Multiple sequence alignment - TraesCS5D01G337100

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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 TraesCS5D01G337100 chr5D 100.000 4339 0 0 1 4339 426045092 426040754 0.000000e+00 8013.0
1 TraesCS5D01G337100 chr5D 91.309 2543 189 14 1810 4339 426033986 426031463 0.000000e+00 3443.0
2 TraesCS5D01G337100 chr5D 90.696 1537 119 8 1 1516 426035512 426033979 0.000000e+00 2025.0
3 TraesCS5D01G337100 chr5B 92.046 4149 250 32 1 4100 515716724 515712607 0.000000e+00 5760.0
4 TraesCS5D01G337100 chr5B 87.948 307 30 7 1515 1817 11532976 11532673 5.340000e-94 355.0
5 TraesCS5D01G337100 chr5A 86.863 883 89 13 650 1518 540354199 540353330 0.000000e+00 963.0
6 TraesCS5D01G337100 chr5A 87.788 434 51 1 3034 3465 540350788 540350355 1.390000e-139 507.0
7 TraesCS5D01G337100 chr5A 87.552 241 26 2 3458 3698 540350159 540349923 4.270000e-70 276.0
8 TraesCS5D01G337100 chr5A 84.232 241 25 6 1810 2049 540353339 540353111 5.650000e-54 222.0
9 TraesCS5D01G337100 chr5A 87.952 83 3 2 1308 1383 422374744 422374826 1.660000e-14 91.6
10 TraesCS5D01G337100 chr3D 84.379 717 83 13 3041 3743 5803869 5804570 0.000000e+00 676.0
11 TraesCS5D01G337100 chr3D 84.043 564 69 15 869 1414 5802734 5803294 1.380000e-144 523.0
12 TraesCS5D01G337100 chr1D 96.474 312 8 3 1512 1821 431522428 431522118 2.990000e-141 512.0
13 TraesCS5D01G337100 chr3B 82.215 596 73 16 869 1437 11944341 11943752 2.350000e-132 483.0
14 TraesCS5D01G337100 chr3B 87.948 307 30 7 1518 1820 524743835 524743532 5.340000e-94 355.0
15 TraesCS5D01G337100 chr3B 85.397 315 35 4 3044 3347 11943366 11943052 2.520000e-82 316.0
16 TraesCS5D01G337100 chr6A 87.987 308 30 7 1515 1817 351703531 351703226 1.480000e-94 357.0
17 TraesCS5D01G337100 chr4B 87.582 306 34 4 1515 1817 549200364 549200060 6.900000e-93 351.0
18 TraesCS5D01G337100 chr3A 87.379 309 35 4 1515 1820 644530228 644530535 6.900000e-93 351.0
19 TraesCS5D01G337100 chr3A 89.873 79 2 1 1308 1380 588384852 588384930 3.570000e-16 97.1
20 TraesCS5D01G337100 chr1B 87.622 307 32 6 1518 1820 528289058 528289362 6.900000e-93 351.0
21 TraesCS5D01G337100 chr2B 87.296 307 32 7 1518 1820 87943370 87943067 1.160000e-90 344.0
22 TraesCS5D01G337100 chr2B 78.109 201 23 14 308 487 418779658 418779858 1.650000e-19 108.0
23 TraesCS5D01G337100 chr2B 89.873 79 2 1 1308 1380 76549493 76549571 3.570000e-16 97.1
24 TraesCS5D01G337100 chr4A 89.888 89 8 1 400 487 698878404 698878492 3.550000e-21 113.0
25 TraesCS5D01G337100 chr1A 89.474 76 2 1 1311 1380 11022971 11022896 1.660000e-14 91.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G337100 chr5D 426040754 426045092 4338 True 8013.0 8013 100.00000 1 4339 1 chr5D.!!$R1 4338
1 TraesCS5D01G337100 chr5D 426031463 426035512 4049 True 2734.0 3443 91.00250 1 4339 2 chr5D.!!$R2 4338
2 TraesCS5D01G337100 chr5B 515712607 515716724 4117 True 5760.0 5760 92.04600 1 4100 1 chr5B.!!$R2 4099
3 TraesCS5D01G337100 chr5A 540349923 540354199 4276 True 492.0 963 86.60875 650 3698 4 chr5A.!!$R1 3048
4 TraesCS5D01G337100 chr3D 5802734 5804570 1836 False 599.5 676 84.21100 869 3743 2 chr3D.!!$F1 2874
5 TraesCS5D01G337100 chr3B 11943052 11944341 1289 True 399.5 483 83.80600 869 3347 2 chr3B.!!$R2 2478

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
511 542 0.537371 ACTGGTGGGGAAAAAGCTCG 60.537 55.000 0.0 0.0 0.0 5.03 F
585 617 0.548989 TCGGGGAAGAGGAGAGAGAG 59.451 60.000 0.0 0.0 0.0 3.20 F
1158 1233 0.554865 ACATCATCCCCCTCCCCAAA 60.555 55.000 0.0 0.0 0.0 3.28 F
1396 1489 0.606604 GTCAAGGGCTCGTGTTCCTA 59.393 55.000 0.0 0.0 0.0 2.94 F
2340 3979 1.267806 CTGCATTTCGTCCTTTGCTGT 59.732 47.619 0.0 0.0 36.1 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1922 3.378742 CAGAGTACCTGCAACGAGTCTAT 59.621 47.826 0.00 0.0 35.89 1.98 R
2070 3559 4.281688 AGCAAATAAGGCAACACACTTCAT 59.718 37.500 0.00 0.0 41.41 2.57 R
2941 4582 2.602257 TACAACATGATGAGGGAGCG 57.398 50.000 10.29 0.0 0.00 5.03 R
3191 4964 0.747283 GGCAGGTCAGATCCAGCAAG 60.747 60.000 8.13 0.0 40.92 4.01 R
4238 6216 0.112606 TAGAGGGCGGAGGATACCTG 59.887 60.000 0.00 0.0 31.76 4.00 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
25 26 4.122776 ACTAATTCATCGGCAGTAGCAAG 58.877 43.478 0.00 0.00 44.61 4.01
28 29 2.299993 TCATCGGCAGTAGCAAGAAG 57.700 50.000 0.00 0.00 44.61 2.85
54 55 7.328737 AGTTGTCGGTAGTAGCTTTATTCATT 58.671 34.615 0.00 0.00 0.00 2.57
132 133 1.520342 CGCCTAAGCTCCTCTGCAC 60.520 63.158 0.00 0.00 36.60 4.57
153 154 4.566759 CACTTGTAACATCGACACCTATGG 59.433 45.833 0.00 0.00 0.00 2.74
190 191 1.388065 CCCACGTGAAAAGGGTTGCA 61.388 55.000 19.30 0.00 37.81 4.08
291 313 1.555967 AAAAATATGCCGGCTGTGGT 58.444 45.000 29.70 10.83 0.00 4.16
347 377 3.923017 AATTGTGTTGCTGGTTCTAGC 57.077 42.857 1.27 1.27 43.95 3.42
385 415 2.281484 ACGCGGTTGCATCCTGTT 60.281 55.556 12.47 0.00 42.97 3.16
511 542 0.537371 ACTGGTGGGGAAAAAGCTCG 60.537 55.000 0.00 0.00 0.00 5.03
558 590 3.415087 GAGGAGGTGGCCATGGCT 61.415 66.667 34.70 16.75 41.60 4.75
583 615 1.327303 CATCGGGGAAGAGGAGAGAG 58.673 60.000 0.00 0.00 0.00 3.20
585 617 0.548989 TCGGGGAAGAGGAGAGAGAG 59.451 60.000 0.00 0.00 0.00 3.20
650 682 2.359404 GGGGAGAGGAGTCCGACA 59.641 66.667 2.76 0.00 37.50 4.35
736 796 2.339556 GGCATTTGCGGGTGTAGCA 61.340 57.895 0.00 0.00 43.26 3.49
795 855 3.803082 CGAGTTACGCGACCGGGA 61.803 66.667 15.93 0.00 39.22 5.14
858 919 7.953493 ACTTTAGACCCTTTCCATTCCATAAAA 59.047 33.333 0.00 0.00 0.00 1.52
954 1029 3.055747 CGCCTTCTCTCCTAAGGTTTCTT 60.056 47.826 3.97 0.00 44.56 2.52
980 1055 1.817572 TACCACCTAGCCACCCCAGA 61.818 60.000 0.00 0.00 0.00 3.86
1010 1085 2.028125 ATCGGATCAATGGCGGACGT 62.028 55.000 0.00 0.00 0.00 4.34
1158 1233 0.554865 ACATCATCCCCCTCCCCAAA 60.555 55.000 0.00 0.00 0.00 3.28
1174 1249 2.426522 CCAAAGTCAAAGCCGAGATCA 58.573 47.619 0.00 0.00 0.00 2.92
1219 1294 1.595109 CAGCACGTCCAGAAGCACA 60.595 57.895 0.00 0.00 0.00 4.57
1388 1481 1.376543 TAGTACTCGTCAAGGGCTCG 58.623 55.000 0.00 0.00 0.00 5.03
1396 1489 0.606604 GTCAAGGGCTCGTGTTCCTA 59.393 55.000 0.00 0.00 0.00 2.94
1558 1659 5.772672 ACAAGGCCACAAACTCATATTACAA 59.227 36.000 5.01 0.00 0.00 2.41
1566 1667 8.450964 CCACAAACTCATATTACAAGTACCAAG 58.549 37.037 0.00 0.00 0.00 3.61
1608 1709 7.576236 TCTTTGTAAATCAGCTTTTCTCTTCG 58.424 34.615 0.00 0.00 0.00 3.79
1665 1767 3.308473 GGAAAGGGTAGGAAGCTGATTGT 60.308 47.826 0.00 0.00 0.00 2.71
1683 1785 9.552114 GCTGATTGTACTATCATTTATGATTGC 57.448 33.333 18.31 11.85 44.70 3.56
1687 1789 9.850628 ATTGTACTATCATTTATGATTGCATGC 57.149 29.630 11.82 11.82 44.70 4.06
1688 1790 8.393671 TGTACTATCATTTATGATTGCATGCA 57.606 30.769 18.46 18.46 44.70 3.96
1689 1791 9.016438 TGTACTATCATTTATGATTGCATGCAT 57.984 29.630 23.37 11.80 44.70 3.96
1716 1818 8.026607 GCATGTTTTAAATAGGTTGCTAGTTCA 58.973 33.333 0.00 0.00 0.00 3.18
1757 1859 2.000447 GTCTCGATTACTGTTGGTGGC 59.000 52.381 0.00 0.00 0.00 5.01
1777 1879 3.243201 GGCCTTGTATAGATGCAAAGTGC 60.243 47.826 0.00 0.00 45.29 4.40
1819 1922 9.151177 CTTGTATAAGTAAATGGGGGAGTACTA 57.849 37.037 0.00 0.00 0.00 1.82
1848 1951 6.265649 ACTCGTTGCAGGTACTCTGATATATT 59.734 38.462 13.57 0.00 46.18 1.28
1850 1953 7.817641 TCGTTGCAGGTACTCTGATATATTAG 58.182 38.462 13.57 0.00 46.18 1.73
1947 2051 6.464749 GGGGGAATGTTGTCGACCTTTATATA 60.465 42.308 14.12 0.00 0.00 0.86
2022 2128 5.350365 GTGCGATCCTAAGTGTTTGTAATCA 59.650 40.000 0.00 0.00 0.00 2.57
2030 2139 7.827236 TCCTAAGTGTTTGTAATCACAATAGGG 59.173 37.037 21.76 12.29 44.01 3.53
2079 3569 9.608617 GCTATTTGATGATATTGATGAAGTGTG 57.391 33.333 0.00 0.00 0.00 3.82
2097 3588 5.713025 AGTGTGTTGCCTTATTTGCTAATG 58.287 37.500 3.49 0.00 0.00 1.90
2182 3814 9.463443 AACTTCAATATTGTGCTTTTCTACAAC 57.537 29.630 14.97 0.00 39.36 3.32
2185 3817 8.795786 TCAATATTGTGCTTTTCTACAACAAC 57.204 30.769 14.97 0.00 39.36 3.32
2188 3820 9.593134 AATATTGTGCTTTTCTACAACAACAAA 57.407 25.926 0.00 0.00 39.36 2.83
2189 3821 7.897575 ATTGTGCTTTTCTACAACAACAAAA 57.102 28.000 0.00 0.00 39.36 2.44
2236 3868 4.579869 CACCCTAGCTTTCTACACATTGT 58.420 43.478 0.00 0.00 0.00 2.71
2247 3879 7.324616 GCTTTCTACACATTGTTGATTTCTGTC 59.675 37.037 0.00 0.00 32.63 3.51
2340 3979 1.267806 CTGCATTTCGTCCTTTGCTGT 59.732 47.619 0.00 0.00 36.10 4.40
2368 4007 5.877012 TCTGAACTATCTGACTTGCATTTCC 59.123 40.000 0.00 0.00 0.00 3.13
2475 4114 5.400066 TGTCGGACTTCTTTGATGTCATA 57.600 39.130 9.88 1.53 38.11 2.15
2564 4203 6.884472 TTCAGTACCTTTATCCCATCAGAA 57.116 37.500 0.00 0.00 0.00 3.02
2572 4211 6.160459 ACCTTTATCCCATCAGAATGTAAGGT 59.840 38.462 0.00 0.00 37.40 3.50
2629 4268 9.743057 CTTTATTCCGGATAATATTTTGCACAA 57.257 29.630 4.15 0.00 30.56 3.33
2906 4547 7.099764 ACAACTCACCTTCAGATTGTACTATG 58.900 38.462 0.00 0.00 0.00 2.23
2995 4636 8.654230 TTTTGCTTAATATGAACTTTTGCACA 57.346 26.923 0.00 0.00 0.00 4.57
3191 4964 0.912486 ACTACCTGGACATCAAGGGC 59.088 55.000 7.26 0.00 0.00 5.19
3268 5041 1.139853 GGAGATCCGCAAGACCTTCAT 59.860 52.381 0.00 0.00 43.02 2.57
3372 5147 9.293404 GGGGTAAACTAAAGAAACAACTATCTT 57.707 33.333 0.00 0.00 37.49 2.40
3421 5196 2.171003 ACCCAGCTTTGTTAATGCCTC 58.829 47.619 0.00 0.00 32.41 4.70
3423 5198 1.468054 CCAGCTTTGTTAATGCCTCGC 60.468 52.381 0.00 0.00 32.41 5.03
3437 5212 0.172803 CCTCGCAGTAGCCGTTAACT 59.827 55.000 3.71 0.00 37.52 2.24
3472 5450 6.018425 TCGAAACTATGCTAGTAGTAAGTCGG 60.018 42.308 14.47 0.00 38.26 4.79
3554 5532 6.976934 ATCTTTATGTTGGTGGTCTTTTGT 57.023 33.333 0.00 0.00 0.00 2.83
3558 5536 2.175202 TGTTGGTGGTCTTTTGTTGCT 58.825 42.857 0.00 0.00 0.00 3.91
3692 5670 4.520111 TGCATGTGCTTCAAGTTTGAGTAT 59.480 37.500 6.55 0.00 42.66 2.12
3720 5698 7.692460 AGTCATGTTGTTATGATGTTGTGAT 57.308 32.000 0.00 0.00 39.13 3.06
3749 5727 1.340017 TGAGCTGCCACCATAGGTTTC 60.340 52.381 0.00 0.00 31.02 2.78
3767 5745 0.038166 TCTGTTCAACCCTGGCATCC 59.962 55.000 0.00 0.00 0.00 3.51
3822 5800 0.759959 TTCTGCCTTGTTCGGTGGTA 59.240 50.000 0.00 0.00 0.00 3.25
3866 5844 7.173907 GTCATCCTATTCAATATGTCAACCCTG 59.826 40.741 0.00 0.00 0.00 4.45
3889 5867 3.265791 CATCTCAGGGCAACTCTAACAC 58.734 50.000 0.00 0.00 0.00 3.32
3902 5880 6.294176 GCAACTCTAACACAGATCACCAAATT 60.294 38.462 0.00 0.00 31.13 1.82
3910 5888 0.179129 GATCACCAAATTGCCCGCAG 60.179 55.000 0.00 0.00 0.00 5.18
3922 5900 1.900351 CCCGCAGAAGTCCAGATCA 59.100 57.895 0.00 0.00 0.00 2.92
3938 5916 3.188048 CAGATCAGACACTCACTTTTGGC 59.812 47.826 0.00 0.00 0.00 4.52
4096 6074 3.038280 TGTTCCGTCCATCCTCATATGT 58.962 45.455 1.90 0.00 0.00 2.29
4115 6093 8.260114 TCATATGTTATGTATCCATGCTACCTG 58.740 37.037 1.90 0.00 32.29 4.00
4127 6105 1.676678 GCTACCTGACTCCGGCATCA 61.677 60.000 0.00 1.27 0.00 3.07
4128 6106 0.103208 CTACCTGACTCCGGCATCAC 59.897 60.000 0.00 0.00 0.00 3.06
4140 6118 0.796312 GGCATCACTGTTGTACCACG 59.204 55.000 0.00 0.00 0.00 4.94
4180 6158 2.365768 GGACCTCCCCCTCTCCAC 60.366 72.222 0.00 0.00 0.00 4.02
4186 6164 2.263099 CTCCCCCTCTCCACCCAGAT 62.263 65.000 0.00 0.00 0.00 2.90
4189 6167 1.692042 CCCTCTCCACCCAGATGCT 60.692 63.158 0.00 0.00 0.00 3.79
4191 6169 1.153208 CTCTCCACCCAGATGCTGC 60.153 63.158 0.00 0.00 0.00 5.25
4212 6190 1.748879 GGCTTTGCATACGCCTCCA 60.749 57.895 12.60 0.00 40.62 3.86
4238 6216 1.595093 CCTGAAATCAACCACGGCCC 61.595 60.000 0.00 0.00 0.00 5.80
4249 6227 2.446036 ACGGCCCAGGTATCCTCC 60.446 66.667 0.00 0.00 0.00 4.30
4265 6251 0.468214 CTCCGCCCTCTACTCATGGA 60.468 60.000 0.00 0.00 0.00 3.41
4292 6278 3.723348 GCCCGACAAGTGTTCGGC 61.723 66.667 5.24 10.44 44.82 5.54
4301 6287 2.126467 CAAGTGTTCGGCCAAATGTTG 58.874 47.619 2.24 0.00 0.00 3.33
4304 6290 2.167487 AGTGTTCGGCCAAATGTTGTTT 59.833 40.909 2.24 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.728971 CAACTCTTCTTGCTACTGCCG 59.271 52.381 0.00 0.00 38.71 5.69
25 26 4.437772 AAGCTACTACCGACAACTCTTC 57.562 45.455 0.00 0.00 0.00 2.87
28 29 6.327934 TGAATAAAGCTACTACCGACAACTC 58.672 40.000 0.00 0.00 0.00 3.01
54 55 4.574421 CGAATATGGATGTTGTAGTTGGCA 59.426 41.667 0.00 0.00 0.00 4.92
132 133 3.555956 GCCATAGGTGTCGATGTTACAAG 59.444 47.826 0.00 0.00 0.00 3.16
153 154 1.299089 GAGTTGCAACCACCAACGC 60.299 57.895 25.62 0.00 45.38 4.84
160 161 1.821759 CACGTGGGAGTTGCAACCA 60.822 57.895 25.62 14.41 0.00 3.67
190 191 2.159819 ATCCACGTTCACGCAGAGCT 62.160 55.000 0.00 0.00 44.43 4.09
291 313 1.074319 GCATAACGCGAGGTTGACGA 61.074 55.000 15.93 0.00 39.75 4.20
347 377 3.242712 GTGTTGCCACGAACATTCTTTTG 59.757 43.478 0.00 0.00 38.11 2.44
535 567 3.086600 GGCCACCTCCTCCTCCAG 61.087 72.222 0.00 0.00 0.00 3.86
558 590 3.074369 TCTTCCCCGATGCTCGCA 61.074 61.111 0.00 0.00 38.82 5.10
583 615 4.166011 GCCGCCAATGTCGTGCTC 62.166 66.667 0.00 0.00 0.00 4.26
609 641 2.441901 CGCTCTGCTCCTCTCCCT 60.442 66.667 0.00 0.00 0.00 4.20
650 682 5.948758 CCTGCTTATCTTCTTTTTCCCTCTT 59.051 40.000 0.00 0.00 0.00 2.85
713 745 4.299796 ACCCGCAAATGCCAGGGT 62.300 61.111 15.68 15.68 45.93 4.34
736 796 2.203394 CCAATGCTAGGGCGCCAT 60.203 61.111 30.85 26.24 42.25 4.40
778 838 3.729906 CTCCCGGTCGCGTAACTCG 62.730 68.421 5.77 4.04 43.12 4.18
782 842 2.879907 CTTCTCCCGGTCGCGTAA 59.120 61.111 5.77 0.00 0.00 3.18
795 855 1.671379 GGGAAACGCCGAAGCTTCT 60.671 57.895 23.50 4.03 37.63 2.85
833 893 7.954666 TTTATGGAATGGAAAGGGTCTAAAG 57.045 36.000 0.00 0.00 0.00 1.85
858 919 2.290960 CGAAGGGGAAGGTGGATTTTCT 60.291 50.000 0.00 0.00 0.00 2.52
954 1029 2.056223 GGCTAGGTGGTACGAGGCA 61.056 63.158 0.00 0.00 34.76 4.75
1158 1233 2.012673 GCAATGATCTCGGCTTTGACT 58.987 47.619 0.00 0.00 0.00 3.41
1174 1249 3.949754 CAGTACTTGATGACCATGGCAAT 59.050 43.478 13.04 5.42 0.00 3.56
1219 1294 1.882989 GAGTCTGTGGCTTCGGCTCT 61.883 60.000 0.00 0.00 41.44 4.09
1299 1374 2.430244 TCGAAGAGGACGCGTTGC 60.430 61.111 15.53 5.97 0.00 4.17
1388 1481 4.099113 ACCGCCTCTAAATAGTAGGAACAC 59.901 45.833 8.99 0.00 31.64 3.32
1396 1489 5.048991 CACAACAAAACCGCCTCTAAATAGT 60.049 40.000 0.00 0.00 0.00 2.12
1596 1697 6.273825 TGATCCAGTATACGAAGAGAAAAGC 58.726 40.000 0.00 0.00 0.00 3.51
1627 1729 4.709397 CCCTTTCCTTGCATGTATTTGGTA 59.291 41.667 0.00 0.00 0.00 3.25
1686 1788 5.581874 AGCAACCTATTTAAAACATGCATGC 59.418 36.000 26.53 11.82 35.11 4.06
1687 1789 7.975616 ACTAGCAACCTATTTAAAACATGCATG 59.024 33.333 25.09 25.09 35.11 4.06
1688 1790 8.066612 ACTAGCAACCTATTTAAAACATGCAT 57.933 30.769 0.00 0.00 35.11 3.96
1689 1791 7.461182 ACTAGCAACCTATTTAAAACATGCA 57.539 32.000 13.57 0.00 35.11 3.96
1791 1893 5.974370 ACTCCCCCATTTACTTATACAAGGA 59.026 40.000 0.00 0.00 35.97 3.36
1819 1922 3.378742 CAGAGTACCTGCAACGAGTCTAT 59.621 47.826 0.00 0.00 35.89 1.98
1865 1968 8.465999 CCAATATTTTGCAGAATACCTGTAACA 58.534 33.333 11.55 0.00 45.11 2.41
1869 1972 7.716799 TTCCAATATTTTGCAGAATACCTGT 57.283 32.000 11.55 0.00 44.71 4.00
1955 2061 8.601546 TGGCAATTAACCCAGAAATTAGAAAAT 58.398 29.630 0.00 0.00 0.00 1.82
2022 2128 9.793259 CATATAATAGTTGTTCCACCCTATTGT 57.207 33.333 0.00 0.00 33.44 2.71
2030 2139 8.894768 AGCTCTTCATATAATAGTTGTTCCAC 57.105 34.615 0.00 0.00 0.00 4.02
2070 3559 4.281688 AGCAAATAAGGCAACACACTTCAT 59.718 37.500 0.00 0.00 41.41 2.57
2079 3569 7.812669 AGTAAACACATTAGCAAATAAGGCAAC 59.187 33.333 0.00 0.00 0.00 4.17
2163 3795 9.593134 TTTTGTTGTTGTAGAAAAGCACAATAT 57.407 25.926 0.00 0.00 37.04 1.28
2182 3814 8.801715 ACTAAGCACAATACTGATTTTTGTTG 57.198 30.769 0.00 0.00 31.48 3.33
2188 3820 9.573133 GCATTTAACTAAGCACAATACTGATTT 57.427 29.630 0.00 0.00 0.00 2.17
2189 3821 8.739039 TGCATTTAACTAAGCACAATACTGATT 58.261 29.630 0.00 0.00 31.05 2.57
2216 3848 5.245531 TCAACAATGTGTAGAAAGCTAGGG 58.754 41.667 0.00 0.00 0.00 3.53
2236 3868 8.786898 CAAATTAACTCAGGAGACAGAAATCAA 58.213 33.333 2.79 0.00 0.00 2.57
2247 3879 7.856145 AGAGTAATGCAAATTAACTCAGGAG 57.144 36.000 15.25 0.00 0.00 3.69
2340 3979 9.453572 AAATGCAAGTCAGATAGTTCAGATTTA 57.546 29.630 0.00 0.00 0.00 1.40
2564 4203 7.168219 TCAAAGAAAGCTCACATACCTTACAT 58.832 34.615 0.00 0.00 0.00 2.29
2572 4211 6.016024 ACAAAGCATCAAAGAAAGCTCACATA 60.016 34.615 0.00 0.00 36.07 2.29
2629 4268 7.790027 AGATCACTAACAGTAGCATTCTCATT 58.210 34.615 0.00 0.00 0.00 2.57
2941 4582 2.602257 TACAACATGATGAGGGAGCG 57.398 50.000 10.29 0.00 0.00 5.03
3191 4964 0.747283 GGCAGGTCAGATCCAGCAAG 60.747 60.000 8.13 0.00 40.92 4.01
3268 5041 1.967779 TGGTGAGGTCGTTCTTGATGA 59.032 47.619 0.00 0.00 0.00 2.92
3343 5116 6.665695 AGTTGTTTCTTTAGTTTACCCCTCA 58.334 36.000 0.00 0.00 0.00 3.86
3372 5147 3.871006 CCTTGCTAGTCATTCGCATTACA 59.129 43.478 0.00 0.00 33.15 2.41
3421 5196 1.425412 AACAGTTAACGGCTACTGCG 58.575 50.000 5.60 0.00 44.34 5.18
3423 5198 3.059188 CCACAAACAGTTAACGGCTACTG 60.059 47.826 5.60 10.34 45.61 2.74
3437 5212 3.880490 AGCATAGTTTCGAACCACAAACA 59.120 39.130 0.00 0.00 35.33 2.83
3472 5450 4.003648 CTGGAACCAGACCAATGTACTTC 58.996 47.826 14.94 0.00 46.30 3.01
3554 5532 7.882791 TCATAATAACCAAGTTCAAGAGAGCAA 59.117 33.333 0.00 0.00 0.00 3.91
3558 5536 9.793259 AAACTCATAATAACCAAGTTCAAGAGA 57.207 29.630 0.00 0.00 30.23 3.10
3692 5670 6.426633 ACAACATCATAACAACATGACTTCGA 59.573 34.615 0.00 0.00 37.74 3.71
3749 5727 0.967380 GGGATGCCAGGGTTGAACAG 60.967 60.000 0.00 0.00 0.00 3.16
3844 5822 5.690097 GCCAGGGTTGACATATTGAATAGGA 60.690 44.000 3.65 0.00 0.00 2.94
3866 5844 0.833287 TAGAGTTGCCCTGAGATGCC 59.167 55.000 0.00 0.00 0.00 4.40
3889 5867 0.179129 GCGGGCAATTTGGTGATCTG 60.179 55.000 0.00 0.00 0.00 2.90
3902 5880 2.244117 GATCTGGACTTCTGCGGGCA 62.244 60.000 0.00 0.00 0.00 5.36
3910 5888 3.509575 AGTGAGTGTCTGATCTGGACTTC 59.490 47.826 16.20 14.09 35.04 3.01
3922 5900 2.508526 GATGGCCAAAAGTGAGTGTCT 58.491 47.619 10.96 0.00 0.00 3.41
3938 5916 3.931907 TTGATGACCCTAGTTGGATGG 57.068 47.619 0.00 0.00 38.35 3.51
4115 6093 0.320771 ACAACAGTGATGCCGGAGTC 60.321 55.000 5.05 1.84 0.00 3.36
4127 6105 1.068127 GTGTCCTCGTGGTACAACAGT 59.932 52.381 0.35 0.00 44.16 3.55
4128 6106 1.604693 GGTGTCCTCGTGGTACAACAG 60.605 57.143 14.97 0.00 44.16 3.16
4170 6148 2.750657 GCATCTGGGTGGAGAGGGG 61.751 68.421 0.00 0.00 0.00 4.79
4186 6164 3.934909 TATGCAAAGCCGGGCAGCA 62.935 57.895 27.58 27.58 44.24 4.41
4189 6167 3.130819 CGTATGCAAAGCCGGGCA 61.131 61.111 23.09 4.17 45.23 5.36
4191 6169 3.887868 GGCGTATGCAAAGCCGGG 61.888 66.667 9.59 0.00 43.09 5.73
4202 6180 0.694444 AGGGTGGAATGGAGGCGTAT 60.694 55.000 0.00 0.00 0.00 3.06
4212 6190 3.165071 GTGGTTGATTTCAGGGTGGAAT 58.835 45.455 0.00 0.00 0.00 3.01
4238 6216 0.112606 TAGAGGGCGGAGGATACCTG 59.887 60.000 0.00 0.00 31.76 4.00
4249 6227 2.045280 CCTCCATGAGTAGAGGGCG 58.955 63.158 7.63 0.00 45.08 6.13
4265 6251 2.365617 CACTTGTCGGGCATAGTATCCT 59.634 50.000 0.00 0.00 0.00 3.24
4274 6260 2.280524 CCGAACACTTGTCGGGCA 60.281 61.111 4.95 0.00 42.70 5.36
4275 6261 3.723348 GCCGAACACTTGTCGGGC 61.723 66.667 14.17 12.63 46.10 6.13


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

AutoCloner maintained by Alex Coulton.