Multiple sequence alignment - TraesCS5D01G098800

Loading Multiple Alignment...

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 TraesCS5D01G098800 chr5D 100.000 5704 0 0 1 5704 110365406 110371109 0.000000e+00 10534.0
1 TraesCS5D01G098800 chr5D 87.422 4023 421 46 78 4053 110347036 110351020 0.000000e+00 4547.0
2 TraesCS5D01G098800 chr5D 74.003 1204 293 15 1939 3135 109943834 109942644 6.690000e-129 472.0
3 TraesCS5D01G098800 chr5D 100.000 28 0 0 5090 5117 461621618 461621591 1.000000e-02 52.8
4 TraesCS5D01G098800 chr5A 96.201 4054 138 10 7 4059 116588164 116584126 0.000000e+00 6619.0
5 TraesCS5D01G098800 chr5A 88.034 1872 207 11 2191 4059 116776535 116774678 0.000000e+00 2200.0
6 TraesCS5D01G098800 chr5A 89.784 1576 153 5 1795 3366 116697564 116695993 0.000000e+00 2012.0
7 TraesCS5D01G098800 chr5A 85.993 1742 197 23 73 1798 116781147 116779437 0.000000e+00 1821.0
8 TraesCS5D01G098800 chr5A 87.154 1300 138 11 503 1798 116698864 116697590 0.000000e+00 1448.0
9 TraesCS5D01G098800 chr5A 93.032 818 52 4 4219 5033 116583898 116583083 0.000000e+00 1190.0
10 TraesCS5D01G098800 chr5A 87.348 656 71 10 3407 4059 116695992 116695346 0.000000e+00 741.0
11 TraesCS5D01G098800 chr5A 92.388 381 27 1 1795 2173 116779411 116779031 5.030000e-150 542.0
12 TraesCS5D01G098800 chr5A 93.141 277 8 4 5437 5704 116582270 116581996 4.140000e-106 396.0
13 TraesCS5D01G098800 chr5A 73.490 811 196 13 2329 3135 117388437 117389232 7.230000e-74 289.0
14 TraesCS5D01G098800 chr5A 83.444 151 12 6 5162 5300 116582884 116582735 1.670000e-25 128.0
15 TraesCS5D01G098800 chr5A 100.000 38 0 0 5346 5383 116582297 116582260 2.850000e-08 71.3
16 TraesCS5D01G098800 chr5B 88.279 5119 483 59 78 5138 122439466 122434407 0.000000e+00 6021.0
17 TraesCS5D01G098800 chr5B 74.421 1208 281 20 1939 3135 122831446 122832636 1.430000e-135 494.0
18 TraesCS5D01G098800 chr5B 95.588 272 8 2 5437 5704 122432050 122431779 3.160000e-117 433.0
19 TraesCS5D01G098800 chr5B 95.556 135 5 1 5257 5390 122434073 122433939 1.240000e-51 215.0
20 TraesCS5D01G098800 chr5B 97.600 125 2 1 5135 5259 122434356 122434233 4.480000e-51 213.0
21 TraesCS5D01G098800 chrUn 87.013 385 46 2 665 1046 480886713 480887096 1.140000e-116 431.0
22 TraesCS5D01G098800 chr3A 88.333 60 5 2 5087 5144 41615101 41615160 2.850000e-08 71.3
23 TraesCS5D01G098800 chr3B 84.058 69 9 2 1855 1922 829213233 829213300 1.330000e-06 65.8
24 TraesCS5D01G098800 chr3B 100.000 31 0 0 1855 1885 817011814 817011784 2.220000e-04 58.4
25 TraesCS5D01G098800 chr3D 100.000 28 0 0 5090 5117 477826650 477826623 1.000000e-02 52.8


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 TraesCS5D01G098800 chr5D 110365406 110371109 5703 False 10534.000000 10534 100.000000 1 5704 1 chr5D.!!$F2 5703
1 TraesCS5D01G098800 chr5D 110347036 110351020 3984 False 4547.000000 4547 87.422000 78 4053 1 chr5D.!!$F1 3975
2 TraesCS5D01G098800 chr5D 109942644 109943834 1190 True 472.000000 472 74.003000 1939 3135 1 chr5D.!!$R1 1196
3 TraesCS5D01G098800 chr5A 116581996 116588164 6168 True 1680.860000 6619 93.163600 7 5704 5 chr5A.!!$R1 5697
4 TraesCS5D01G098800 chr5A 116774678 116781147 6469 True 1521.000000 2200 88.805000 73 4059 3 chr5A.!!$R3 3986
5 TraesCS5D01G098800 chr5A 116695346 116698864 3518 True 1400.333333 2012 88.095333 503 4059 3 chr5A.!!$R2 3556
6 TraesCS5D01G098800 chr5A 117388437 117389232 795 False 289.000000 289 73.490000 2329 3135 1 chr5A.!!$F1 806
7 TraesCS5D01G098800 chr5B 122431779 122439466 7687 True 1720.500000 6021 94.255750 78 5704 4 chr5B.!!$R1 5626
8 TraesCS5D01G098800 chr5B 122831446 122832636 1190 False 494.000000 494 74.421000 1939 3135 1 chr5B.!!$F1 1196

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
588 602 0.754587 TGGTGCAGGCAATTCACACA 60.755 50.0 0.00 0.0 32.89 3.72 F
1107 1127 0.596600 TGTCGAGTCCAGTCGCAAAC 60.597 55.0 0.00 0.0 39.90 2.93 F
1428 1448 0.555769 AGGTGGTGTCCATTGTTGGT 59.444 50.0 0.00 0.0 44.06 3.67 F
1976 2030 0.317519 CGCGTATCATCACCGTAGCA 60.318 55.0 0.00 0.0 0.00 3.49 F
3380 5914 0.912486 GGGTAGCCTCACTTGACCAT 59.088 55.0 2.95 0.0 29.60 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1411 1.358725 CTTTAGCTGCTGCGCCGTTA 61.359 55.000 13.43 0.0 45.42 3.18 R
1976 2030 3.063510 TGCTGAGAGCTGCAATACTTT 57.936 42.857 1.02 0.0 44.50 2.66 R
3401 5935 0.031314 CCTCATCCACTGGATCGACG 59.969 60.000 7.69 0.0 40.98 5.12 R
3542 6116 0.685097 TGTCCCAGCAGGTGAAGTAC 59.315 55.000 0.00 0.0 36.75 2.73 R
4724 7383 0.107456 CTCGGCTAATCATGGCACCT 59.893 55.000 0.00 0.0 34.13 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
20 21 2.413310 AACGTTTTCCACTGGTGTCT 57.587 45.000 0.00 0.00 0.00 3.41
257 268 3.305398 AATCACGGTCTCTGTCTTCAC 57.695 47.619 0.00 0.00 0.00 3.18
460 474 9.965902 ATCTATGGTGATTTATATCTTTCCACC 57.034 33.333 0.00 0.00 41.98 4.61
550 564 7.984617 GGCTTATGACTTCTTCTCTTGACTAAT 59.015 37.037 0.00 0.00 0.00 1.73
588 602 0.754587 TGGTGCAGGCAATTCACACA 60.755 50.000 0.00 0.00 32.89 3.72
604 618 5.246981 TCACACATCCTTTCCTTCTTGAT 57.753 39.130 0.00 0.00 0.00 2.57
657 671 6.699575 ACCATCTGTGCTTTTTATATGGTC 57.300 37.500 0.00 0.00 41.24 4.02
998 1018 1.492764 TATCCGAGTTTGAGGACCCC 58.507 55.000 0.00 0.00 39.66 4.95
1058 1078 1.359475 GTCCTACGACATCGAGGGC 59.641 63.158 8.54 8.25 43.02 5.19
1090 1110 1.426251 TTCATGCTGTCCCTGGGTGT 61.426 55.000 13.56 0.00 0.00 4.16
1100 1120 1.908793 CCTGGGTGTCGAGTCCAGT 60.909 63.158 20.43 0.00 44.78 4.00
1107 1127 0.596600 TGTCGAGTCCAGTCGCAAAC 60.597 55.000 0.00 0.00 39.90 2.93
1108 1128 1.371267 TCGAGTCCAGTCGCAAACG 60.371 57.895 0.00 0.00 39.90 3.60
1109 1129 2.372690 CGAGTCCAGTCGCAAACGG 61.373 63.158 0.00 0.00 40.63 4.44
1110 1130 2.665185 AGTCCAGTCGCAAACGGC 60.665 61.111 0.00 0.00 46.74 5.68
1268 1288 6.777580 AGGTACAAGGTTGATGATGTTTTCTT 59.222 34.615 0.00 0.00 0.00 2.52
1296 1316 2.368221 GAGCAGGACAAGCATAGATCCT 59.632 50.000 0.00 0.00 42.52 3.24
1354 1374 2.192979 GCATCGATGGCCCAAGGA 59.807 61.111 26.00 0.00 0.00 3.36
1391 1411 2.375174 TGCTAACAGAAGGGGAATGTGT 59.625 45.455 0.00 0.00 0.00 3.72
1428 1448 0.555769 AGGTGGTGTCCATTGTTGGT 59.444 50.000 0.00 0.00 44.06 3.67
1494 1514 1.457346 AGCTCGAAGGGCAATTTGAG 58.543 50.000 12.36 12.36 41.73 3.02
1808 1862 3.762407 TTGCTTACTACTGCTTCACCA 57.238 42.857 0.00 0.00 0.00 4.17
1813 1867 4.799586 GCTTACTACTGCTTCACCAGTTGA 60.800 45.833 9.93 0.00 43.19 3.18
1976 2030 0.317519 CGCGTATCATCACCGTAGCA 60.318 55.000 0.00 0.00 0.00 3.49
2007 2061 2.144730 GCTCTCAGCACCATGATCATC 58.855 52.381 4.86 0.00 41.89 2.92
2216 4748 3.300388 AGAAGAATGGCTGAGGATACGA 58.700 45.455 0.00 0.00 46.39 3.43
2633 5165 2.658285 CCGTATGATAAGGTTCGTCGG 58.342 52.381 0.00 0.00 0.00 4.79
2792 5326 6.418057 AGAGTGCTGGATCTAGAAAATAGG 57.582 41.667 10.75 0.00 0.00 2.57
2812 5346 3.387699 AGGGAGGTTTTGGAACACAATTG 59.612 43.478 3.24 3.24 39.29 2.32
2827 5361 9.522804 GGAACACAATTGTCTTAAACACATAAA 57.477 29.630 8.48 0.00 37.70 1.40
2938 5472 7.181125 ACAGACCTTAGACTTAAGATGGACATT 59.819 37.037 10.09 0.00 38.88 2.71
3125 5659 3.686726 GCACTCTGACCAAACTAAGGATG 59.313 47.826 0.00 0.00 0.00 3.51
3299 5833 2.106684 ACTTGACTCTTGGTTTCCTCCC 59.893 50.000 0.00 0.00 0.00 4.30
3303 5837 1.076438 CTCTTGGTTTCCTCCCCCTT 58.924 55.000 0.00 0.00 0.00 3.95
3306 5840 0.938192 TTGGTTTCCTCCCCCTTGTT 59.062 50.000 0.00 0.00 0.00 2.83
3308 5842 1.133294 TGGTTTCCTCCCCCTTGTTTC 60.133 52.381 0.00 0.00 0.00 2.78
3380 5914 0.912486 GGGTAGCCTCACTTGACCAT 59.088 55.000 2.95 0.00 29.60 3.55
3392 5926 5.827756 TCACTTGACCATCTCTCTTACCTA 58.172 41.667 0.00 0.00 0.00 3.08
3393 5927 5.888724 TCACTTGACCATCTCTCTTACCTAG 59.111 44.000 0.00 0.00 0.00 3.02
3399 5933 4.140805 ACCATCTCTCTTACCTAGGCATCT 60.141 45.833 9.30 0.00 0.00 2.90
3401 5935 5.417580 CCATCTCTCTTACCTAGGCATCTAC 59.582 48.000 9.30 0.00 0.00 2.59
3405 5939 3.136763 TCTTACCTAGGCATCTACGTCG 58.863 50.000 9.30 0.00 0.00 5.12
3551 6125 4.652822 ACCTGAAGGAATTGTACTTCACC 58.347 43.478 2.62 0.00 45.76 4.02
3648 6222 1.026182 TGCGCATGATGTGTTCCCTC 61.026 55.000 5.66 0.00 0.00 4.30
3651 6225 1.676916 CGCATGATGTGTTCCCTCTGT 60.677 52.381 0.00 0.00 0.00 3.41
3681 6255 4.096984 GTCTTGATTTCGGCATCCAGAATT 59.903 41.667 1.65 0.00 29.19 2.17
3683 6257 5.885352 TCTTGATTTCGGCATCCAGAATTTA 59.115 36.000 0.00 0.00 0.00 1.40
3684 6258 5.499139 TGATTTCGGCATCCAGAATTTAC 57.501 39.130 0.00 0.00 0.00 2.01
3734 6308 0.800012 TTTGTTATGGCGCGAAGGTC 59.200 50.000 12.10 0.00 0.00 3.85
3735 6309 0.036765 TTGTTATGGCGCGAAGGTCT 60.037 50.000 12.10 0.00 0.00 3.85
3779 6353 1.531423 CTGTCAAGAATGCAGCTGGT 58.469 50.000 17.12 0.00 0.00 4.00
3797 6371 4.070716 CTGGTTGTCTTTCAGATGAGCTT 58.929 43.478 0.00 0.00 0.00 3.74
3824 6398 5.362143 TCTTGAAGTGAGTAGATGGGATGAG 59.638 44.000 0.00 0.00 0.00 2.90
3887 6461 2.821969 GGAGGTTGATGCTGACAATTGT 59.178 45.455 11.78 11.78 0.00 2.71
3916 6490 0.524862 ACGCCGTTGAGGTACTACTG 59.475 55.000 0.00 0.00 41.55 2.74
3931 6508 4.576216 ACTACTGATTCTCGTATGCCAG 57.424 45.455 0.00 0.00 0.00 4.85
3932 6509 2.898729 ACTGATTCTCGTATGCCAGG 57.101 50.000 0.00 0.00 0.00 4.45
3939 6516 0.176680 CTCGTATGCCAGGACTGCTT 59.823 55.000 0.00 0.00 0.00 3.91
4020 6597 5.070847 GGAATGTAGGATGGGCATGAAAATT 59.929 40.000 0.00 0.00 0.00 1.82
4083 6661 2.289945 CCGGGATCCTTGATCTTCCATC 60.290 54.545 12.58 0.00 38.91 3.51
4088 6666 5.073691 GGGATCCTTGATCTTCCATCCTTAA 59.926 44.000 12.58 0.00 38.91 1.85
4127 6705 2.444421 CTCTCTTGCCAATGAAGCCTT 58.556 47.619 0.00 0.00 0.00 4.35
4149 6727 7.705325 GCCTTCTAGTTTCATAGAATCGTGTAA 59.295 37.037 0.00 0.00 40.18 2.41
4217 6796 5.181811 CAGACTGATGAACCTGCACAATTTA 59.818 40.000 0.00 0.00 0.00 1.40
4253 6899 8.028938 TGCTTCTATAGGAAAATTTGAGCAAAC 58.971 33.333 0.00 0.00 33.07 2.93
4265 6911 3.921119 TGAGCAAACGCAGATTGATTT 57.079 38.095 3.50 0.00 39.43 2.17
4323 6969 6.968131 TTAGTTCATTGAGAAACCAGATCG 57.032 37.500 0.00 0.00 38.13 3.69
4369 7015 5.368256 TGCATCTTTTCTTCTTCTTCTGC 57.632 39.130 0.00 0.00 0.00 4.26
4375 7021 5.584649 TCTTTTCTTCTTCTTCTGCGAAACA 59.415 36.000 0.00 0.00 0.00 2.83
4474 7122 1.391157 TTTGCTCTGGTGTTGGTGCC 61.391 55.000 0.00 0.00 0.00 5.01
4487 7143 4.332819 GTGTTGGTGCCACTATCAGTATTC 59.667 45.833 0.00 0.00 0.00 1.75
4494 7150 6.109359 GTGCCACTATCAGTATTCTGTCTTT 58.891 40.000 0.00 0.00 41.91 2.52
4622 7280 3.691049 TTCAACTTTCTCAGTTTGCCG 57.309 42.857 0.00 0.00 43.89 5.69
4629 7287 4.583073 ACTTTCTCAGTTTGCCGGTTATTT 59.417 37.500 1.90 0.00 27.32 1.40
4724 7383 3.716006 GCTGAAACTCGCTGCGCA 61.716 61.111 18.65 10.98 0.00 6.09
4740 7399 1.789078 CGCAGGTGCCATGATTAGCC 61.789 60.000 0.00 0.00 37.91 3.93
4776 7435 2.143925 GTGTGGACTGCTCTTACCAAC 58.856 52.381 0.00 0.00 34.11 3.77
4858 7518 2.014068 GCTCGAAGACCCCATTTGGAG 61.014 57.143 0.00 0.00 37.39 3.86
4859 7519 1.279271 CTCGAAGACCCCATTTGGAGT 59.721 52.381 0.00 0.00 37.39 3.85
4877 7537 3.008049 GGAGTTCTGGAAGTTGCTCCTAA 59.992 47.826 9.20 0.00 40.84 2.69
4923 7583 0.994263 GCGAAACAGAAATGGCATGC 59.006 50.000 9.90 9.90 0.00 4.06
4976 7636 1.486211 TGGCGGAAACCCTTTTCAAA 58.514 45.000 0.00 0.00 42.72 2.69
4997 7657 4.900635 ATTGCCAGTTCCATTTCGTATC 57.099 40.909 0.00 0.00 0.00 2.24
5035 7695 1.745232 TGTTTAACGCATGCTAGGGG 58.255 50.000 17.13 1.61 0.00 4.79
5036 7696 1.279558 TGTTTAACGCATGCTAGGGGA 59.720 47.619 17.13 0.00 0.00 4.81
5058 7802 6.463331 GGGATTGAACATGATAACATTGGCAT 60.463 38.462 0.00 0.00 34.15 4.40
5105 7849 3.870419 CACTAGTGACTACTACCTCCGTC 59.130 52.174 18.45 0.00 38.36 4.79
5383 10668 6.463995 TTCAAACTGTAATTTCAGTGGCTT 57.536 33.333 17.24 6.64 46.25 4.35
5384 10669 6.463995 TCAAACTGTAATTTCAGTGGCTTT 57.536 33.333 17.24 6.32 46.25 3.51
5385 10670 6.872920 TCAAACTGTAATTTCAGTGGCTTTT 58.127 32.000 17.24 5.99 46.25 2.27
5386 10671 7.327214 TCAAACTGTAATTTCAGTGGCTTTTT 58.673 30.769 17.24 5.35 46.25 1.94
5411 10696 5.766150 TTGAGTGGTTGTAATTTCAGTGG 57.234 39.130 0.00 0.00 0.00 4.00
5412 10697 3.568007 TGAGTGGTTGTAATTTCAGTGGC 59.432 43.478 0.00 0.00 0.00 5.01
5413 10698 3.821033 GAGTGGTTGTAATTTCAGTGGCT 59.179 43.478 0.00 0.00 0.00 4.75
5414 10699 4.980573 AGTGGTTGTAATTTCAGTGGCTA 58.019 39.130 0.00 0.00 0.00 3.93
5415 10700 5.003804 AGTGGTTGTAATTTCAGTGGCTAG 58.996 41.667 0.00 0.00 0.00 3.42
5416 10701 5.001232 GTGGTTGTAATTTCAGTGGCTAGA 58.999 41.667 0.00 0.00 0.00 2.43
5417 10702 5.648092 GTGGTTGTAATTTCAGTGGCTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
5418 10703 6.151144 GTGGTTGTAATTTCAGTGGCTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
5419 10704 6.719370 TGGTTGTAATTTCAGTGGCTAGATTT 59.281 34.615 0.00 0.00 0.00 2.17
5420 10705 7.232534 TGGTTGTAATTTCAGTGGCTAGATTTT 59.767 33.333 0.00 0.00 0.00 1.82
5421 10706 8.088365 GGTTGTAATTTCAGTGGCTAGATTTTT 58.912 33.333 0.00 0.00 0.00 1.94
5445 10730 4.900635 TCTTGAGAAACTTTTCAGTGGC 57.099 40.909 4.58 0.00 39.61 5.01
5446 10731 4.526970 TCTTGAGAAACTTTTCAGTGGCT 58.473 39.130 4.58 0.00 39.61 4.75
5447 10732 5.680619 TCTTGAGAAACTTTTCAGTGGCTA 58.319 37.500 4.58 0.00 39.61 3.93
5448 10733 6.299141 TCTTGAGAAACTTTTCAGTGGCTAT 58.701 36.000 4.58 0.00 39.61 2.97
5508 10793 2.301870 ACCCAACGAGACAGAAGCATAA 59.698 45.455 0.00 0.00 0.00 1.90
5666 10962 1.662686 AAGGGAGAAGAGAACCCCAG 58.337 55.000 0.00 0.00 44.21 4.45
5668 10964 1.152271 AGGGAGAAGAGAACCCCAGAA 59.848 52.381 0.00 0.00 44.21 3.02
5669 10965 1.557371 GGGAGAAGAGAACCCCAGAAG 59.443 57.143 0.00 0.00 38.69 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.422127 CAGACACCAGTGGAAAACGTTT 59.578 45.455 18.40 7.96 34.19 3.60
1 2 2.014128 CAGACACCAGTGGAAAACGTT 58.986 47.619 18.40 0.00 34.19 3.99
2 3 1.208535 TCAGACACCAGTGGAAAACGT 59.791 47.619 18.40 4.40 34.19 3.99
4 5 2.919228 AGTCAGACACCAGTGGAAAAC 58.081 47.619 18.40 5.08 34.19 2.43
5 6 3.644966 AAGTCAGACACCAGTGGAAAA 57.355 42.857 18.40 0.00 34.19 2.29
6 7 3.278574 CAAAGTCAGACACCAGTGGAAA 58.721 45.455 18.40 0.00 34.19 3.13
9 10 2.332063 ACAAAGTCAGACACCAGTGG 57.668 50.000 7.91 7.91 34.19 4.00
10 11 4.631131 TGATACAAAGTCAGACACCAGTG 58.369 43.478 2.66 0.00 0.00 3.66
11 12 4.955811 TGATACAAAGTCAGACACCAGT 57.044 40.909 2.66 0.00 0.00 4.00
12 13 6.401474 CGATTTGATACAAAGTCAGACACCAG 60.401 42.308 2.66 0.00 0.00 4.00
13 14 5.408299 CGATTTGATACAAAGTCAGACACCA 59.592 40.000 2.66 0.00 0.00 4.17
14 15 5.163854 CCGATTTGATACAAAGTCAGACACC 60.164 44.000 2.66 0.00 0.00 4.16
15 16 5.671329 GCCGATTTGATACAAAGTCAGACAC 60.671 44.000 2.66 0.00 0.00 3.67
16 17 4.391830 GCCGATTTGATACAAAGTCAGACA 59.608 41.667 2.66 0.00 0.00 3.41
17 18 4.492570 CGCCGATTTGATACAAAGTCAGAC 60.493 45.833 0.00 0.00 0.00 3.51
18 19 3.616821 CGCCGATTTGATACAAAGTCAGA 59.383 43.478 0.00 0.00 0.00 3.27
19 20 3.242413 CCGCCGATTTGATACAAAGTCAG 60.242 47.826 0.00 0.00 0.00 3.51
20 21 2.675844 CCGCCGATTTGATACAAAGTCA 59.324 45.455 0.00 0.00 0.00 3.41
257 268 4.019860 CCATGGTGTCTGATATAAGAGGGG 60.020 50.000 2.57 0.00 0.00 4.79
511 525 5.324409 AGTCATAAGCCACCAAATGAGAAA 58.676 37.500 0.00 0.00 0.00 2.52
550 564 1.792367 CACGATTGCAAAGTCAGTCGA 59.208 47.619 21.02 0.00 45.21 4.20
588 602 7.609532 CAGTCAAGTTATCAAGAAGGAAAGGAT 59.390 37.037 0.00 0.00 0.00 3.24
604 618 5.748152 GCACATTTCAAAAGCAGTCAAGTTA 59.252 36.000 0.00 0.00 0.00 2.24
657 671 2.110967 CAGGTGCCCGCAGAATCTG 61.111 63.158 5.78 5.78 34.12 2.90
780 794 2.086610 AGTTTTTGTGTCCCTGCCAT 57.913 45.000 0.00 0.00 0.00 4.40
998 1018 0.390866 AGCACTTGGACAGCTCATCG 60.391 55.000 0.00 0.00 32.05 3.84
1058 1078 1.200716 AGCATGAAACTGTCAATGCCG 59.799 47.619 14.78 0.00 40.50 5.69
1090 1110 1.371267 CGTTTGCGACTGGACTCGA 60.371 57.895 0.00 0.00 41.33 4.04
1100 1120 3.597728 GGGGTTTGCCGTTTGCGA 61.598 61.111 0.00 0.00 45.60 5.10
1119 1139 3.710722 AGGAGTCCCTTGCAGCCG 61.711 66.667 5.25 0.00 40.78 5.52
1268 1288 2.922503 TTGTCCTGCTCGGCCTGA 60.923 61.111 0.00 0.00 0.00 3.86
1354 1374 8.621532 TCTGTTAGCAACTTGATGAGTTTATT 57.378 30.769 0.00 0.00 46.34 1.40
1391 1411 1.358725 CTTTAGCTGCTGCGCCGTTA 61.359 55.000 13.43 0.00 45.42 3.18
1428 1448 2.091333 AGTCTTTCCAAGGCCTCCAAAA 60.091 45.455 5.23 5.96 32.16 2.44
1494 1514 2.092211 CACCGACACGAAAGCTTGATAC 59.908 50.000 0.00 0.00 0.00 2.24
1808 1862 8.409358 AAACATGTATTCCTAAAGCTTCAACT 57.591 30.769 0.00 0.00 0.00 3.16
1976 2030 3.063510 TGCTGAGAGCTGCAATACTTT 57.936 42.857 1.02 0.00 44.50 2.66
2007 2061 7.280876 TGCACTAAGAGGCTTTATTTCATACAG 59.719 37.037 0.00 0.00 0.00 2.74
2216 4748 6.899393 TCAAGTGCTGAACCAATAGAATTT 57.101 33.333 0.00 0.00 0.00 1.82
2607 5139 3.363970 CGAACCTTATCATACGGCAATGC 60.364 47.826 0.00 0.00 0.00 3.56
2633 5165 4.020751 TGAGCATGATAGTTCAGGGATAGC 60.021 45.833 0.00 0.00 34.26 2.97
2792 5326 4.099419 AGACAATTGTGTTCCAAAACCTCC 59.901 41.667 17.58 0.00 38.41 4.30
2812 5346 7.649057 AGAAAGCCTGTTTATGTGTTTAAGAC 58.351 34.615 0.00 0.00 0.00 3.01
3299 5833 5.560724 TCAAATCTCTGTAGGAAACAAGGG 58.439 41.667 0.00 0.00 37.74 3.95
3303 5837 7.487822 AGATCTCAAATCTCTGTAGGAAACA 57.512 36.000 0.00 0.00 36.42 2.83
3367 5901 4.142049 GGTAAGAGAGATGGTCAAGTGAGG 60.142 50.000 0.00 0.00 0.00 3.86
3380 5914 4.102838 ACGTAGATGCCTAGGTAAGAGAGA 59.897 45.833 11.31 0.00 40.86 3.10
3392 5926 0.955178 CTGGATCGACGTAGATGCCT 59.045 55.000 23.31 0.00 38.05 4.75
3393 5927 0.669077 ACTGGATCGACGTAGATGCC 59.331 55.000 23.31 18.86 38.05 4.40
3399 5933 1.947456 CTCATCCACTGGATCGACGTA 59.053 52.381 7.69 0.00 40.98 3.57
3401 5935 0.031314 CCTCATCCACTGGATCGACG 59.969 60.000 7.69 0.00 40.98 5.12
3405 5939 3.634397 TGTTTCCTCATCCACTGGATC 57.366 47.619 7.69 0.00 40.98 3.36
3449 6023 5.483583 AGATATCCAGAGAAATAGCAGGGAC 59.516 44.000 0.00 0.00 0.00 4.46
3452 6026 7.002250 TGAAGATATCCAGAGAAATAGCAGG 57.998 40.000 0.00 0.00 0.00 4.85
3542 6116 0.685097 TGTCCCAGCAGGTGAAGTAC 59.315 55.000 0.00 0.00 36.75 2.73
3628 6202 1.137404 GGGAACACATCATGCGCAC 59.863 57.895 14.90 0.00 0.00 5.34
3648 6222 2.224079 CGAAATCAAGACCACCACACAG 59.776 50.000 0.00 0.00 0.00 3.66
3651 6225 1.890876 CCGAAATCAAGACCACCACA 58.109 50.000 0.00 0.00 0.00 4.17
3681 6255 3.198068 GGAGATGCTTGAGCGAATGTAA 58.802 45.455 0.00 0.00 45.83 2.41
3683 6257 1.065926 TGGAGATGCTTGAGCGAATGT 60.066 47.619 0.00 0.00 45.83 2.71
3684 6258 1.329906 GTGGAGATGCTTGAGCGAATG 59.670 52.381 0.00 0.00 45.83 2.67
3734 6308 2.612115 AAGGCCTCCACCTCCCAG 60.612 66.667 5.23 0.00 39.93 4.45
3735 6309 2.935481 CAAGGCCTCCACCTCCCA 60.935 66.667 5.23 0.00 39.93 4.37
3779 6353 6.352016 AGAGTAAGCTCATCTGAAAGACAA 57.648 37.500 0.00 0.00 42.30 3.18
3797 6371 5.827756 TCCCATCTACTCACTTCAAGAGTA 58.172 41.667 0.00 0.00 44.10 2.59
3824 6398 4.166144 TCCCCATCCTTAACAATCTCTTCC 59.834 45.833 0.00 0.00 0.00 3.46
3899 6473 3.130693 AGAATCAGTAGTACCTCAACGGC 59.869 47.826 0.00 0.00 35.61 5.68
3900 6474 4.496010 CGAGAATCAGTAGTACCTCAACGG 60.496 50.000 0.00 0.00 34.69 4.44
3902 6476 5.564048 ACGAGAATCAGTAGTACCTCAAC 57.436 43.478 0.00 0.00 33.17 3.18
3916 6490 2.748605 CAGTCCTGGCATACGAGAATC 58.251 52.381 0.00 0.00 0.00 2.52
4046 6624 2.963101 TCCCGGACACTAATGTATCCAG 59.037 50.000 0.73 0.00 39.66 3.86
4062 6640 1.131638 TGGAAGATCAAGGATCCCGG 58.868 55.000 8.55 0.21 39.66 5.73
4064 6642 2.985311 AGGATGGAAGATCAAGGATCCC 59.015 50.000 8.55 0.00 39.66 3.85
4083 6661 7.495055 AGCTGCAAAATATCCAAGAATTAAGG 58.505 34.615 1.02 0.00 0.00 2.69
4088 6666 6.127793 AGAGAGCTGCAAAATATCCAAGAAT 58.872 36.000 1.02 0.00 0.00 2.40
4165 6744 3.286353 TCCATGCAGAAACAGTCAAACA 58.714 40.909 0.00 0.00 0.00 2.83
4200 6779 8.796475 GTCCATATATAAATTGTGCAGGTTCAT 58.204 33.333 0.00 0.00 0.00 2.57
4298 6944 7.066284 CCGATCTGGTTTCTCAATGAACTAAAT 59.934 37.037 0.00 0.00 33.88 1.40
4323 6969 4.171416 GCGCAAGTAGCAGCAGCC 62.171 66.667 0.30 0.00 46.13 4.85
4357 7003 4.997905 TGATGTTTCGCAGAAGAAGAAG 57.002 40.909 0.00 0.00 45.90 2.85
4369 7015 9.817365 GGAAGAAATACATATGATGATGTTTCG 57.183 33.333 10.38 0.00 40.54 3.46
4375 7021 9.512588 GAAGTGGGAAGAAATACATATGATGAT 57.487 33.333 10.38 0.00 0.00 2.45
4474 7122 8.954950 AATGGAAAGACAGAATACTGATAGTG 57.045 34.615 0.00 0.00 46.03 2.74
4487 7143 5.505173 ACACTGAACAAATGGAAAGACAG 57.495 39.130 0.00 0.00 0.00 3.51
4494 7150 3.289407 TGTGGACACTGAACAAATGGA 57.711 42.857 3.91 0.00 0.00 3.41
4606 7264 2.052782 AACCGGCAAACTGAGAAAGT 57.947 45.000 0.00 0.00 42.60 2.66
4622 7280 9.984190 TTTTTCCTAACAATACCACAAATAACC 57.016 29.630 0.00 0.00 0.00 2.85
4724 7383 0.107456 CTCGGCTAATCATGGCACCT 59.893 55.000 0.00 0.00 34.13 4.00
4776 7435 8.889849 ATCTTCAACGACCAAAATATAAAACG 57.110 30.769 0.00 0.00 0.00 3.60
4858 7518 5.123027 CAGATTTAGGAGCAACTTCCAGAAC 59.877 44.000 0.00 0.00 39.84 3.01
4859 7519 5.248640 CAGATTTAGGAGCAACTTCCAGAA 58.751 41.667 0.00 0.00 39.84 3.02
4877 7537 1.272425 TGGTCCATTTTCCCGCAGATT 60.272 47.619 0.00 0.00 0.00 2.40
4923 7583 4.275936 ACCAAAAGAACAGAACTGGAATCG 59.724 41.667 6.76 0.00 34.19 3.34
4976 7636 4.526970 AGATACGAAATGGAACTGGCAAT 58.473 39.130 0.00 0.00 0.00 3.56
5018 7678 2.948979 CAATCCCCTAGCATGCGTTAAA 59.051 45.455 13.01 0.00 0.00 1.52
5035 7695 8.332464 CAAATGCCAATGTTATCATGTTCAATC 58.668 33.333 0.00 0.00 34.19 2.67
5036 7696 7.825270 ACAAATGCCAATGTTATCATGTTCAAT 59.175 29.630 0.00 0.00 34.19 2.57
5058 7802 5.184096 TCAGAAACAACAAGGCTGTTACAAA 59.816 36.000 0.00 0.00 44.15 2.83
5105 7849 8.846607 GCCTACAAAAACGTGTTATATTTTGAG 58.153 33.333 21.46 15.15 42.48 3.02
5254 8080 5.163963 GCAATTGTTTTGCTATGGTTGTAGC 60.164 40.000 7.40 0.00 45.71 3.58
5255 8081 5.348451 GGCAATTGTTTTGCTATGGTTGTAG 59.652 40.000 7.40 0.00 44.36 2.74
5386 10671 7.038659 CCACTGAAATTACAACCACTCAAAAA 58.961 34.615 0.00 0.00 0.00 1.94
5387 10672 6.568869 CCACTGAAATTACAACCACTCAAAA 58.431 36.000 0.00 0.00 0.00 2.44
5388 10673 5.451242 GCCACTGAAATTACAACCACTCAAA 60.451 40.000 0.00 0.00 0.00 2.69
5389 10674 4.037446 GCCACTGAAATTACAACCACTCAA 59.963 41.667 0.00 0.00 0.00 3.02
5390 10675 3.568007 GCCACTGAAATTACAACCACTCA 59.432 43.478 0.00 0.00 0.00 3.41
5391 10676 3.821033 AGCCACTGAAATTACAACCACTC 59.179 43.478 0.00 0.00 0.00 3.51
5392 10677 3.832527 AGCCACTGAAATTACAACCACT 58.167 40.909 0.00 0.00 0.00 4.00
5393 10678 5.001232 TCTAGCCACTGAAATTACAACCAC 58.999 41.667 0.00 0.00 0.00 4.16
5394 10679 5.235850 TCTAGCCACTGAAATTACAACCA 57.764 39.130 0.00 0.00 0.00 3.67
5395 10680 6.759497 AATCTAGCCACTGAAATTACAACC 57.241 37.500 0.00 0.00 0.00 3.77
5420 10705 6.589907 GCCACTGAAAAGTTTCTCAAGAAAAA 59.410 34.615 6.76 0.00 44.58 1.94
5421 10706 6.071391 AGCCACTGAAAAGTTTCTCAAGAAAA 60.071 34.615 6.76 0.00 44.58 2.29
5422 10707 5.418840 AGCCACTGAAAAGTTTCTCAAGAAA 59.581 36.000 1.06 1.06 41.29 2.52
5423 10708 4.949856 AGCCACTGAAAAGTTTCTCAAGAA 59.050 37.500 5.45 0.00 38.02 2.52
5424 10709 4.526970 AGCCACTGAAAAGTTTCTCAAGA 58.473 39.130 5.45 0.00 38.02 3.02
5425 10710 4.907879 AGCCACTGAAAAGTTTCTCAAG 57.092 40.909 5.45 0.00 38.02 3.02
5426 10711 8.635765 AATATAGCCACTGAAAAGTTTCTCAA 57.364 30.769 5.45 0.00 38.02 3.02
5427 10712 8.514594 CAAATATAGCCACTGAAAAGTTTCTCA 58.485 33.333 5.45 0.00 38.02 3.27
5428 10713 7.486232 GCAAATATAGCCACTGAAAAGTTTCTC 59.514 37.037 5.45 0.00 38.02 2.87
5429 10714 7.039784 TGCAAATATAGCCACTGAAAAGTTTCT 60.040 33.333 5.45 0.00 38.02 2.52
5430 10715 7.090173 TGCAAATATAGCCACTGAAAAGTTTC 58.910 34.615 0.00 0.00 37.69 2.78
5431 10716 6.991938 TGCAAATATAGCCACTGAAAAGTTT 58.008 32.000 0.00 0.00 0.00 2.66
5432 10717 6.588719 TGCAAATATAGCCACTGAAAAGTT 57.411 33.333 0.00 0.00 0.00 2.66
5433 10718 6.588719 TTGCAAATATAGCCACTGAAAAGT 57.411 33.333 0.00 0.00 0.00 2.66
5434 10719 6.477688 CCATTGCAAATATAGCCACTGAAAAG 59.522 38.462 1.71 0.00 0.00 2.27
5435 10720 6.070881 ACCATTGCAAATATAGCCACTGAAAA 60.071 34.615 1.71 0.00 0.00 2.29
5436 10721 5.421693 ACCATTGCAAATATAGCCACTGAAA 59.578 36.000 1.71 0.00 0.00 2.69
5437 10722 4.955450 ACCATTGCAAATATAGCCACTGAA 59.045 37.500 1.71 0.00 0.00 3.02
5438 10723 4.535781 ACCATTGCAAATATAGCCACTGA 58.464 39.130 1.71 0.00 0.00 3.41
5439 10724 4.924305 ACCATTGCAAATATAGCCACTG 57.076 40.909 1.71 0.00 0.00 3.66
5440 10725 5.010012 GCTTACCATTGCAAATATAGCCACT 59.990 40.000 1.71 0.00 0.00 4.00
5441 10726 5.221224 TGCTTACCATTGCAAATATAGCCAC 60.221 40.000 1.71 0.00 36.15 5.01
5442 10727 4.892345 TGCTTACCATTGCAAATATAGCCA 59.108 37.500 1.71 0.00 36.15 4.75
5443 10728 5.452078 TGCTTACCATTGCAAATATAGCC 57.548 39.130 1.71 0.00 36.15 3.93
5666 10962 4.760047 TCCTTGCGGCCGAGCTTC 62.760 66.667 33.48 11.67 38.13 3.86
5668 10964 4.767255 CTTCCTTGCGGCCGAGCT 62.767 66.667 33.48 0.00 38.13 4.09


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

AutoCloner maintained by Alex Coulton.