Multiple sequence alignment - TraesCS6D01G199700

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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 TraesCS6D01G199700 chr6D 100.000 6255 0 0 1 6255 277669940 277663686 0.000000e+00 11551.0
1 TraesCS6D01G199700 chr6B 95.453 2617 76 17 3487 6086 439394883 439392293 0.000000e+00 4133.0
2 TraesCS6D01G199700 chr6B 92.337 2845 100 31 1 2777 439398527 439395733 0.000000e+00 3938.0
3 TraesCS6D01G199700 chr6B 95.231 713 10 4 2776 3488 439395651 439394963 0.000000e+00 1107.0
4 TraesCS6D01G199700 chr6B 92.857 42 3 0 5063 5104 670023355 670023396 1.880000e-05 62.1
5 TraesCS6D01G199700 chr6A 95.570 2235 51 10 3076 5299 400117530 400115333 0.000000e+00 3535.0
6 TraesCS6D01G199700 chr6A 92.629 1750 85 17 146 1863 400120687 400118950 0.000000e+00 2477.0
7 TraesCS6D01G199700 chr6A 96.614 1211 33 3 1863 3070 400118923 400117718 0.000000e+00 2002.0
8 TraesCS6D01G199700 chr6A 93.653 646 23 5 5611 6253 400115295 400114665 0.000000e+00 950.0
9 TraesCS6D01G199700 chr6A 97.059 136 4 0 1 136 400121026 400120891 4.880000e-56 230.0
10 TraesCS6D01G199700 chr6A 83.333 60 8 2 5074 5131 205095268 205095209 3.000000e-03 54.7
11 TraesCS6D01G199700 chr5D 90.798 163 12 3 987 1149 546657242 546657083 1.370000e-51 215.0
12 TraesCS6D01G199700 chr4A 92.617 149 11 0 998 1146 622281848 622281996 1.370000e-51 215.0
13 TraesCS6D01G199700 chr4A 100.000 32 0 0 5073 5104 101753399 101753430 6.770000e-05 60.2
14 TraesCS6D01G199700 chr4A 100.000 32 0 0 5073 5104 127810346 127810315 6.770000e-05 60.2
15 TraesCS6D01G199700 chr5B 91.946 149 12 0 1001 1149 689858174 689858026 6.350000e-50 209.0
16 TraesCS6D01G199700 chr1D 80.405 148 28 1 2715 2862 300722351 300722497 1.840000e-20 111.0
17 TraesCS6D01G199700 chr1D 78.417 139 22 6 2716 2849 196973583 196973448 4.020000e-12 84.2
18 TraesCS6D01G199700 chr7D 83.000 100 16 1 2697 2796 126482634 126482536 8.640000e-14 89.8
19 TraesCS6D01G199700 chr7D 79.381 97 18 2 2698 2793 126708495 126708590 4.050000e-07 67.6
20 TraesCS6D01G199700 chr3D 76.829 164 33 4 2701 2862 582777318 582777158 3.110000e-13 87.9
21 TraesCS6D01G199700 chr2A 86.420 81 9 2 2701 2780 712343075 712342996 3.110000e-13 87.9
22 TraesCS6D01G199700 chr5A 76.875 160 26 9 2701 2854 242858349 242858503 5.200000e-11 80.5
23 TraesCS6D01G199700 chrUn 82.857 70 12 0 2793 2862 41472383 41472314 5.230000e-06 63.9
24 TraesCS6D01G199700 chr3B 100.000 34 0 0 5071 5104 667641838 667641805 5.230000e-06 63.9
25 TraesCS6D01G199700 chr3B 100.000 31 0 0 5074 5104 688230997 688230967 2.440000e-04 58.4
26 TraesCS6D01G199700 chr3B 100.000 31 0 0 5074 5104 688290673 688290643 2.440000e-04 58.4


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 TraesCS6D01G199700 chr6D 277663686 277669940 6254 True 11551.000000 11551 100.000000 1 6255 1 chr6D.!!$R1 6254
1 TraesCS6D01G199700 chr6B 439392293 439398527 6234 True 3059.333333 4133 94.340333 1 6086 3 chr6B.!!$R1 6085
2 TraesCS6D01G199700 chr6A 400114665 400121026 6361 True 1838.800000 3535 95.105000 1 6253 5 chr6A.!!$R2 6252

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
478 690 0.249868 CAGAAGCCTCCGTGACAACA 60.250 55.000 0.00 0.00 0.00 3.33 F
908 1184 0.452585 CTTCCTTCGTCGTCCTCCTC 59.547 60.000 0.00 0.00 0.00 3.71 F
1554 1835 2.336945 TGGAGTCATGGATCATGCAC 57.663 50.000 0.00 3.59 41.18 4.57 F
3086 3667 0.187117 TTTCCACCATGTGCCTTCCA 59.813 50.000 0.00 0.00 31.34 3.53 F
3602 4264 0.668706 CACAGCCTGTTCCTGACTCG 60.669 60.000 0.00 0.00 34.47 4.18 F
3943 4605 1.715931 ACCAGGAATTTCCACCATGGA 59.284 47.619 21.47 0.00 46.61 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1983 0.517755 ACAACGAAACAACGCACACA 59.482 45.000 0.00 0.0 36.70 3.72 R
1734 2019 0.976641 TTGTCGATCAACAGGAGGCT 59.023 50.000 0.00 0.0 0.00 4.58 R
3384 3965 3.698040 GTGCTTCATCAATCATCCCACTT 59.302 43.478 0.00 0.0 0.00 3.16 R
4643 5307 0.671251 CTCTATGACGGTCCCTGCTC 59.329 60.000 5.55 0.0 0.00 4.26 R
4663 5327 1.095600 ACGACTGCTGCTTCGATCTA 58.904 50.000 24.29 0.0 38.63 1.98 R
5390 6063 1.340600 ACGTTCATGGGTTATGGGGTG 60.341 52.381 0.00 0.0 37.39 4.61 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
46 47 1.552792 TCAACACGATCCACTATGGCA 59.447 47.619 0.00 0.00 37.47 4.92
146 347 6.301169 AGCTTATTTCCAGCTAACTACTGT 57.699 37.500 0.00 0.00 46.18 3.55
147 348 7.419711 AGCTTATTTCCAGCTAACTACTGTA 57.580 36.000 0.00 0.00 46.18 2.74
374 586 5.233225 TCACTCAATCAGCAACTGAGTTAG 58.767 41.667 0.00 4.33 45.85 2.34
385 597 3.802948 ACTGAGTTAGTATCCCGCAAG 57.197 47.619 0.00 0.00 38.04 4.01
478 690 0.249868 CAGAAGCCTCCGTGACAACA 60.250 55.000 0.00 0.00 0.00 3.33
490 702 2.220133 CGTGACAACAAACTAACCTCGG 59.780 50.000 0.00 0.00 0.00 4.63
530 742 1.587547 GATCCACCGGAAATCAGAGC 58.412 55.000 9.46 0.00 34.34 4.09
620 832 1.227350 CTGCAGCGATCCGATGGAA 60.227 57.895 0.00 0.00 43.43 3.53
683 896 4.035102 GCCGGGGAGCAGGAAACT 62.035 66.667 2.18 0.00 46.44 2.66
734 947 4.988716 AGCCCGTGACGACCCTCA 62.989 66.667 6.54 0.00 0.00 3.86
736 949 4.436998 CCCGTGACGACCCTCAGC 62.437 72.222 6.54 0.00 0.00 4.26
752 1000 4.173924 GCTCTGGGCTCTGGGCTC 62.174 72.222 8.30 0.00 42.93 4.70
753 1001 2.365370 CTCTGGGCTCTGGGCTCT 60.365 66.667 0.00 0.00 43.07 4.09
900 1176 1.014564 GGTTCCAGCTTCCTTCGTCG 61.015 60.000 0.00 0.00 0.00 5.12
908 1184 0.452585 CTTCCTTCGTCGTCCTCCTC 59.547 60.000 0.00 0.00 0.00 3.71
1023 1299 3.207669 GCCATCCGGAAGCAGCTG 61.208 66.667 21.49 10.11 0.00 4.24
1230 1508 3.429085 GGCTCGCTGATATGTTTTTGTG 58.571 45.455 0.00 0.00 0.00 3.33
1357 1637 6.542735 TGTGCGTGTAATTTTAGGGCAATATA 59.457 34.615 0.00 0.00 0.00 0.86
1358 1638 7.229707 TGTGCGTGTAATTTTAGGGCAATATAT 59.770 33.333 0.00 0.00 0.00 0.86
1407 1687 7.120726 ACATTAGTTCAGTTTATTTCCCCTTCG 59.879 37.037 0.00 0.00 0.00 3.79
1447 1727 3.938963 TGAAGAAGTTTTGAGTGCTCGTT 59.061 39.130 0.00 0.00 0.00 3.85
1554 1835 2.336945 TGGAGTCATGGATCATGCAC 57.663 50.000 0.00 3.59 41.18 4.57
1599 1880 8.589629 GCTACATTTTGCTTGTCAAGATTATTG 58.410 33.333 16.99 9.59 35.84 1.90
1616 1897 9.512588 AAGATTATTGTGACCTCCATATTGATC 57.487 33.333 0.00 0.00 0.00 2.92
1698 1983 6.465439 AAGCTTTAGGTTTGCAAAAGTAGT 57.535 33.333 14.67 0.00 33.67 2.73
1700 1985 5.359860 AGCTTTAGGTTTGCAAAAGTAGTGT 59.640 36.000 14.67 0.00 33.67 3.55
1729 2014 7.015289 CGTTGTTTCGTTGTATGAGATTTGAT 58.985 34.615 0.00 0.00 0.00 2.57
1841 2126 8.264347 TGTGAAGCATTAGGTTTGTGATATAGA 58.736 33.333 0.00 0.00 35.19 1.98
1903 2218 7.283354 CCTTTCCTAATCAACCAAATCTAGGTC 59.717 40.741 0.00 0.00 38.76 3.85
1992 2308 7.421955 TTTTGTTTTAAACGCTTTACTCGTC 57.578 32.000 3.28 0.00 39.48 4.20
1994 2310 4.810491 TGTTTTAAACGCTTTACTCGTCCT 59.190 37.500 3.28 0.00 39.48 3.85
1995 2311 5.982516 TGTTTTAAACGCTTTACTCGTCCTA 59.017 36.000 3.28 0.00 39.48 2.94
1996 2312 6.478344 TGTTTTAAACGCTTTACTCGTCCTAA 59.522 34.615 3.28 0.00 39.48 2.69
2094 2410 4.956085 AGTAACAGTGAAGCACATACACA 58.044 39.130 0.00 0.00 36.74 3.72
2154 2470 1.068610 CATGTTTGCAGTTGGGTACGG 60.069 52.381 0.00 0.00 0.00 4.02
2232 2548 6.356556 CCAAAGGTATGGACAACTATGATCA 58.643 40.000 0.00 0.00 43.54 2.92
2249 2565 8.900781 ACTATGATCATGAATTGGAAGAAACTG 58.099 33.333 18.72 0.00 0.00 3.16
2456 2772 9.255304 GGTGAAAGATAATGTTTACTTGCAAAA 57.745 29.630 0.00 0.00 31.00 2.44
2555 2871 6.040391 TCCTTTTTGTTTCTCCCACAACTATG 59.960 38.462 0.00 0.00 33.81 2.23
2558 2874 7.883391 TTTTGTTTCTCCCACAACTATGTTA 57.117 32.000 0.00 0.00 37.82 2.41
3086 3667 0.187117 TTTCCACCATGTGCCTTCCA 59.813 50.000 0.00 0.00 31.34 3.53
3299 3880 1.605738 CCTGCAGCCTCCTTTGCTT 60.606 57.895 8.66 0.00 40.87 3.91
3341 3922 9.859427 AATCATTGTTTATCTGGTGTTGTATTG 57.141 29.630 0.00 0.00 0.00 1.90
3384 3965 5.184864 ACAACATTTGTTCTGAACAGGTGAA 59.815 36.000 28.38 19.57 42.22 3.18
3602 4264 0.668706 CACAGCCTGTTCCTGACTCG 60.669 60.000 0.00 0.00 34.47 4.18
3714 4376 6.328934 TGCATGGAGACCTACTTATTGGATTA 59.671 38.462 0.00 0.00 0.00 1.75
3723 4385 8.492415 ACCTACTTATTGGATTAGCTATGTGA 57.508 34.615 0.00 0.00 0.00 3.58
3728 4390 8.543774 ACTTATTGGATTAGCTATGTGATAGGG 58.456 37.037 0.00 0.00 33.43 3.53
3943 4605 1.715931 ACCAGGAATTTCCACCATGGA 59.284 47.619 21.47 0.00 46.61 3.41
4094 4757 9.720569 GTGCGTGTTTATTTATACATGTTTTTG 57.279 29.630 2.30 0.00 34.52 2.44
4150 4813 8.113675 GGTTTAATGTAACTTGCAAACTTGTTG 58.886 33.333 11.00 0.00 0.00 3.33
4322 4985 6.910536 ATAATCTTTTGAGTGAAGCGTAGG 57.089 37.500 0.00 0.00 0.00 3.18
4560 5224 4.899352 AGTCTCCTAACAGAGCAACAAT 57.101 40.909 0.00 0.00 33.66 2.71
4643 5307 3.071786 ACAGAACGTGATAGAGCATCG 57.928 47.619 0.00 0.00 42.67 3.84
4663 5327 0.033011 AGCAGGGACCGTCATAGAGT 60.033 55.000 0.00 0.00 0.00 3.24
4892 5556 9.602568 TCTAGTTACCGCATAATGTTTGAATTA 57.397 29.630 0.00 0.00 0.00 1.40
5136 5800 6.017192 AGATTGTTTAGGTCACTACAGAGGA 58.983 40.000 0.00 0.00 0.00 3.71
5269 5942 2.628178 CCGTTGAGATGGGCACTAGATA 59.372 50.000 0.00 0.00 0.00 1.98
5276 5949 1.578897 TGGGCACTAGATACAGGCAA 58.421 50.000 0.00 0.00 0.00 4.52
5301 5974 5.105595 GCTTGCATTAGATTTTCTGAGGGTT 60.106 40.000 0.00 0.00 0.00 4.11
5401 6074 3.555966 CATCTTCCTTCACCCCATAACC 58.444 50.000 0.00 0.00 0.00 2.85
5419 6092 4.963276 AACCCATGAACGTGATATGTTG 57.037 40.909 0.00 0.00 0.00 3.33
5452 6125 4.217550 TCTGTTATGGCTTTAACCAGTTGC 59.782 41.667 7.96 0.00 44.71 4.17
5471 6144 5.415701 AGTTGCCAACCTTATGTACTTCATG 59.584 40.000 3.45 0.00 37.91 3.07
5486 6159 3.245586 ACTTCATGGTATCCCTTGCCAAA 60.246 43.478 0.00 0.00 43.93 3.28
5530 6205 9.730705 TCAAGTTATTCTGTCTTGAATTGAGAT 57.269 29.630 4.68 0.00 42.61 2.75
5560 6235 4.569719 ATTGACCCTGAAACCGTAGAAT 57.430 40.909 0.00 0.00 0.00 2.40
5741 6416 2.014010 TGGATGGCTTGGCTCTTTTT 57.986 45.000 0.00 0.00 0.00 1.94
5925 6600 2.149578 GCTAGGCTGATCGCATCAAAT 58.850 47.619 0.00 0.00 41.67 2.32
5957 6634 5.337788 ACCTCTATTTTTGGTGGGCATTAA 58.662 37.500 0.00 0.00 32.16 1.40
5971 6648 6.211384 GGTGGGCATTAAATATTTCCTAGCAT 59.789 38.462 3.39 0.00 0.00 3.79
5986 6663 0.333993 AGCATCTGAGGGCAAATGGT 59.666 50.000 6.83 0.00 0.00 3.55
6002 6682 5.730568 GCAAATGGTTCCTAGAATAAGTGCG 60.731 44.000 0.00 0.00 0.00 5.34
6039 6719 5.473162 CCACCTTGTCATCATAAAGAACACA 59.527 40.000 0.00 0.00 0.00 3.72
6088 6768 3.328382 TCAATAGGTTCCTGTTGTCCG 57.672 47.619 21.50 3.59 36.80 4.79
6089 6769 2.901192 TCAATAGGTTCCTGTTGTCCGA 59.099 45.455 21.50 6.00 36.80 4.55
6090 6770 3.000727 CAATAGGTTCCTGTTGTCCGAC 58.999 50.000 16.58 0.00 32.80 4.79
6091 6771 2.005370 TAGGTTCCTGTTGTCCGACT 57.995 50.000 1.12 0.00 0.00 4.18
6092 6772 0.680061 AGGTTCCTGTTGTCCGACTC 59.320 55.000 0.00 0.00 0.00 3.36
6093 6773 0.680061 GGTTCCTGTTGTCCGACTCT 59.320 55.000 0.00 0.00 0.00 3.24
6094 6774 1.605712 GGTTCCTGTTGTCCGACTCTG 60.606 57.143 0.00 0.00 0.00 3.35
6095 6775 1.068741 GTTCCTGTTGTCCGACTCTGT 59.931 52.381 0.00 0.00 0.00 3.41
6096 6776 0.959553 TCCTGTTGTCCGACTCTGTC 59.040 55.000 0.00 0.00 0.00 3.51
6097 6777 0.673985 CCTGTTGTCCGACTCTGTCA 59.326 55.000 0.00 0.00 32.09 3.58
6132 6812 1.463553 AAAAAGGAGCCGTGCTTGGG 61.464 55.000 0.00 0.00 39.88 4.12
6196 6876 6.650120 TGAAGGGTTGAGATTAGAACATACC 58.350 40.000 0.00 0.00 0.00 2.73
6201 6881 6.542735 GGGTTGAGATTAGAACATACCCTTTC 59.457 42.308 0.00 0.00 40.61 2.62
6205 6885 8.964476 TGAGATTAGAACATACCCTTTCATTC 57.036 34.615 0.00 0.00 0.00 2.67
6217 6897 3.366374 CCCTTTCATTCAACCGCTTCTTC 60.366 47.826 0.00 0.00 0.00 2.87
6253 6933 9.042008 GTTTGTCTGTGATTACCATCGTAATAT 57.958 33.333 0.00 0.00 43.71 1.28
6254 6934 8.812147 TTGTCTGTGATTACCATCGTAATATC 57.188 34.615 0.00 0.00 43.71 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 9.017509 TGCACTCTTCAAAGATAATTTGAATCT 57.982 29.630 14.22 0.77 44.41 2.40
143 344 9.912634 AAAACATTCTGTTGTTCCAATATACAG 57.087 29.630 0.00 0.00 40.14 2.74
283 494 7.243487 CGTAGTACTGTAGTTGGAATTTCGTA 58.757 38.462 5.39 0.00 0.00 3.43
374 586 3.746045 TTCATCTACCTTGCGGGATAC 57.254 47.619 2.42 0.00 38.76 2.24
385 597 6.650807 TCGAATGCCTCATTATTTCATCTACC 59.349 38.462 0.00 0.00 33.90 3.18
530 742 2.966309 GCGGCTCGTGGACTTTTGG 61.966 63.158 0.00 0.00 0.00 3.28
598 810 0.938637 CATCGGATCGCTGCAGTCTC 60.939 60.000 16.64 9.45 0.00 3.36
620 832 0.827925 TCAGGTGGTCTCTTCAGCGT 60.828 55.000 0.00 0.00 37.66 5.07
681 894 0.329596 GAGTCCCCAATTGCTCCAGT 59.670 55.000 0.00 0.00 0.00 4.00
683 896 1.299648 CGAGTCCCCAATTGCTCCA 59.700 57.895 0.00 0.00 0.00 3.86
736 949 2.365370 AGAGCCCAGAGCCCAGAG 60.365 66.667 0.00 0.00 45.47 3.35
900 1176 4.637873 GCGATTAGCGAGGAGGAC 57.362 61.111 0.00 0.00 44.57 3.85
1230 1508 3.843999 TCTTCTGCAAAACACCAACAAC 58.156 40.909 0.00 0.00 0.00 3.32
1357 1637 2.505407 TCATCTCCACAAATCCGTCCAT 59.495 45.455 0.00 0.00 0.00 3.41
1358 1638 1.905894 TCATCTCCACAAATCCGTCCA 59.094 47.619 0.00 0.00 0.00 4.02
1386 1666 3.756963 GCGAAGGGGAAATAAACTGAACT 59.243 43.478 0.00 0.00 0.00 3.01
1407 1687 1.742831 TCAATCCAAACCGCACTATGC 59.257 47.619 0.00 0.00 40.69 3.14
1422 1702 5.142962 CGAGCACTCAAAACTTCTTCAATC 58.857 41.667 0.00 0.00 0.00 2.67
1425 1705 3.531538 ACGAGCACTCAAAACTTCTTCA 58.468 40.909 0.00 0.00 0.00 3.02
1447 1727 5.366768 CCAATCTATTCTACCCTCACCTCAA 59.633 44.000 0.00 0.00 0.00 3.02
1513 1794 3.959495 ACAATCATCCAAGCCCAGTAT 57.041 42.857 0.00 0.00 0.00 2.12
1554 1835 4.795970 AGCTAAGTTGTGTCGTTCAAAG 57.204 40.909 0.00 0.00 0.00 2.77
1599 1880 7.572523 TCATTTTGATCAATATGGAGGTCAC 57.427 36.000 27.86 0.00 32.82 3.67
1698 1983 0.517755 ACAACGAAACAACGCACACA 59.482 45.000 0.00 0.00 36.70 3.72
1700 1985 2.608090 TCATACAACGAAACAACGCACA 59.392 40.909 0.00 0.00 36.70 4.57
1729 2014 3.031013 TCGATCAACAGGAGGCTCAATA 58.969 45.455 17.69 0.00 0.00 1.90
1734 2019 0.976641 TTGTCGATCAACAGGAGGCT 59.023 50.000 0.00 0.00 0.00 4.58
1841 2126 0.990818 GGATTCAGAGGGGAAGCCCT 60.991 60.000 2.01 0.00 45.36 5.19
1903 2218 5.959583 AAGGTGACCTAATAAGAGAAGGG 57.040 43.478 3.68 0.00 34.52 3.95
1932 2247 4.963373 TCAAACCTCGTTTTCTCACCATA 58.037 39.130 0.00 0.00 33.10 2.74
1945 2260 7.873739 AAAAAGATAAAGCATTCAAACCTCG 57.126 32.000 0.00 0.00 0.00 4.63
1992 2308 7.202016 TGTTAACTCAAGACTGCAATTTAGG 57.798 36.000 7.22 0.00 0.00 2.69
1994 2310 7.500892 TCCTTGTTAACTCAAGACTGCAATTTA 59.499 33.333 7.22 0.00 45.11 1.40
1995 2311 6.321181 TCCTTGTTAACTCAAGACTGCAATTT 59.679 34.615 7.22 0.00 45.11 1.82
1996 2312 5.827797 TCCTTGTTAACTCAAGACTGCAATT 59.172 36.000 7.22 0.00 45.11 2.32
2094 2410 6.172630 GCATGGGAATGTAACCAAAAGAAAT 58.827 36.000 0.00 0.00 40.73 2.17
2154 2470 3.006247 GGAAGCAACAGAACAGATCCTC 58.994 50.000 0.00 0.00 0.00 3.71
2232 2548 8.787852 GTCTTTCTACAGTTTCTTCCAATTCAT 58.212 33.333 0.00 0.00 0.00 2.57
2249 2565 5.513495 CGCACTCAACTATCAGTCTTTCTAC 59.487 44.000 0.00 0.00 0.00 2.59
2456 2772 4.263418 ACTCGAGTACCTCTTTACTCTGGT 60.263 45.833 18.46 0.00 44.05 4.00
3086 3667 9.736023 GCCTTCAAATGAGAATAAAATCGTTAT 57.264 29.630 0.00 0.00 0.00 1.89
3299 3880 6.701340 ACAATGATTTGTGCTCTAGTAGTCA 58.299 36.000 0.00 0.00 44.36 3.41
3384 3965 3.698040 GTGCTTCATCAATCATCCCACTT 59.302 43.478 0.00 0.00 0.00 3.16
3602 4264 1.336755 ACGTGAGTGGACATTTTTGCC 59.663 47.619 0.00 0.00 46.97 4.52
3714 4376 4.396357 AGAGTAGCCCTATCACATAGCT 57.604 45.455 0.00 0.00 37.58 3.32
3723 4385 3.014304 TCACGACAAGAGTAGCCCTAT 57.986 47.619 0.00 0.00 0.00 2.57
3728 4390 4.049186 TGAAACTTCACGACAAGAGTAGC 58.951 43.478 5.32 0.00 31.01 3.58
3855 4517 1.675714 CCACATATGTCACACAGGCGT 60.676 52.381 5.07 0.00 0.00 5.68
3943 4605 5.540337 CCCATACACCACTATACTCATGACT 59.460 44.000 0.00 0.00 0.00 3.41
4150 4813 8.202745 AGCATAGCTATAAACAACAAGTTCTC 57.797 34.615 5.77 0.00 36.84 2.87
4322 4985 3.600388 ACTAACATGTAACTCTGCAGGC 58.400 45.455 15.13 0.24 0.00 4.85
4643 5307 0.671251 CTCTATGACGGTCCCTGCTC 59.329 60.000 5.55 0.00 0.00 4.26
4663 5327 1.095600 ACGACTGCTGCTTCGATCTA 58.904 50.000 24.29 0.00 38.63 1.98
4892 5556 3.887716 GCAACAGAGGAAGGAATATGCAT 59.112 43.478 3.79 3.79 0.00 3.96
5109 5773 8.478877 CCTCTGTAGTGACCTAAACAATCTTAT 58.521 37.037 0.00 0.00 0.00 1.73
5110 5774 7.672660 TCCTCTGTAGTGACCTAAACAATCTTA 59.327 37.037 0.00 0.00 0.00 2.10
5111 5775 6.497259 TCCTCTGTAGTGACCTAAACAATCTT 59.503 38.462 0.00 0.00 0.00 2.40
5112 5776 6.017192 TCCTCTGTAGTGACCTAAACAATCT 58.983 40.000 0.00 0.00 0.00 2.40
5113 5777 6.282199 TCCTCTGTAGTGACCTAAACAATC 57.718 41.667 0.00 0.00 0.00 2.67
5114 5778 6.270231 ACTTCCTCTGTAGTGACCTAAACAAT 59.730 38.462 0.00 0.00 0.00 2.71
5115 5779 5.601313 ACTTCCTCTGTAGTGACCTAAACAA 59.399 40.000 0.00 0.00 0.00 2.83
5116 5780 5.145564 ACTTCCTCTGTAGTGACCTAAACA 58.854 41.667 0.00 0.00 0.00 2.83
5169 5833 8.595533 CGCACGCTATTGATATAATTAAGTCAT 58.404 33.333 4.57 0.35 0.00 3.06
5170 5834 7.810759 TCGCACGCTATTGATATAATTAAGTCA 59.189 33.333 0.00 0.00 0.00 3.41
5276 5949 4.643784 CCCTCAGAAAATCTAATGCAAGCT 59.356 41.667 0.00 0.00 0.00 3.74
5301 5974 3.135348 CCATTCTTGTCATCCTAGGCAGA 59.865 47.826 2.96 0.87 0.00 4.26
5390 6063 1.340600 ACGTTCATGGGTTATGGGGTG 60.341 52.381 0.00 0.00 37.39 4.61
5401 6074 4.394610 TGGTTCAACATATCACGTTCATGG 59.605 41.667 0.00 0.00 0.00 3.66
5419 6092 9.516314 GTTAAAGCCATAACAGATAAATGGTTC 57.484 33.333 2.80 0.00 41.87 3.62
5452 6125 6.710744 GGATACCATGAAGTACATAAGGTTGG 59.289 42.308 0.00 0.00 36.85 3.77
5486 6159 3.485463 TGAGAAATCAACAGGGACGTT 57.515 42.857 0.00 0.00 0.00 3.99
5530 6205 5.472137 CGGTTTCAGGGTCAATTTTTCTCTA 59.528 40.000 0.00 0.00 0.00 2.43
5531 6206 4.278419 CGGTTTCAGGGTCAATTTTTCTCT 59.722 41.667 0.00 0.00 0.00 3.10
5533 6208 3.958147 ACGGTTTCAGGGTCAATTTTTCT 59.042 39.130 0.00 0.00 0.00 2.52
5535 6210 5.134661 TCTACGGTTTCAGGGTCAATTTTT 58.865 37.500 0.00 0.00 0.00 1.94
5536 6211 4.721132 TCTACGGTTTCAGGGTCAATTTT 58.279 39.130 0.00 0.00 0.00 1.82
5636 6311 4.964262 AGGGCATTGGTTGAATGTTGATAT 59.036 37.500 0.00 0.00 43.17 1.63
5741 6416 2.300152 AGGTGATCTTTCTGTCGCAGAA 59.700 45.455 15.33 15.33 46.93 3.02
5925 6600 6.940298 CCACCAAAAATAGAGGTACTTCTTGA 59.060 38.462 13.27 0.00 41.55 3.02
5957 6634 4.352001 TGCCCTCAGATGCTAGGAAATATT 59.648 41.667 0.00 0.00 34.58 1.28
5971 6648 1.075601 AGGAACCATTTGCCCTCAGA 58.924 50.000 0.00 0.00 0.00 3.27
5986 6663 5.790593 ACTTCAACGCACTTATTCTAGGAA 58.209 37.500 0.00 0.00 0.00 3.36
6002 6682 4.398044 TGACAAGGTGGAAGAAACTTCAAC 59.602 41.667 12.46 11.07 0.00 3.18
6039 6719 8.598041 AGAAAATCAGTACCTTGAGATACAACT 58.402 33.333 0.00 0.00 34.56 3.16
6091 6771 6.544928 TTCTGGTAATTGCTCTATGACAGA 57.455 37.500 0.00 0.00 0.00 3.41
6092 6772 7.615582 TTTTCTGGTAATTGCTCTATGACAG 57.384 36.000 0.00 0.00 0.00 3.51
6093 6773 7.121168 CCTTTTTCTGGTAATTGCTCTATGACA 59.879 37.037 0.00 0.00 0.00 3.58
6094 6774 7.336931 TCCTTTTTCTGGTAATTGCTCTATGAC 59.663 37.037 0.00 0.00 0.00 3.06
6095 6775 7.402054 TCCTTTTTCTGGTAATTGCTCTATGA 58.598 34.615 0.00 0.00 0.00 2.15
6096 6776 7.630242 TCCTTTTTCTGGTAATTGCTCTATG 57.370 36.000 0.00 0.00 0.00 2.23
6097 6777 6.319911 GCTCCTTTTTCTGGTAATTGCTCTAT 59.680 38.462 0.00 0.00 0.00 1.98
6132 6812 7.266400 TGTGAACTTTTTAAAATGGGGTGTAC 58.734 34.615 15.81 9.47 0.00 2.90
6154 6834 6.016943 ACCCTTCATTTGCATCAAAATTTGTG 60.017 34.615 5.56 5.03 36.90 3.33
6168 6848 7.452880 TGTTCTAATCTCAACCCTTCATTTG 57.547 36.000 0.00 0.00 0.00 2.32
6196 6876 3.366374 GGAAGAAGCGGTTGAATGAAAGG 60.366 47.826 3.70 0.00 0.00 3.11
6201 6881 0.811281 GGGGAAGAAGCGGTTGAATG 59.189 55.000 3.70 0.00 0.00 2.67
6205 6885 0.825840 TTTGGGGGAAGAAGCGGTTG 60.826 55.000 3.70 0.00 0.00 3.77
6217 6897 1.106944 ACAGACAAACGCTTTGGGGG 61.107 55.000 12.79 6.01 44.81 5.40


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

AutoCloner maintained by Alex Coulton.