTA 59.084 33.333 0.00 0.00 31.69 2.90
4372 4594 5.850046 AAAGATATACTCCCCCATTCCAG 57.150 43.478 0.00 0.00 0.00 3.86
4472 4707 6.314784 CAAAATCCAGAGATTAACGACCAAC 58.685 40.000 0.00 0.00 42.03 3.77
4628 4868 9.310449 ACTTAGACTTGTTACTCTTGAGGATTA 57.690 33.333 2.55 0.00 0.00 1.75
4663 4903 4.884668 TGGTTAGGAGTCGTTCAAAGAT 57.115 40.909 0.00 0.00 0.00 2.40
4737 4977 6.343703 TCACCACAAGATCTAATGAGTGATG 58.656 40.000 17.32 10.73 32.53 3.07
4765 7545 5.333035 CGAGTTTCGATGAACTTAGCACAAA 60.333 40.000 4.09 0.00 43.74 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.959293 AGTGAAGATGGCATGACAATGA 58.041 40.909 4.70 0.00 35.67 2.57
16 17 3.054875 AGTTGCTAGTGAAGATGGCATGA 60.055 43.478 3.81 0.00 32.87 3.07
65 66 1.066573 CAATGGAGTTCGAGGCAGAGT 60.067 52.381 0.00 0.00 0.00 3.24
81 82 4.490743 TCTTGCAATGCTGATTGTCAATG 58.509 39.130 6.82 0.00 41.09 2.82
91 92 4.031314 CACGAATGATTTCTTGCAATGCTG 59.969 41.667 6.82 0.00 0.00 4.41
92 93 4.171005 CACGAATGATTTCTTGCAATGCT 58.829 39.130 6.82 0.00 0.00 3.79
102 103 4.668576 TCACTTGAGCACGAATGATTTC 57.331 40.909 0.00 0.00 0.00 2.17
103 104 5.437289 TTTCACTTGAGCACGAATGATTT 57.563 34.783 0.00 0.00 0.00 2.17
104 105 5.437289 TTTTCACTTGAGCACGAATGATT 57.563 34.783 0.00 0.00 0.00 2.57
105 106 4.083110 CCTTTTCACTTGAGCACGAATGAT 60.083 41.667 0.00 0.00 0.00 2.45
106 107 3.250762 CCTTTTCACTTGAGCACGAATGA 59.749 43.478 0.00 0.00 0.00 2.57
107 108 3.003689 ACCTTTTCACTTGAGCACGAATG 59.996 43.478 0.00 0.00 0.00 2.67
108 109 3.214328 ACCTTTTCACTTGAGCACGAAT 58.786 40.909 0.00 0.00 0.00 3.34
109 110 2.612212 GACCTTTTCACTTGAGCACGAA 59.388 45.455 0.00 0.00 0.00 3.85
110 111 2.158957 AGACCTTTTCACTTGAGCACGA 60.159 45.455 0.00 0.00 0.00 4.35
111 112 2.213499 AGACCTTTTCACTTGAGCACG 58.787 47.619 0.00 0.00 0.00 5.34
117 118 6.003950 TCAAGGGATTAGACCTTTTCACTTG 58.996 40.000 7.31 7.31 45.81 3.16
152 153 7.309012 CCATCATGGATCCATTGTTAAGACATC 60.309 40.741 25.20 0.00 40.96 3.06
157 158 5.387788 TCCCATCATGGATCCATTGTTAAG 58.612 41.667 25.20 12.51 40.96 1.85
178 180 3.681897 CGCTTACCATATTGAGATGCTCC 59.318 47.826 0.00 0.00 0.00 4.70
193 195 6.517374 CGTGACAAACTTTAATAACGCTTACC 59.483 38.462 0.00 0.00 0.00 2.85
204 206 7.658167 TCACATATTCTCCGTGACAAACTTTAA 59.342 33.333 0.00 0.00 34.83 1.52
217 219 7.542025 TCTATCACATCATCACATATTCTCCG 58.458 38.462 0.00 0.00 0.00 4.63
246 248 2.440539 AGTGTTCTCGCTCGACATTT 57.559 45.000 0.00 0.00 0.00 2.32
256 258 5.120053 TGCACACATGTTAATAGTGTTCTCG 59.880 40.000 13.06 0.00 43.40 4.04
270 272 2.106511 AGGGTCTTAGTTGCACACATGT 59.893 45.455 0.00 0.00 0.00 3.21
276 278 2.949644 ACAAACAGGGTCTTAGTTGCAC 59.050 45.455 0.00 0.00 0.00 4.57
292 294 3.339141 TGAAGCAAAACCCCAAACAAAC 58.661 40.909 0.00 0.00 0.00 2.93
296 298 1.138859 AGCTGAAGCAAAACCCCAAAC 59.861 47.619 4.90 0.00 45.16 2.93
297 299 1.494960 AGCTGAAGCAAAACCCCAAA 58.505 45.000 4.90 0.00 45.16 3.28
332 334 3.555966 CCACAAAAGCTCCTAATAGGGG 58.444 50.000 6.46 3.74 39.50 4.79
333 335 3.053619 ACCCACAAAAGCTCCTAATAGGG 60.054 47.826 6.46 0.00 35.59 3.53
334 336 4.236527 ACCCACAAAAGCTCCTAATAGG 57.763 45.455 0.00 0.00 36.46 2.57
335 337 6.590234 AAAACCCACAAAAGCTCCTAATAG 57.410 37.500 0.00 0.00 0.00 1.73
336 338 6.987403 AAAAACCCACAAAAGCTCCTAATA 57.013 33.333 0.00 0.00 0.00 0.98
337 339 5.887214 AAAAACCCACAAAAGCTCCTAAT 57.113 34.783 0.00 0.00 0.00 1.73
367 407 6.098982 TCAGCCTTTCCAACTTTTCCATTTTA 59.901 34.615 0.00 0.00 0.00 1.52
371 411 3.575805 TCAGCCTTTCCAACTTTTCCAT 58.424 40.909 0.00 0.00 0.00 3.41
380 420 4.584327 GCTTTTACTTCAGCCTTTCCAA 57.416 40.909 0.00 0.00 0.00 3.53
395 435 2.223852 GCCTCGTTTGTTTGGGCTTTTA 60.224 45.455 0.00 0.00 39.68 1.52
405 445 1.034838 TGTGCAAGGCCTCGTTTGTT 61.035 50.000 5.23 0.00 0.00 2.83
436 481 6.590292 CCGATGCGTCCAACTCTTAATATATT 59.410 38.462 2.97 2.97 0.00 1.28
440 485 3.131577 ACCGATGCGTCCAACTCTTAATA 59.868 43.478 0.00 0.00 0.00 0.98
444 489 0.892755 TACCGATGCGTCCAACTCTT 59.107 50.000 0.00 0.00 0.00 2.85
449 494 1.545136 TGTAGTTACCGATGCGTCCAA 59.455 47.619 0.00 0.00 0.00 3.53
451 496 2.190981 CTTGTAGTTACCGATGCGTCC 58.809 52.381 0.00 0.00 0.00 4.79
522 567 3.596214 GAGAATAGAAAACCGAGTGGCA 58.404 45.455 0.00 0.00 39.70 4.92
528 573 3.322211 TTGGCGAGAATAGAAAACCGA 57.678 42.857 0.00 0.00 0.00 4.69
1044 1159 1.820519 GGCAAAGGAATCACTCATGCA 59.179 47.619 0.00 0.00 35.88 3.96
1077 1192 5.469421 CCTGTGCCAAAATGAAATAAGCAAA 59.531 36.000 0.00 0.00 0.00 3.68
1210 1325 3.154473 CTCCTCCGGATTCCGCCA 61.154 66.667 19.80 7.16 46.86 5.69
1286 1401 0.883833 CACCTGCTCCAAATCCACAC 59.116 55.000 0.00 0.00 0.00 3.82
1519 1634 2.180017 CTTGGAATGTGCAGCGGC 59.820 61.111 0.31 0.31 41.68 6.53
1535 1650 5.871396 ACGAACAATATATCCAGTGGACT 57.129 39.130 15.86 7.70 32.98 3.85
1662 1777 7.236529 AGTATTCCTGGTTTCATATGCATCAT 58.763 34.615 0.19 0.00 0.00 2.45
1690 1805 2.936498 AGAACGGAACAAATAGGATGCG 59.064 45.455 0.00 0.00 0.00 4.73
1783 1899 7.060633 GTGTGCATCGTCGAATTTTCTAAAAAT 59.939 33.333 0.00 0.00 0.00 1.82
2035 2151 6.345096 TCATATGCCTCTGTAATCGAATCA 57.655 37.500 0.00 0.00 0.00 2.57
2195 2314 2.886523 CCAACTGCAATTGAGGAACTGA 59.113 45.455 9.94 0.00 41.55 3.41
2196 2315 2.624838 ACCAACTGCAATTGAGGAACTG 59.375 45.455 9.94 0.00 41.55 3.16
2990 3109 1.792367 CAACGCGTGAATCTGAACAGA 59.208 47.619 14.98 6.98 42.37 3.41
3551 3673 6.064846 AGTGCATAAGCCTTTTCAATATCG 57.935 37.500 0.00 0.00 41.13 2.92
3572 3694 0.172352 GCTCTTCAGCAGCGAGTAGT 59.828 55.000 0.00 0.00 46.06 2.73
3625 3747 1.368950 CCGTGATCCGCATCCTCAT 59.631 57.895 0.00 0.00 34.38 2.90
3669 3791 2.527624 ACCCTCAGCAGCCTCACA 60.528 61.111 0.00 0.00 0.00 3.58
3841 3963 3.624777 CCACCTTGGACTTGCAAGATAT 58.375 45.455 32.50 10.86 40.96 1.63
3953 4131 7.389803 TTCCACAACATGATGTTTATGGTAG 57.610 36.000 25.97 11.36 41.45 3.18
3973 4151 0.603707 CAGCCTTTCGACAGCTTCCA 60.604 55.000 0.44 0.00 33.70 3.53
4009 4188 3.496692 CCTGGGAAGACATCAACTGAACA 60.497 47.826 0.00 0.00 0.00 3.18
4010 4189 3.077359 CCTGGGAAGACATCAACTGAAC 58.923 50.000 0.00 0.00 0.00 3.18
4053 4232 2.337879 TTTGGTCAGCGTCCAAGCCT 62.338 55.000 9.43 0.00 44.26 4.58
4293 4515 3.369175 GGATCTCCCCAGCTTCATTTTT 58.631 45.455 0.00 0.00 0.00 1.94
4294 4516 2.684927 CGGATCTCCCCAGCTTCATTTT 60.685 50.000 0.00 0.00 0.00 1.82
4295 4517 1.133976 CGGATCTCCCCAGCTTCATTT 60.134 52.381 0.00 0.00 0.00 2.32
4296 4518 0.471617 CGGATCTCCCCAGCTTCATT 59.528 55.000 0.00 0.00 0.00 2.57
4297 4519 0.692419 ACGGATCTCCCCAGCTTCAT 60.692 55.000 0.00 0.00 0.00 2.57
4298 4520 1.306141 ACGGATCTCCCCAGCTTCA 60.306 57.895 0.00 0.00 0.00 3.02
4299 4521 1.144936 CACGGATCTCCCCAGCTTC 59.855 63.158 0.00 0.00 0.00 3.86
4300 4522 2.370445 CCACGGATCTCCCCAGCTT 61.370 63.158 0.00 0.00 0.00 3.74
4301 4523 2.765807 CCACGGATCTCCCCAGCT 60.766 66.667 0.00 0.00 0.00 4.24
4302 4524 2.764128 TCCACGGATCTCCCCAGC 60.764 66.667 0.00 0.00 0.00 4.85
4303 4525 0.687757 TTCTCCACGGATCTCCCCAG 60.688 60.000 0.00 0.00 0.00 4.45
4304 4526 0.031111 ATTCTCCACGGATCTCCCCA 60.031 55.000 0.00 0.00 0.00 4.96
4305 4527 0.394565 CATTCTCCACGGATCTCCCC 59.605 60.000 0.00 0.00 0.00 4.81
4306 4528 0.250081 GCATTCTCCACGGATCTCCC 60.250 60.000 0.00 0.00 0.00 4.30
4307 4529 0.755686 AGCATTCTCCACGGATCTCC 59.244 55.000 0.00 0.00 0.00 3.71
4308 4530 2.611225 AAGCATTCTCCACGGATCTC 57.389 50.000 0.00 0.00 0.00 2.75
4309 4531 2.766263 TGTAAGCATTCTCCACGGATCT 59.234 45.455 0.00 0.00 0.00 2.75
4350 4572 5.486332 TCTGGAATGGGGGAGTATATCTTT 58.514 41.667 0.00 0.00 0.00 2.52
4498 4733 2.510918 GCGGGAGTAAAGGTCGCC 60.511 66.667 0.00 0.00 40.44 5.54
4628 4868 3.646162 TCCTAACCATTACGAGGATGCAT 59.354 43.478 0.00 0.00 33.05 3.96
4638 4878 6.161381 TCTTTGAACGACTCCTAACCATTAC 58.839 40.000 0.00 0.00 0.00 1.89
4681 4921 7.214467 ACCATTACAAATTTGTTCATCGACT 57.786 32.000 27.66 3.41 42.35 4.18
4737 4977 1.997669 AGTTCATCGAAACTCGCTCC 58.002 50.000 0.00 0.00 40.21 4.70


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

AutoCloner maintained by Alex Coulton.