Multiple sequence alignment - TraesCS4A01G188200

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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 TraesCS4A01G188200 chr4A 100.000 5029 0 0 1 5029 467141674 467146702 0.000000e+00 9287
1 TraesCS4A01G188200 chr4A 89.347 291 28 3 4740 5029 300004195 300003907 3.700000e-96 363
2 TraesCS4A01G188200 chr4A 95.122 82 4 0 4948 5029 622161417 622161498 4.090000e-26 130
3 TraesCS4A01G188200 chr4A 92.000 75 5 1 4737 4811 298815245 298815318 2.480000e-18 104
4 TraesCS4A01G188200 chr4D 97.660 3505 63 11 1534 5029 109362716 109359222 0.000000e+00 6000
5 TraesCS4A01G188200 chr4D 95.153 1506 57 4 1 1500 109364210 109362715 0.000000e+00 2362
6 TraesCS4A01G188200 chr4B 97.177 2763 62 6 1534 4282 167344698 167347458 0.000000e+00 4656
7 TraesCS4A01G188200 chr4B 93.828 1523 60 7 3 1500 167343186 167344699 0.000000e+00 2261
8 TraesCS4A01G188200 chr4B 92.992 371 13 6 4347 4713 167347512 167347873 3.450000e-146 529
9 TraesCS4A01G188200 chr2B 90.722 291 23 3 4740 5029 485685939 485685652 7.900000e-103 385
10 TraesCS4A01G188200 chr1B 90.034 291 25 3 4740 5029 200035928 200035641 1.710000e-99 374
11 TraesCS4A01G188200 chrUn 91.481 270 18 4 4740 5007 53051509 53051243 2.860000e-97 366
12 TraesCS4A01G188200 chr6A 87.285 291 27 7 4740 5029 239316231 239316512 1.750000e-84 324
13 TraesCS4A01G188200 chr6A 93.860 114 6 1 4600 4713 273934854 273934966 2.410000e-38 171
14 TraesCS4A01G188200 chr6A 93.860 114 6 1 4600 4713 274008719 274008831 2.410000e-38 171
15 TraesCS4A01G188200 chr6B 93.780 209 12 1 4505 4713 715738096 715737889 3.780000e-81 313
16 TraesCS4A01G188200 chr3A 95.614 114 5 0 4600 4713 250042975 250043088 3.090000e-42 183
17 TraesCS4A01G188200 chr7B 95.122 82 4 0 4948 5029 511463856 511463775 4.090000e-26 130
18 TraesCS4A01G188200 chr3D 93.902 82 5 0 4948 5029 124495750 124495669 1.900000e-24 124


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 TraesCS4A01G188200 chr4A 467141674 467146702 5028 False 9287 9287 100.000000 1 5029 1 chr4A.!!$F2 5028
1 TraesCS4A01G188200 chr4D 109359222 109364210 4988 True 4181 6000 96.406500 1 5029 2 chr4D.!!$R1 5028
2 TraesCS4A01G188200 chr4B 167343186 167347873 4687 False 2482 4656 94.665667 3 4713 3 chr4B.!!$F1 4710

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
28 29 0.592500 CCATCACCTGATCGTCGTCG 60.593 60.0 0.0 0.0 38.55 5.12 F
693 694 0.612229 AGTGCAGGGAGTGTGATCAG 59.388 55.0 0.0 0.0 0.00 2.90 F
2082 2127 0.685458 TAGGACGGTTAGGGTGGAGC 60.685 60.0 0.0 0.0 0.00 4.70 F
2849 2894 0.329596 AGGATGTTGCCAGGAGAACC 59.670 55.0 0.0 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1089 1115 1.894756 CCGGACCTCGCCAAACAAA 60.895 57.895 0.00 0.0 37.59 2.83 R
2492 2537 1.448717 GCCACCTTCGAGCTCCTTC 60.449 63.158 8.47 0.0 0.00 3.46 R
3108 3153 0.324943 GCCTGTAACTCCAGCCTCAA 59.675 55.000 0.00 0.0 0.00 3.02 R
4139 4185 0.742990 ACATGAACATGGGTACGCGG 60.743 55.000 12.47 2.8 42.91 6.46 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
28 29 0.592500 CCATCACCTGATCGTCGTCG 60.593 60.000 0.00 0.00 38.55 5.12
137 138 1.221414 CGAGCCTGCAATTACCTAGC 58.779 55.000 0.00 0.00 0.00 3.42
140 141 0.938008 GCCTGCAATTACCTAGCGAC 59.062 55.000 0.00 0.00 0.00 5.19
144 145 1.206523 GCAATTACCTAGCGACGTCC 58.793 55.000 10.58 2.76 0.00 4.79
146 147 2.728922 CAATTACCTAGCGACGTCCTC 58.271 52.381 10.58 1.88 0.00 3.71
194 195 1.130373 TGAATTTGCTGGATTCGCGAC 59.870 47.619 9.15 0.00 36.52 5.19
217 218 7.158099 ACAAATTTTGAGGAACATACCTAGC 57.842 36.000 15.81 0.00 40.73 3.42
252 253 6.851330 GGTTTAGTGTTCACGAGAAATTTCTG 59.149 38.462 25.12 17.93 37.73 3.02
255 256 4.511826 AGTGTTCACGAGAAATTTCTGGAC 59.488 41.667 29.90 19.50 37.73 4.02
276 277 1.197430 ACTAGCTCAAGGTGCAGGCT 61.197 55.000 0.00 0.00 37.08 4.58
308 309 6.646240 GCATTTTTGCTGGATTCTCTGTTTTA 59.354 34.615 0.00 0.00 0.00 1.52
339 340 9.736819 TTTGGGTAATAATTTATCTGGGGAATT 57.263 29.630 0.00 0.00 0.00 2.17
395 396 6.388619 ACCATCATTGTAGTTTAGGAACCT 57.611 37.500 0.00 0.00 36.39 3.50
399 400 6.938698 TCATTGTAGTTTAGGAACCTGGTA 57.061 37.500 0.00 0.00 36.39 3.25
417 418 8.554490 ACCTGGTATCTATTTTAGTGTCTGAT 57.446 34.615 0.00 0.00 0.00 2.90
531 532 5.932455 TGGATCACATTTATCAGCTCATGA 58.068 37.500 0.00 0.00 43.70 3.07
614 615 5.513962 GGGGAATAAGAGATTAAGAGGGCAG 60.514 48.000 0.00 0.00 0.00 4.85
693 694 0.612229 AGTGCAGGGAGTGTGATCAG 59.388 55.000 0.00 0.00 0.00 2.90
762 763 2.031870 AGGAAAGCTGTGGTTGTTTCC 58.968 47.619 4.80 4.80 45.67 3.13
786 787 7.014518 TCCAATGAGATTGTTGACAAATTCAGT 59.985 33.333 14.60 11.24 39.55 3.41
917 943 3.673543 ACTGGACCCCTTTGTAAAACA 57.326 42.857 0.00 0.00 0.00 2.83
981 1007 1.556451 TCTGTCACAGGCTGCATACAT 59.444 47.619 15.89 0.00 31.51 2.29
1032 1058 2.476619 ACACGCTGATTCAGAAAAGACG 59.523 45.455 17.87 11.85 32.44 4.18
1033 1059 2.069273 ACGCTGATTCAGAAAAGACGG 58.931 47.619 17.87 0.00 32.44 4.79
1034 1060 2.288825 ACGCTGATTCAGAAAAGACGGA 60.289 45.455 17.87 0.00 32.44 4.69
1035 1061 2.346847 CGCTGATTCAGAAAAGACGGAG 59.653 50.000 17.87 0.00 32.44 4.63
1036 1062 3.589988 GCTGATTCAGAAAAGACGGAGA 58.410 45.455 17.87 0.00 32.44 3.71
1037 1063 4.187694 GCTGATTCAGAAAAGACGGAGAT 58.812 43.478 17.87 0.00 32.44 2.75
1089 1115 5.997746 TGAATCTGTTAAAGCTGCAGTAAGT 59.002 36.000 16.64 1.03 0.00 2.24
1098 1124 2.127251 GCTGCAGTAAGTTTGTTTGGC 58.873 47.619 16.64 0.00 0.00 4.52
1104 1130 2.876550 AGTAAGTTTGTTTGGCGAGGTC 59.123 45.455 0.00 0.00 0.00 3.85
1194 1220 8.980143 TTAGCAGAAAATTGTGGCTTTAATAC 57.020 30.769 0.00 0.00 36.10 1.89
1272 1298 9.579768 ACTGCAGCTATCTAAGAATAATAATCG 57.420 33.333 15.27 0.00 0.00 3.34
1280 1306 6.387465 TCTAAGAATAATAATCGAGTGCGGG 58.613 40.000 0.00 0.00 38.28 6.13
1366 1392 7.880105 TCTGTGATCAGATGTGTAGATCATAC 58.120 38.462 0.00 0.00 46.71 2.39
1369 1395 7.723172 TGTGATCAGATGTGTAGATCATACTCT 59.277 37.037 0.00 0.00 46.71 3.24
1407 1433 3.129813 TCATCAGATTGTAGCGTACCGTT 59.870 43.478 0.00 0.00 0.00 4.44
1423 1449 5.612788 CGTACCGTTTACTTTTCTTTTGTCG 59.387 40.000 0.00 0.00 0.00 4.35
1498 1524 5.523916 TGTAGTTCAGTTTCAGAAAGCACTC 59.476 40.000 0.00 0.00 0.00 3.51
1499 1525 4.517285 AGTTCAGTTTCAGAAAGCACTCA 58.483 39.130 0.00 0.00 0.00 3.41
1500 1526 4.574013 AGTTCAGTTTCAGAAAGCACTCAG 59.426 41.667 0.00 0.00 0.00 3.35
1501 1527 2.874701 TCAGTTTCAGAAAGCACTCAGC 59.125 45.455 0.00 0.00 46.19 4.26
1516 1542 4.688413 GCACTCAGCTATTATAGAGGTTGC 59.312 45.833 3.04 1.28 41.15 4.17
1517 1543 5.740224 GCACTCAGCTATTATAGAGGTTGCA 60.740 44.000 3.04 0.00 41.15 4.08
1518 1544 6.283694 CACTCAGCTATTATAGAGGTTGCAA 58.716 40.000 3.04 0.00 32.52 4.08
1519 1545 6.201806 CACTCAGCTATTATAGAGGTTGCAAC 59.798 42.308 21.59 21.59 32.52 4.17
1520 1546 6.127054 ACTCAGCTATTATAGAGGTTGCAACA 60.127 38.462 29.55 10.82 32.52 3.33
1521 1547 6.830912 TCAGCTATTATAGAGGTTGCAACAT 58.169 36.000 29.55 24.42 0.00 2.71
1522 1548 6.931281 TCAGCTATTATAGAGGTTGCAACATC 59.069 38.462 31.34 31.34 39.82 3.06
1523 1549 6.148480 CAGCTATTATAGAGGTTGCAACATCC 59.852 42.308 33.68 19.16 40.35 3.51
1524 1550 5.997746 GCTATTATAGAGGTTGCAACATCCA 59.002 40.000 33.68 24.85 40.35 3.41
1525 1551 6.073003 GCTATTATAGAGGTTGCAACATCCAC 60.073 42.308 33.68 15.66 40.35 4.02
1526 1552 5.435686 TTATAGAGGTTGCAACATCCACT 57.564 39.130 33.68 22.68 40.35 4.00
1527 1553 2.664402 AGAGGTTGCAACATCCACTT 57.336 45.000 33.68 17.41 40.35 3.16
1528 1554 2.949447 AGAGGTTGCAACATCCACTTT 58.051 42.857 33.68 17.07 40.35 2.66
1529 1555 3.299503 AGAGGTTGCAACATCCACTTTT 58.700 40.909 33.68 16.40 40.35 2.27
1530 1556 4.469657 AGAGGTTGCAACATCCACTTTTA 58.530 39.130 33.68 0.00 40.35 1.52
1531 1557 4.520492 AGAGGTTGCAACATCCACTTTTAG 59.480 41.667 33.68 0.00 40.35 1.85
1532 1558 4.469657 AGGTTGCAACATCCACTTTTAGA 58.530 39.130 29.55 0.00 0.00 2.10
1596 1622 9.997482 TGTATTTGTAGAAACTGTCTTTTGTTC 57.003 29.630 0.00 0.00 37.84 3.18
1643 1669 1.340889 TGGACATTTTTGGCAGCTGTC 59.659 47.619 12.53 12.53 36.38 3.51
1694 1720 4.637534 ACTAGACATGATGTGCCATGAAAC 59.362 41.667 1.23 0.00 44.98 2.78
1902 1936 0.773644 AGTGACACCTGAAGGGCAAT 59.226 50.000 0.84 0.00 40.27 3.56
2009 2050 2.124983 GCGCTGCTTCCAGATCCA 60.125 61.111 0.00 0.00 41.77 3.41
2010 2051 2.467826 GCGCTGCTTCCAGATCCAC 61.468 63.158 0.00 0.00 41.77 4.02
2011 2052 1.220206 CGCTGCTTCCAGATCCACT 59.780 57.895 0.00 0.00 41.77 4.00
2013 2054 1.134699 CGCTGCTTCCAGATCCACTAA 60.135 52.381 0.00 0.00 41.77 2.24
2014 2055 2.559440 GCTGCTTCCAGATCCACTAAG 58.441 52.381 0.00 0.00 41.77 2.18
2015 2056 2.559440 CTGCTTCCAGATCCACTAAGC 58.441 52.381 10.95 10.95 41.77 3.09
2016 2057 2.170187 CTGCTTCCAGATCCACTAAGCT 59.830 50.000 16.12 0.00 41.77 3.74
2017 2058 2.093288 TGCTTCCAGATCCACTAAGCTG 60.093 50.000 16.12 0.00 39.54 4.24
2018 2059 2.559440 CTTCCAGATCCACTAAGCTGC 58.441 52.381 0.00 0.00 0.00 5.25
2019 2060 1.571955 TCCAGATCCACTAAGCTGCA 58.428 50.000 1.02 0.00 0.00 4.41
2045 2086 2.285256 GCTGTGAGCATAATCAACGACG 60.285 50.000 0.00 0.00 41.89 5.12
2050 2092 2.535984 GAGCATAATCAACGACGACAGG 59.464 50.000 0.00 0.00 0.00 4.00
2082 2127 0.685458 TAGGACGGTTAGGGTGGAGC 60.685 60.000 0.00 0.00 0.00 4.70
2105 2150 3.123620 GCGCTTCCACCAGCAGAG 61.124 66.667 0.00 0.00 40.09 3.35
2135 2180 1.431633 TCCACTGTAGGAGGGTTCTCA 59.568 52.381 0.00 0.00 41.69 3.27
2136 2181 1.550976 CCACTGTAGGAGGGTTCTCAC 59.449 57.143 0.00 0.00 41.69 3.51
2149 2194 3.371285 GGGTTCTCACGTATCTTGCTTTC 59.629 47.826 0.00 0.00 0.00 2.62
2151 2196 4.092091 GGTTCTCACGTATCTTGCTTTCTG 59.908 45.833 0.00 0.00 0.00 3.02
2387 2432 1.221293 CCAAGCCCTCTCTGAGCTG 59.779 63.158 0.00 0.00 36.84 4.24
2467 2512 4.941873 GTCAAAAGAACTGAATATCCGGGT 59.058 41.667 0.00 0.00 0.00 5.28
2492 2537 6.853279 ACAGAAAATGCAAATATTCGAACG 57.147 33.333 0.00 0.00 0.00 3.95
2531 2576 0.741221 GCTCTAGTGAAGCCGTTGGG 60.741 60.000 0.00 0.00 0.00 4.12
2770 2815 5.316167 TGCAATGGTTCAAGAGTCACTTAT 58.684 37.500 0.00 0.00 37.03 1.73
2849 2894 0.329596 AGGATGTTGCCAGGAGAACC 59.670 55.000 0.00 0.00 0.00 3.62
2927 2972 2.912956 TGATCCTGTAGCTTTCAAGGGT 59.087 45.455 0.00 0.00 0.00 4.34
2933 2978 2.708861 TGTAGCTTTCAAGGGTCTCCAA 59.291 45.455 0.00 0.00 34.83 3.53
2993 3038 3.193263 GCAGAAGAAGATCGAAGATGCA 58.807 45.455 0.00 0.00 45.12 3.96
3108 3153 6.688578 TCTCTTAGCAGTTTAGTTGAATCGT 58.311 36.000 0.00 0.00 0.00 3.73
3251 3296 1.625315 ACTGCAGTAGCCACAGAATCA 59.375 47.619 20.16 0.00 41.13 2.57
3261 3306 2.426024 GCCACAGAATCAGATGCAACAT 59.574 45.455 0.00 0.00 0.00 2.71
3368 3413 1.668919 CGTGCAGCCGAGTTAAGAGAA 60.669 52.381 0.00 0.00 0.00 2.87
3512 3557 2.075426 AAAAGGCAAGTGCTGTCCGC 62.075 55.000 2.85 0.00 41.70 5.54
3563 3608 3.193691 TCACGATCTCAAAGGAGGAGTTC 59.806 47.826 0.00 0.00 41.69 3.01
3752 3797 2.613977 GCTAAAGAAGGCAGAGACAGCA 60.614 50.000 0.00 0.00 0.00 4.41
3822 3867 6.806739 AGAGAAGGAAGAACAAAACAAAAACG 59.193 34.615 0.00 0.00 0.00 3.60
3888 3933 2.630158 CTCCATCTCACAAGGCTTCTG 58.370 52.381 0.00 0.00 0.00 3.02
4139 4185 3.315191 TGTGCTGAACTCCTAACTTTTGC 59.685 43.478 0.00 0.00 0.00 3.68
4142 4188 1.877443 TGAACTCCTAACTTTTGCCGC 59.123 47.619 0.00 0.00 0.00 6.53
4373 4454 6.254281 TGCTTTCTTCACTTAATTACTGCC 57.746 37.500 0.00 0.00 0.00 4.85
4391 4472 2.223688 TGCCGCATATCCAAATTTTCCG 60.224 45.455 0.00 0.00 0.00 4.30
4598 4687 5.097742 TCCACAACCACATTATGTAGAGG 57.902 43.478 0.00 0.00 0.00 3.69
4832 4921 0.389757 GGGAAGCGACCTATCAGTCC 59.610 60.000 0.00 0.00 32.91 3.85
4914 5003 4.273480 GCGCCTTCACATGTAATCTATTGT 59.727 41.667 0.00 0.00 0.00 2.71
4949 5038 9.195411 CATGTGTTTTGCTACAAAATTATGTCT 57.805 29.630 8.57 0.00 34.75 3.41
4971 5060 7.557358 TGTCTCAACCATCTGTATTTGCATTAT 59.443 33.333 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 3.351020 ACGATAATTTCCTCGAGGACG 57.649 47.619 33.75 30.50 45.39 4.79
194 195 7.156876 TGCTAGGTATGTTCCTCAAAATTTG 57.843 36.000 0.00 0.00 38.86 2.32
217 218 6.073494 TCGTGAACACTAAACCATACAACATG 60.073 38.462 3.51 0.00 0.00 3.21
252 253 1.825474 TGCACCTTGAGCTAGTAGTCC 59.175 52.381 0.00 0.00 0.00 3.85
255 256 1.472376 GCCTGCACCTTGAGCTAGTAG 60.472 57.143 0.00 0.00 0.00 2.57
293 294 9.320295 ACCCAAATTATTAAAACAGAGAATCCA 57.680 29.630 0.00 0.00 33.66 3.41
324 325 3.222603 GCCGTCAATTCCCCAGATAAAT 58.777 45.455 0.00 0.00 0.00 1.40
339 340 0.950836 CAACAGAAATGTGGCCGTCA 59.049 50.000 0.00 0.00 0.00 4.35
395 396 9.421399 TCTCATCAGACACTAAAATAGATACCA 57.579 33.333 0.00 0.00 0.00 3.25
399 400 8.986991 AGGTTCTCATCAGACACTAAAATAGAT 58.013 33.333 0.00 0.00 0.00 1.98
411 412 4.394300 CCATGACAAAGGTTCTCATCAGAC 59.606 45.833 0.00 0.00 0.00 3.51
417 418 3.689347 CCATCCATGACAAAGGTTCTCA 58.311 45.455 0.00 0.00 0.00 3.27
423 424 1.462616 TTCGCCATCCATGACAAAGG 58.537 50.000 0.00 0.00 0.00 3.11
573 574 0.544357 CCCCTACCACACTGTCTCCA 60.544 60.000 0.00 0.00 0.00 3.86
576 577 0.192566 TTCCCCCTACCACACTGTCT 59.807 55.000 0.00 0.00 0.00 3.41
762 763 9.681692 TTACTGAATTTGTCAACAATCTCATTG 57.318 29.630 0.00 0.00 37.93 2.82
981 1007 3.634448 CCATAATCCCGTTGCCACAATAA 59.366 43.478 0.00 0.00 0.00 1.40
1032 1058 7.164803 CCCTTGTATCTATTTCTCCAATCTCC 58.835 42.308 0.00 0.00 0.00 3.71
1033 1059 6.652900 GCCCTTGTATCTATTTCTCCAATCTC 59.347 42.308 0.00 0.00 0.00 2.75
1034 1060 6.331307 AGCCCTTGTATCTATTTCTCCAATCT 59.669 38.462 0.00 0.00 0.00 2.40
1035 1061 6.538263 AGCCCTTGTATCTATTTCTCCAATC 58.462 40.000 0.00 0.00 0.00 2.67
1036 1062 6.466470 GGAGCCCTTGTATCTATTTCTCCAAT 60.466 42.308 0.00 0.00 37.93 3.16
1037 1063 5.163195 GGAGCCCTTGTATCTATTTCTCCAA 60.163 44.000 0.00 0.00 37.93 3.53
1089 1115 1.894756 CCGGACCTCGCCAAACAAA 60.895 57.895 0.00 0.00 37.59 2.83
1098 1124 4.592426 GAGGAAAACCGGACCTCG 57.408 61.111 9.46 0.00 40.28 4.63
1104 1130 3.010420 GGATCTTTCAGAGGAAAACCGG 58.990 50.000 0.00 0.00 42.18 5.28
1194 1220 6.293081 GCATGCAGGCCTATCATATAATTACG 60.293 42.308 13.44 6.11 0.00 3.18
1272 1298 3.111853 TCATCAATGATACCCGCACTC 57.888 47.619 0.00 0.00 0.00 3.51
1314 1340 4.892934 CCCTATTTATGCTTAGGTTGGCAA 59.107 41.667 0.00 0.00 41.90 4.52
1369 1395 6.345096 TCTGATGACTTCACTGTTGATACA 57.655 37.500 0.00 0.00 0.00 2.29
1407 1433 4.037089 GGGAAGGCGACAAAAGAAAAGTAA 59.963 41.667 0.00 0.00 0.00 2.24
1423 1449 3.006752 TGTCAAATGAACATTGGGAAGGC 59.993 43.478 0.69 0.00 0.00 4.35
1498 1524 6.148480 GGATGTTGCAACCTCTATAATAGCTG 59.852 42.308 27.05 0.00 0.00 4.24
1499 1525 6.183361 TGGATGTTGCAACCTCTATAATAGCT 60.183 38.462 27.05 0.00 0.00 3.32
1500 1526 5.997746 TGGATGTTGCAACCTCTATAATAGC 59.002 40.000 27.05 13.16 0.00 2.97
1501 1527 7.220030 AGTGGATGTTGCAACCTCTATAATAG 58.780 38.462 27.05 0.00 30.47 1.73
1502 1528 7.136822 AGTGGATGTTGCAACCTCTATAATA 57.863 36.000 27.05 8.56 30.47 0.98
1503 1529 6.006275 AGTGGATGTTGCAACCTCTATAAT 57.994 37.500 27.05 13.85 30.47 1.28
1504 1530 5.435686 AGTGGATGTTGCAACCTCTATAA 57.564 39.130 27.05 9.90 30.47 0.98
1505 1531 5.435686 AAGTGGATGTTGCAACCTCTATA 57.564 39.130 27.05 15.21 30.87 1.31
1506 1532 4.307032 AAGTGGATGTTGCAACCTCTAT 57.693 40.909 27.05 15.47 30.87 1.98
1507 1533 3.788227 AAGTGGATGTTGCAACCTCTA 57.212 42.857 27.05 21.56 30.87 2.43
1508 1534 2.664402 AAGTGGATGTTGCAACCTCT 57.336 45.000 27.05 16.21 32.88 3.69
1509 1535 3.733443 AAAAGTGGATGTTGCAACCTC 57.267 42.857 26.14 24.07 0.00 3.85
1510 1536 4.278419 GTCTAAAAGTGGATGTTGCAACCT 59.722 41.667 26.14 17.24 0.00 3.50
1511 1537 4.037446 TGTCTAAAAGTGGATGTTGCAACC 59.963 41.667 26.14 12.24 0.00 3.77
1512 1538 4.976116 GTGTCTAAAAGTGGATGTTGCAAC 59.024 41.667 22.83 22.83 0.00 4.17
1513 1539 4.642437 TGTGTCTAAAAGTGGATGTTGCAA 59.358 37.500 0.00 0.00 0.00 4.08
1514 1540 4.203226 TGTGTCTAAAAGTGGATGTTGCA 58.797 39.130 0.00 0.00 0.00 4.08
1515 1541 4.829064 TGTGTCTAAAAGTGGATGTTGC 57.171 40.909 0.00 0.00 0.00 4.17
1516 1542 5.278463 CCCTTGTGTCTAAAAGTGGATGTTG 60.278 44.000 0.00 0.00 0.00 3.33
1517 1543 4.827284 CCCTTGTGTCTAAAAGTGGATGTT 59.173 41.667 0.00 0.00 0.00 2.71
1518 1544 4.104102 TCCCTTGTGTCTAAAAGTGGATGT 59.896 41.667 0.00 0.00 0.00 3.06
1519 1545 4.651778 TCCCTTGTGTCTAAAAGTGGATG 58.348 43.478 0.00 0.00 0.00 3.51
1520 1546 4.993705 TCCCTTGTGTCTAAAAGTGGAT 57.006 40.909 0.00 0.00 0.00 3.41
1521 1547 4.781775 TTCCCTTGTGTCTAAAAGTGGA 57.218 40.909 0.00 0.00 0.00 4.02
1522 1548 4.887655 ACTTTCCCTTGTGTCTAAAAGTGG 59.112 41.667 0.00 0.00 36.06 4.00
1523 1549 5.821204 CACTTTCCCTTGTGTCTAAAAGTG 58.179 41.667 10.32 10.32 43.84 3.16
1524 1550 5.751586 TCACTTTCCCTTGTGTCTAAAAGT 58.248 37.500 0.00 0.00 37.41 2.66
1525 1551 6.884280 ATCACTTTCCCTTGTGTCTAAAAG 57.116 37.500 0.00 0.00 35.82 2.27
1526 1552 7.654022 AAATCACTTTCCCTTGTGTCTAAAA 57.346 32.000 0.00 0.00 35.82 1.52
1527 1553 7.654022 AAAATCACTTTCCCTTGTGTCTAAA 57.346 32.000 0.00 0.00 35.82 1.85
1528 1554 7.776030 TGTAAAATCACTTTCCCTTGTGTCTAA 59.224 33.333 0.00 0.00 35.82 2.10
1529 1555 7.284074 TGTAAAATCACTTTCCCTTGTGTCTA 58.716 34.615 0.00 0.00 35.82 2.59
1530 1556 6.126409 TGTAAAATCACTTTCCCTTGTGTCT 58.874 36.000 0.00 0.00 35.82 3.41
1531 1557 6.385649 TGTAAAATCACTTTCCCTTGTGTC 57.614 37.500 0.00 0.00 35.82 3.67
1532 1558 6.323739 ACATGTAAAATCACTTTCCCTTGTGT 59.676 34.615 0.00 0.00 35.82 3.72
1619 1645 2.170187 AGCTGCCAAAAATGTCCAAACA 59.830 40.909 0.00 0.00 40.38 2.83
1643 1669 8.119226 CAGAAGTTTCTCTTAAGACAAACTGTG 58.881 37.037 28.59 24.65 40.65 3.66
1720 1746 7.546250 AAGATAAAGGATGTGTCGATAGGAT 57.454 36.000 0.00 0.00 0.00 3.24
1727 1753 7.491372 TGCTTTACTAAGATAAAGGATGTGTCG 59.509 37.037 7.24 0.00 40.88 4.35
1734 1760 9.569122 AACTTTGTGCTTTACTAAGATAAAGGA 57.431 29.630 7.93 2.16 42.39 3.36
2105 2150 1.473278 CCTACAGTGGAGACGACTTCC 59.527 57.143 3.07 0.00 0.00 3.46
2135 2180 7.094631 TGTGTAATACAGAAAGCAAGATACGT 58.905 34.615 0.00 0.00 33.42 3.57
2136 2181 7.520119 TGTGTAATACAGAAAGCAAGATACG 57.480 36.000 0.00 0.00 33.42 3.06
2149 2194 8.988934 GGTTATGTACCATCATGTGTAATACAG 58.011 37.037 0.00 0.00 46.92 2.74
2254 2299 9.238368 CCCTCTACCACAGACAAAATTTAAATA 57.762 33.333 0.01 0.00 0.00 1.40
2467 2512 8.231161 TCGTTCGAATATTTGCATTTTCTGTTA 58.769 29.630 0.00 0.00 0.00 2.41
2492 2537 1.448717 GCCACCTTCGAGCTCCTTC 60.449 63.158 8.47 0.00 0.00 3.46
2849 2894 6.405538 AGCTTCTTCCAGAGATTCTTTACAG 58.594 40.000 0.00 0.00 33.49 2.74
2927 2972 4.156922 GTCTCATCGAGTTTCTCTTGGAGA 59.843 45.833 0.00 0.00 36.86 3.71
2933 2978 7.338196 TCAGAATAAGTCTCATCGAGTTTCTCT 59.662 37.037 0.00 0.00 36.66 3.10
2993 3038 7.732222 AACAGACTCCAAATCTCTATCTCTT 57.268 36.000 0.00 0.00 0.00 2.85
3108 3153 0.324943 GCCTGTAACTCCAGCCTCAA 59.675 55.000 0.00 0.00 0.00 3.02
3251 3296 5.296283 GTCATCAGAAGCTAATGTTGCATCT 59.704 40.000 0.00 0.00 38.75 2.90
3261 3306 5.181009 CAACATCAGGTCATCAGAAGCTAA 58.819 41.667 0.00 0.00 0.00 3.09
3512 3557 4.268687 GGCTCGGATATTGAGGCG 57.731 61.111 14.04 0.00 46.97 5.52
3563 3608 3.166489 ACCTTTCGGCTTAGAGATTCG 57.834 47.619 0.00 0.00 0.00 3.34
3752 3797 1.656441 CGCCTTGTTTGCTGCTTCT 59.344 52.632 0.00 0.00 0.00 2.85
3822 3867 3.412879 GAGGCACGTAGGTCTCGGC 62.413 68.421 0.00 0.00 0.00 5.54
4139 4185 0.742990 ACATGAACATGGGTACGCGG 60.743 55.000 12.47 2.80 42.91 6.46
4142 4188 6.481976 ACATATACAACATGAACATGGGTACG 59.518 38.462 17.25 12.72 42.91 3.67
4350 4431 5.106712 CGGCAGTAATTAAGTGAAGAAAGCA 60.107 40.000 1.11 0.00 0.00 3.91
4373 4454 4.027572 ACACGGAAAATTTGGATATGCG 57.972 40.909 0.00 0.00 0.00 4.73
4391 4472 6.907212 CAGAAGCGACATGGAATTAATTACAC 59.093 38.462 15.42 2.76 32.51 2.90
4501 4590 2.224018 TGTTGAACCTGGCAAATGCTTC 60.224 45.455 5.25 2.14 41.70 3.86
4502 4591 1.761784 TGTTGAACCTGGCAAATGCTT 59.238 42.857 5.25 0.00 41.70 3.91
4598 4687 7.260603 AGCTTGCTGTTTAATCCAAATATCAC 58.739 34.615 0.00 0.00 0.00 3.06
4914 5003 6.463360 TGTAGCAAAACACATGTCAGAGATA 58.537 36.000 0.00 0.00 0.00 1.98
4971 5060 6.875948 TTACATTTCAGAAGCTTACAGCAA 57.124 33.333 0.00 0.00 45.56 3.91


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

AutoCloner maintained by Alex Coulton.