Multiple sequence alignment - TraesCS6B01G435500

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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 TraesCS6B01G435500 chr6B 100.000 2510 0 0 1 2510 703390427 703387918 0.000000e+00 4636.0
1 TraesCS6B01G435500 chr6B 87.009 331 23 13 1999 2317 703667471 703667149 3.070000e-94 355.0
2 TraesCS6B01G435500 chr6B 91.154 260 23 0 1745 2004 703667849 703667590 1.100000e-93 353.0
3 TraesCS6B01G435500 chr6B 91.787 207 16 1 2305 2510 703666249 703666043 1.140000e-73 287.0
4 TraesCS6B01G435500 chr6D 92.152 1529 76 14 1 1513 461502341 461500841 0.000000e+00 2119.0
5 TraesCS6B01G435500 chr6D 90.722 679 40 11 1850 2510 461498138 461497465 0.000000e+00 883.0
6 TraesCS6B01G435500 chr6D 89.820 167 15 1 1500 1666 461498300 461498136 1.960000e-51 213.0
7 TraesCS6B01G435500 chr6A 92.799 1361 75 12 309 1666 608285980 608284640 0.000000e+00 1949.0
8 TraesCS6B01G435500 chr6A 89.198 611 45 8 1920 2510 608154565 608153956 0.000000e+00 743.0
9 TraesCS6B01G435500 chr6A 92.555 497 22 2 1170 1666 608156818 608156337 0.000000e+00 699.0
10 TraesCS6B01G435500 chr6A 91.111 90 8 0 994 1083 608296575 608296486 3.390000e-24 122.0
11 TraesCS6B01G435500 chr6A 86.585 82 7 3 772 853 608296720 608296643 1.240000e-13 87.9
12 TraesCS6B01G435500 chr5B 75.116 647 127 24 862 1488 700418004 700417372 3.180000e-69 272.0
13 TraesCS6B01G435500 chr5D 73.408 801 172 25 862 1642 548954131 548953352 6.890000e-66 261.0
14 TraesCS6B01G435500 chr3B 92.500 120 7 2 40 158 825536797 825536915 1.190000e-38 171.0
15 TraesCS6B01G435500 chrUn 91.667 120 8 2 40 158 209290233 209290115 5.550000e-37 165.0
16 TraesCS6B01G435500 chr7B 91.667 120 8 2 40 158 642250366 642250248 5.550000e-37 165.0
17 TraesCS6B01G435500 chr4A 92.308 52 3 1 862 913 620290586 620290636 3.460000e-09 73.1


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 TraesCS6B01G435500 chr6B 703387918 703390427 2509 True 4636.000000 4636 100.000000 1 2510 1 chr6B.!!$R1 2509
1 TraesCS6B01G435500 chr6B 703666043 703667849 1806 True 331.666667 355 89.983333 1745 2510 3 chr6B.!!$R2 765
2 TraesCS6B01G435500 chr6D 461497465 461502341 4876 True 1071.666667 2119 90.898000 1 2510 3 chr6D.!!$R1 2509
3 TraesCS6B01G435500 chr6A 608284640 608285980 1340 True 1949.000000 1949 92.799000 309 1666 1 chr6A.!!$R1 1357
4 TraesCS6B01G435500 chr6A 608153956 608156818 2862 True 721.000000 743 90.876500 1170 2510 2 chr6A.!!$R2 1340
5 TraesCS6B01G435500 chr5B 700417372 700418004 632 True 272.000000 272 75.116000 862 1488 1 chr5B.!!$R1 626
6 TraesCS6B01G435500 chr5D 548953352 548954131 779 True 261.000000 261 73.408000 862 1642 1 chr5D.!!$R1 780

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
633 634 0.395311 CATTGATGGACAGGCTGGCT 60.395 55.0 21.79 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1735 4335 0.847373 TTAGGGACCAAACTGCCACA 59.153 50.0 0.0 0.0 0.0 4.17 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
17 18 2.738480 GGTGTGTGGCTGTACCGA 59.262 61.111 0.00 0.00 43.94 4.69
52 53 2.107041 TAACACCAGTGGCAGTCGGG 62.107 60.000 9.78 6.48 34.19 5.14
71 72 3.430453 GGGATTTCACAACTGGGATTCA 58.570 45.455 0.00 0.00 0.00 2.57
80 81 4.763793 CACAACTGGGATTCAGACTTTCAT 59.236 41.667 0.00 0.00 46.18 2.57
88 89 7.689299 TGGGATTCAGACTTTCATAGAAGAAA 58.311 34.615 0.00 0.00 36.21 2.52
96 97 7.604164 CAGACTTTCATAGAAGAAACTGCCTTA 59.396 37.037 0.00 0.00 34.11 2.69
99 100 7.389053 ACTTTCATAGAAGAAACTGCCTTACTG 59.611 37.037 0.00 0.00 34.11 2.74
103 104 4.464947 AGAAGAAACTGCCTTACTGCTTT 58.535 39.130 0.00 0.00 0.00 3.51
133 134 1.224069 CTGCCAGGTGTCACTCAACG 61.224 60.000 2.35 0.00 39.03 4.10
158 159 6.051179 AGTGGGTCTCCAGATTAAAAGTAC 57.949 41.667 0.00 0.00 45.05 2.73
159 160 5.785940 AGTGGGTCTCCAGATTAAAAGTACT 59.214 40.000 0.00 0.00 45.05 2.73
160 161 6.070710 AGTGGGTCTCCAGATTAAAAGTACTC 60.071 42.308 0.00 0.00 45.05 2.59
161 162 5.189145 TGGGTCTCCAGATTAAAAGTACTCC 59.811 44.000 0.00 0.00 38.32 3.85
162 163 5.349809 GGTCTCCAGATTAAAAGTACTCCG 58.650 45.833 0.00 0.00 0.00 4.63
177 178 3.308035 ACTCCGTATATGACCAGGTCA 57.692 47.619 25.06 25.06 46.90 4.02
179 180 1.951602 TCCGTATATGACCAGGTCACG 59.048 52.381 25.35 21.60 45.65 4.35
182 183 3.504906 CCGTATATGACCAGGTCACGTAT 59.495 47.826 25.35 20.17 45.65 3.06
185 186 5.106277 CGTATATGACCAGGTCACGTATGAT 60.106 44.000 25.35 9.59 45.65 2.45
228 229 1.140252 CCTGGTGGGTTAGGAATACCG 59.860 57.143 0.00 0.00 41.83 4.02
229 230 1.835531 CTGGTGGGTTAGGAATACCGT 59.164 52.381 0.00 0.00 41.83 4.83
233 234 3.264947 GTGGGTTAGGAATACCGTTGTC 58.735 50.000 0.00 0.00 41.83 3.18
241 242 3.778629 AGGAATACCGTTGTCCACCTAAT 59.221 43.478 0.00 0.00 41.83 1.73
242 243 4.964262 AGGAATACCGTTGTCCACCTAATA 59.036 41.667 0.00 0.00 41.83 0.98
243 244 5.426185 AGGAATACCGTTGTCCACCTAATAA 59.574 40.000 0.00 0.00 41.83 1.40
244 245 5.756833 GGAATACCGTTGTCCACCTAATAAG 59.243 44.000 0.00 0.00 0.00 1.73
284 285 6.472016 TGTTTCAGCTACATGGATAACTTGA 58.528 36.000 0.00 0.00 0.00 3.02
286 287 7.119699 TGTTTCAGCTACATGGATAACTTGAAG 59.880 37.037 0.00 0.00 0.00 3.02
290 291 6.201806 CAGCTACATGGATAACTTGAAGCTAC 59.798 42.308 0.00 0.00 0.00 3.58
359 360 1.963855 TTGGTGTTCATGCCCGTCG 60.964 57.895 0.00 0.00 0.00 5.12
370 371 3.041940 CCCGTCGTGTTCAGCACC 61.042 66.667 0.00 0.00 44.97 5.01
375 376 1.069090 TCGTGTTCAGCACCCACTC 59.931 57.895 0.00 0.00 44.97 3.51
419 420 2.045926 GCCATTGGCCTCGTGACT 60.046 61.111 17.28 0.00 44.06 3.41
451 452 2.898181 TTGCTGTTGTGCGATGTATG 57.102 45.000 0.00 0.00 35.36 2.39
452 453 0.447406 TGCTGTTGTGCGATGTATGC 59.553 50.000 0.00 0.00 35.36 3.14
453 454 0.729116 GCTGTTGTGCGATGTATGCT 59.271 50.000 0.00 0.00 0.00 3.79
454 455 1.530441 GCTGTTGTGCGATGTATGCTG 60.530 52.381 0.00 0.00 0.00 4.41
455 456 0.447406 TGTTGTGCGATGTATGCTGC 59.553 50.000 0.00 0.00 0.00 5.25
456 457 0.447406 GTTGTGCGATGTATGCTGCA 59.553 50.000 4.13 4.13 34.44 4.41
481 482 2.124151 GGCCATGCCCCAGTACAG 60.124 66.667 0.00 0.00 44.06 2.74
545 546 2.606725 CGACAGGAAAGATCAGCATCAC 59.393 50.000 0.00 0.00 0.00 3.06
564 565 2.770802 CACTGACCCCATTCTGAGATCT 59.229 50.000 0.00 0.00 0.00 2.75
585 586 6.121776 TCTACAAATAATGCATATCCCGGT 57.878 37.500 0.00 0.00 0.00 5.28
596 597 0.539986 TATCCCGGTTCCTGTCTTGC 59.460 55.000 0.00 0.00 0.00 4.01
597 598 1.201429 ATCCCGGTTCCTGTCTTGCT 61.201 55.000 0.00 0.00 0.00 3.91
598 599 1.672356 CCCGGTTCCTGTCTTGCTG 60.672 63.158 0.00 0.00 0.00 4.41
599 600 2.328099 CCGGTTCCTGTCTTGCTGC 61.328 63.158 0.00 0.00 0.00 5.25
600 601 1.302033 CGGTTCCTGTCTTGCTGCT 60.302 57.895 0.00 0.00 0.00 4.24
601 602 1.294659 CGGTTCCTGTCTTGCTGCTC 61.295 60.000 0.00 0.00 0.00 4.26
618 619 3.473625 TGCTCCTGCTCATGTATCATTG 58.526 45.455 0.00 0.00 40.48 2.82
633 634 0.395311 CATTGATGGACAGGCTGGCT 60.395 55.000 21.79 0.00 0.00 4.75
651 652 2.423185 GGCTGTGTAATGCTGCATGTTA 59.577 45.455 17.00 3.61 33.36 2.41
689 690 9.825972 AAATCTTTTTGATACGTACAATCTGTG 57.174 29.630 0.00 0.00 34.45 3.66
835 848 8.700644 CGTATTCAAAATATACAGAGCACCTAC 58.299 37.037 0.00 0.00 0.00 3.18
941 957 2.450160 CGCTTCGGTGCATAAATTTCC 58.550 47.619 0.00 0.00 0.00 3.13
996 1016 2.479275 ACGAAGCTTTTTACGCTCCTTC 59.521 45.455 0.00 0.00 36.56 3.46
1438 1475 6.237887 AGAAGAATCTCATGGAGAAAGAGG 57.762 41.667 0.00 0.00 42.27 3.69
1503 1540 0.237235 TTCTGTTGTTCAATCGGCGC 59.763 50.000 0.00 0.00 0.00 6.53
1593 4192 1.349688 TCCACCGCTTCCTTACATGTT 59.650 47.619 2.30 0.00 0.00 2.71
1595 4194 1.135689 CACCGCTTCCTTACATGTTGC 60.136 52.381 2.30 0.00 0.00 4.17
1598 4197 1.196808 CGCTTCCTTACATGTTGCGTT 59.803 47.619 2.30 0.00 37.62 4.84
1602 4202 2.695359 TCCTTACATGTTGCGTTCCTC 58.305 47.619 2.30 0.00 0.00 3.71
1606 4206 4.378459 CCTTACATGTTGCGTTCCTCTTTC 60.378 45.833 2.30 0.00 0.00 2.62
1620 4220 3.384467 TCCTCTTTCCCTTTGCTTGTTTG 59.616 43.478 0.00 0.00 0.00 2.93
1623 4223 5.243730 CCTCTTTCCCTTTGCTTGTTTGATA 59.756 40.000 0.00 0.00 0.00 2.15
1631 4231 7.039152 TCCCTTTGCTTGTTTGATAATCAATCA 60.039 33.333 0.00 0.00 43.03 2.57
1658 4258 8.761689 TCTGCAATATATATTACCTCATCAGCA 58.238 33.333 7.65 8.82 0.00 4.41
1660 4260 9.333724 TGCAATATATATTACCTCATCAGCATG 57.666 33.333 7.65 0.00 37.54 4.06
1661 4261 9.334947 GCAATATATATTACCTCATCAGCATGT 57.665 33.333 7.65 0.00 37.40 3.21
1670 4270 8.579850 TTACCTCATCAGCATGTTAATTTTCT 57.420 30.769 0.00 0.00 37.40 2.52
1671 4271 9.679661 TTACCTCATCAGCATGTTAATTTTCTA 57.320 29.630 0.00 0.00 37.40 2.10
1672 4272 8.757982 ACCTCATCAGCATGTTAATTTTCTAT 57.242 30.769 0.00 0.00 37.40 1.98
1673 4273 9.193806 ACCTCATCAGCATGTTAATTTTCTATT 57.806 29.630 0.00 0.00 37.40 1.73
1674 4274 9.674824 CCTCATCAGCATGTTAATTTTCTATTC 57.325 33.333 0.00 0.00 37.40 1.75
1675 4275 9.674824 CTCATCAGCATGTTAATTTTCTATTCC 57.325 33.333 0.00 0.00 37.40 3.01
1676 4276 9.187996 TCATCAGCATGTTAATTTTCTATTCCA 57.812 29.630 0.00 0.00 37.40 3.53
1677 4277 9.241317 CATCAGCATGTTAATTTTCTATTCCAC 57.759 33.333 0.00 0.00 37.40 4.02
1678 4278 8.347004 TCAGCATGTTAATTTTCTATTCCACA 57.653 30.769 0.00 0.00 37.40 4.17
1679 4279 8.801299 TCAGCATGTTAATTTTCTATTCCACAA 58.199 29.630 0.00 0.00 37.40 3.33
1680 4280 9.590451 CAGCATGTTAATTTTCTATTCCACAAT 57.410 29.630 0.00 0.00 0.00 2.71
1681 4281 9.807649 AGCATGTTAATTTTCTATTCCACAATC 57.192 29.630 0.00 0.00 0.00 2.67
1682 4282 9.585099 GCATGTTAATTTTCTATTCCACAATCA 57.415 29.630 0.00 0.00 0.00 2.57
1723 4323 5.531122 ACATACATGTCTACGCTACCATT 57.469 39.130 0.00 0.00 35.87 3.16
1724 4324 5.914033 ACATACATGTCTACGCTACCATTT 58.086 37.500 0.00 0.00 35.87 2.32
1725 4325 5.983720 ACATACATGTCTACGCTACCATTTC 59.016 40.000 0.00 0.00 35.87 2.17
1726 4326 4.737855 ACATGTCTACGCTACCATTTCT 57.262 40.909 0.00 0.00 0.00 2.52
1727 4327 5.086104 ACATGTCTACGCTACCATTTCTT 57.914 39.130 0.00 0.00 0.00 2.52
1728 4328 6.216801 ACATGTCTACGCTACCATTTCTTA 57.783 37.500 0.00 0.00 0.00 2.10
1729 4329 6.040878 ACATGTCTACGCTACCATTTCTTAC 58.959 40.000 0.00 0.00 0.00 2.34
1730 4330 5.909621 TGTCTACGCTACCATTTCTTACT 57.090 39.130 0.00 0.00 0.00 2.24
1731 4331 5.647589 TGTCTACGCTACCATTTCTTACTG 58.352 41.667 0.00 0.00 0.00 2.74
1732 4332 5.184479 TGTCTACGCTACCATTTCTTACTGT 59.816 40.000 0.00 0.00 0.00 3.55
1733 4333 6.098017 GTCTACGCTACCATTTCTTACTGTT 58.902 40.000 0.00 0.00 0.00 3.16
1734 4334 7.094248 TGTCTACGCTACCATTTCTTACTGTTA 60.094 37.037 0.00 0.00 0.00 2.41
1735 4335 7.919621 GTCTACGCTACCATTTCTTACTGTTAT 59.080 37.037 0.00 0.00 0.00 1.89
1736 4336 6.903883 ACGCTACCATTTCTTACTGTTATG 57.096 37.500 0.00 0.00 0.00 1.90
1737 4337 6.403878 ACGCTACCATTTCTTACTGTTATGT 58.596 36.000 0.00 0.00 0.00 2.29
1738 4338 6.312918 ACGCTACCATTTCTTACTGTTATGTG 59.687 38.462 0.00 0.00 0.00 3.21
1739 4339 6.238103 CGCTACCATTTCTTACTGTTATGTGG 60.238 42.308 0.00 0.00 0.00 4.17
1740 4340 5.897377 ACCATTTCTTACTGTTATGTGGC 57.103 39.130 0.00 0.00 0.00 5.01
1741 4341 5.321102 ACCATTTCTTACTGTTATGTGGCA 58.679 37.500 0.00 0.00 0.00 4.92
1742 4342 5.415701 ACCATTTCTTACTGTTATGTGGCAG 59.584 40.000 0.00 0.00 38.58 4.85
1743 4343 5.415701 CCATTTCTTACTGTTATGTGGCAGT 59.584 40.000 0.00 0.00 46.33 4.40
1744 4344 6.071952 CCATTTCTTACTGTTATGTGGCAGTT 60.072 38.462 2.48 0.00 42.61 3.16
1745 4345 6.952773 TTTCTTACTGTTATGTGGCAGTTT 57.047 33.333 2.48 0.00 42.61 2.66
1746 4346 5.940192 TCTTACTGTTATGTGGCAGTTTG 57.060 39.130 2.48 0.00 42.61 2.93
1747 4347 4.759693 TCTTACTGTTATGTGGCAGTTTGG 59.240 41.667 2.48 0.00 42.61 3.28
1786 4386 6.105333 TCATGTACATCGATTCATTGTGACA 58.895 36.000 5.07 0.00 0.00 3.58
1788 4388 3.997319 ACATCGATTCATTGTGACACG 57.003 42.857 0.00 0.00 0.00 4.49
1808 4408 6.646636 ACACGTTCTGAGTTTTATTTTCTCG 58.353 36.000 0.00 0.00 0.00 4.04
1814 4414 7.653767 TCTGAGTTTTATTTTCTCGTTCTCC 57.346 36.000 0.00 0.00 0.00 3.71
1817 4417 8.084590 TGAGTTTTATTTTCTCGTTCTCCTTC 57.915 34.615 0.00 0.00 0.00 3.46
1828 4428 7.596749 TCTCGTTCTCCTTCAAAATATGAAC 57.403 36.000 0.00 0.00 43.08 3.18
1829 4429 7.158697 TCTCGTTCTCCTTCAAAATATGAACA 58.841 34.615 0.00 0.00 43.08 3.18
1831 4431 9.098355 CTCGTTCTCCTTCAAAATATGAACATA 57.902 33.333 0.00 0.00 43.08 2.29
1870 4473 8.408043 TGGGAATACATAAATTTGCTAGGATG 57.592 34.615 0.00 0.00 0.00 3.51
1979 6284 6.012508 TCCAGAGAGTTACCAAATCTTCCAAT 60.013 38.462 0.00 0.00 0.00 3.16
1984 6289 8.794335 AGAGTTACCAAATCTTCCAATACTTC 57.206 34.615 0.00 0.00 0.00 3.01
2131 6580 3.397482 ACGGCTAATTCTCATCAGCATC 58.603 45.455 0.00 0.00 35.69 3.91
2238 6690 7.539366 TCCTTTTGTAAATAATGTGTTAAGCGC 59.461 33.333 0.00 0.00 0.00 5.92
2421 7786 2.737252 GACACTTCTCGCACTTAAAGGG 59.263 50.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.772853 TAGCACCATGCCGGCCATC 62.773 63.158 26.77 7.05 46.52 3.51
17 18 3.357444 TTAGCACCATGCCGGCCAT 62.357 57.895 26.77 14.88 46.52 4.40
39 40 0.321564 TGAAATCCCGACTGCCACTG 60.322 55.000 0.00 0.00 0.00 3.66
52 53 5.006386 AGTCTGAATCCCAGTTGTGAAATC 58.994 41.667 0.00 0.00 43.38 2.17
71 72 6.120507 AGGCAGTTTCTTCTATGAAAGTCT 57.879 37.500 0.00 0.00 37.46 3.24
80 81 4.891992 AGCAGTAAGGCAGTTTCTTCTA 57.108 40.909 0.00 0.00 35.83 2.10
88 89 3.604582 GATCTCAAAGCAGTAAGGCAGT 58.395 45.455 0.00 0.00 35.83 4.40
96 97 2.675317 GCAGTACGGATCTCAAAGCAGT 60.675 50.000 0.00 0.00 0.00 4.40
99 100 1.291132 GGCAGTACGGATCTCAAAGC 58.709 55.000 0.00 0.00 0.00 3.51
103 104 0.324368 ACCTGGCAGTACGGATCTCA 60.324 55.000 14.43 0.00 0.00 3.27
152 153 5.301298 GACCTGGTCATATACGGAGTACTTT 59.699 44.000 21.70 0.00 38.01 2.66
158 159 2.031069 CGTGACCTGGTCATATACGGAG 60.031 54.545 30.50 11.93 44.63 4.63
159 160 1.951602 CGTGACCTGGTCATATACGGA 59.048 52.381 30.50 3.93 44.63 4.69
160 161 1.679680 ACGTGACCTGGTCATATACGG 59.320 52.381 30.50 17.56 44.63 4.02
161 162 4.214758 TCATACGTGACCTGGTCATATACG 59.785 45.833 30.50 28.10 44.63 3.06
162 163 5.700722 TCATACGTGACCTGGTCATATAC 57.299 43.478 30.50 17.31 44.63 1.47
194 195 0.923358 ACCAGGGTTCAAGTTGTGGA 59.077 50.000 14.55 0.00 0.00 4.02
196 197 1.032014 CCACCAGGGTTCAAGTTGTG 58.968 55.000 2.11 0.00 0.00 3.33
197 198 3.513209 CCACCAGGGTTCAAGTTGT 57.487 52.632 2.11 0.00 0.00 3.32
228 229 4.523083 TGGATGCTTATTAGGTGGACAAC 58.477 43.478 0.00 0.00 0.00 3.32
229 230 4.853468 TGGATGCTTATTAGGTGGACAA 57.147 40.909 0.00 0.00 0.00 3.18
233 234 3.632145 GTGGTTGGATGCTTATTAGGTGG 59.368 47.826 0.00 0.00 0.00 4.61
241 242 2.969821 AACCTGTGGTTGGATGCTTA 57.030 45.000 0.71 0.00 45.07 3.09
242 243 3.848353 AACCTGTGGTTGGATGCTT 57.152 47.368 0.71 0.00 45.07 3.91
262 263 6.094048 GCTTCAAGTTATCCATGTAGCTGAAA 59.906 38.462 0.00 0.00 35.42 2.69
267 268 6.049149 TGTAGCTTCAAGTTATCCATGTAGC 58.951 40.000 0.00 0.00 37.63 3.58
284 285 6.072508 ACGTGAATTGATCAATGTTGTAGCTT 60.073 34.615 21.39 3.31 40.50 3.74
286 287 5.631026 ACGTGAATTGATCAATGTTGTAGC 58.369 37.500 21.39 7.33 40.50 3.58
290 291 6.077197 ACGTAACGTGAATTGATCAATGTTG 58.923 36.000 21.39 13.58 40.50 3.33
332 333 1.503818 ATGAACACCAACGACACCGC 61.504 55.000 0.00 0.00 39.95 5.68
419 420 0.538584 ACAGCAATGCGAGGAGATCA 59.461 50.000 0.00 0.00 0.00 2.92
481 482 3.433615 GTCTGTATCTGGTTGTGCTGTTC 59.566 47.826 0.00 0.00 0.00 3.18
524 525 2.606725 GTGATGCTGATCTTTCCTGTCG 59.393 50.000 0.00 0.00 0.00 4.35
564 565 5.708230 GGAACCGGGATATGCATTATTTGTA 59.292 40.000 3.54 0.00 0.00 2.41
585 586 0.035881 CAGGAGCAGCAAGACAGGAA 59.964 55.000 0.00 0.00 0.00 3.36
596 597 2.904697 TGATACATGAGCAGGAGCAG 57.095 50.000 0.00 0.00 45.49 4.24
597 598 3.135167 TCAATGATACATGAGCAGGAGCA 59.865 43.478 0.00 0.00 45.49 4.26
598 599 3.736720 TCAATGATACATGAGCAGGAGC 58.263 45.455 0.00 0.00 42.56 4.70
599 600 4.695928 CCATCAATGATACATGAGCAGGAG 59.304 45.833 0.00 0.00 0.00 3.69
600 601 4.348754 TCCATCAATGATACATGAGCAGGA 59.651 41.667 0.00 0.00 0.00 3.86
601 602 4.454847 GTCCATCAATGATACATGAGCAGG 59.545 45.833 0.00 0.00 0.00 4.85
720 721 8.301720 AGTACAAGTATTCACACTTATGAACGA 58.698 33.333 0.00 0.00 41.29 3.85
730 731 7.275999 GCCTAGAAAGAGTACAAGTATTCACAC 59.724 40.741 0.00 0.00 0.00 3.82
835 848 7.586300 CGGTATTAAAATTAATGGTCTTGCTCG 59.414 37.037 8.34 0.00 35.20 5.03
1182 1219 3.560278 CGTTTAGCGGCGGCGATT 61.560 61.111 36.87 23.61 46.35 3.34
1438 1475 4.984785 GGCCAAATTTTTGTTCTCTGAGTC 59.015 41.667 0.00 0.61 36.45 3.36
1503 1540 5.657302 AGTACCCAACCATGTCTACTAAGAG 59.343 44.000 0.00 0.00 30.45 2.85
1593 4192 1.604604 CAAAGGGAAAGAGGAACGCA 58.395 50.000 0.00 0.00 0.00 5.24
1595 4194 1.897560 AGCAAAGGGAAAGAGGAACG 58.102 50.000 0.00 0.00 0.00 3.95
1598 4197 3.312736 AACAAGCAAAGGGAAAGAGGA 57.687 42.857 0.00 0.00 0.00 3.71
1602 4202 7.153985 TGATTATCAAACAAGCAAAGGGAAAG 58.846 34.615 0.00 0.00 0.00 2.62
1606 4206 7.098477 TGATTGATTATCAAACAAGCAAAGGG 58.902 34.615 14.09 0.00 40.12 3.95
1631 4231 9.775854 GCTGATGAGGTAATATATATTGCAGAT 57.224 33.333 20.74 11.36 31.09 2.90
1646 4246 9.851686 ATAGAAAATTAACATGCTGATGAGGTA 57.148 29.630 0.00 0.00 33.36 3.08
1656 4256 9.585099 TGATTGTGGAATAGAAAATTAACATGC 57.415 29.630 0.00 0.00 0.00 4.06
1701 4301 5.531122 AATGGTAGCGTAGACATGTATGT 57.469 39.130 2.50 0.00 45.16 2.29
1702 4302 6.216569 AGAAATGGTAGCGTAGACATGTATG 58.783 40.000 2.50 0.00 0.00 2.39
1703 4303 6.406692 AGAAATGGTAGCGTAGACATGTAT 57.593 37.500 0.00 0.00 0.00 2.29
1704 4304 5.847111 AGAAATGGTAGCGTAGACATGTA 57.153 39.130 0.00 0.00 0.00 2.29
1705 4305 4.737855 AGAAATGGTAGCGTAGACATGT 57.262 40.909 0.00 0.00 0.00 3.21
1706 4306 6.199154 CAGTAAGAAATGGTAGCGTAGACATG 59.801 42.308 0.00 0.00 0.00 3.21
1707 4307 6.127423 ACAGTAAGAAATGGTAGCGTAGACAT 60.127 38.462 0.00 0.00 0.00 3.06
1708 4308 5.184479 ACAGTAAGAAATGGTAGCGTAGACA 59.816 40.000 0.00 0.00 0.00 3.41
1709 4309 5.648572 ACAGTAAGAAATGGTAGCGTAGAC 58.351 41.667 0.00 0.00 0.00 2.59
1710 4310 5.909621 ACAGTAAGAAATGGTAGCGTAGA 57.090 39.130 0.00 0.00 0.00 2.59
1711 4311 7.705325 ACATAACAGTAAGAAATGGTAGCGTAG 59.295 37.037 0.00 0.00 0.00 3.51
1712 4312 7.490079 CACATAACAGTAAGAAATGGTAGCGTA 59.510 37.037 0.00 0.00 0.00 4.42
1713 4313 6.312918 CACATAACAGTAAGAAATGGTAGCGT 59.687 38.462 0.00 0.00 0.00 5.07
1714 4314 6.238103 CCACATAACAGTAAGAAATGGTAGCG 60.238 42.308 0.00 0.00 0.00 4.26
1715 4315 6.458342 GCCACATAACAGTAAGAAATGGTAGC 60.458 42.308 0.00 0.00 0.00 3.58
1716 4316 6.597672 TGCCACATAACAGTAAGAAATGGTAG 59.402 38.462 0.00 0.00 0.00 3.18
1717 4317 6.477253 TGCCACATAACAGTAAGAAATGGTA 58.523 36.000 0.00 0.00 0.00 3.25
1718 4318 5.321102 TGCCACATAACAGTAAGAAATGGT 58.679 37.500 0.00 0.00 0.00 3.55
1719 4319 5.415701 ACTGCCACATAACAGTAAGAAATGG 59.584 40.000 0.00 0.00 45.09 3.16
1720 4320 6.500684 ACTGCCACATAACAGTAAGAAATG 57.499 37.500 0.00 0.00 45.09 2.32
1721 4321 7.370383 CAAACTGCCACATAACAGTAAGAAAT 58.630 34.615 0.00 0.00 46.17 2.17
1722 4322 6.238897 CCAAACTGCCACATAACAGTAAGAAA 60.239 38.462 0.00 0.00 46.17 2.52
1723 4323 5.240623 CCAAACTGCCACATAACAGTAAGAA 59.759 40.000 0.00 0.00 46.17 2.52
1724 4324 4.759693 CCAAACTGCCACATAACAGTAAGA 59.240 41.667 0.00 0.00 46.17 2.10
1725 4325 4.518970 ACCAAACTGCCACATAACAGTAAG 59.481 41.667 0.00 0.00 46.17 2.34
1726 4326 4.465886 ACCAAACTGCCACATAACAGTAA 58.534 39.130 0.00 0.00 46.17 2.24
1727 4327 4.069304 GACCAAACTGCCACATAACAGTA 58.931 43.478 0.00 0.00 46.17 2.74
1729 4329 2.228822 GGACCAAACTGCCACATAACAG 59.771 50.000 0.00 0.00 39.86 3.16
1730 4330 2.235016 GGACCAAACTGCCACATAACA 58.765 47.619 0.00 0.00 0.00 2.41
1731 4331 1.544246 GGGACCAAACTGCCACATAAC 59.456 52.381 0.00 0.00 0.00 1.89
1732 4332 1.427368 AGGGACCAAACTGCCACATAA 59.573 47.619 0.00 0.00 0.00 1.90
1733 4333 1.072266 AGGGACCAAACTGCCACATA 58.928 50.000 0.00 0.00 0.00 2.29
1734 4334 1.072266 TAGGGACCAAACTGCCACAT 58.928 50.000 0.00 0.00 0.00 3.21
1735 4335 0.847373 TTAGGGACCAAACTGCCACA 59.153 50.000 0.00 0.00 0.00 4.17
1736 4336 1.989706 TTTAGGGACCAAACTGCCAC 58.010 50.000 0.00 0.00 0.00 5.01
1737 4337 2.757894 TTTTAGGGACCAAACTGCCA 57.242 45.000 0.00 0.00 0.00 4.92
1786 4386 6.839820 ACGAGAAAATAAAACTCAGAACGT 57.160 33.333 0.00 0.00 0.00 3.99
1788 4388 8.010540 GGAGAACGAGAAAATAAAACTCAGAAC 58.989 37.037 0.00 0.00 0.00 3.01
1845 4445 8.004215 ACATCCTAGCAAATTTATGTATTCCCA 58.996 33.333 1.10 0.00 0.00 4.37
1862 4465 6.149474 TGCAAGAACTAAAAAGACATCCTAGC 59.851 38.462 0.00 0.00 0.00 3.42
1870 4473 5.048434 AGGATGCTGCAAGAACTAAAAAGAC 60.048 40.000 6.36 0.00 34.07 3.01
1944 6249 8.792830 TTGGTAACTCTCTGGAAATGAAATAG 57.207 34.615 0.00 0.00 37.61 1.73
2046 6477 5.208294 ACTAGATGTCCCTAAGTTCCAGA 57.792 43.478 0.00 0.00 0.00 3.86
2047 6478 5.941555 AACTAGATGTCCCTAAGTTCCAG 57.058 43.478 0.00 0.00 0.00 3.86
2084 6533 6.606796 TGAAAATTATATGCCTCTTTCCTGCA 59.393 34.615 0.00 0.00 39.68 4.41
2100 6549 8.902806 TGATGAGAATTAGCCGTTGAAAATTAT 58.097 29.630 0.00 0.00 0.00 1.28
2131 6580 8.101654 ACTCTAACTACTGCTCCTATAATTCG 57.898 38.462 0.00 0.00 0.00 3.34
2374 7739 9.108284 CACTTCATGAAAAAGGGTATTGTTTTT 57.892 29.630 9.88 0.00 38.31 1.94
2421 7786 4.142227 TGTTGTACGAAGATAGGAGCCTTC 60.142 45.833 0.00 0.00 36.38 3.46


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

AutoCloner maintained by Alex Coulton.