Multiple sequence alignment - TraesCS1D01G069100

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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 TraesCS1D01G069100 chr1D 100.000 4407 0 0 1 4407 50107545 50111951 0.000000e+00 8139.0
1 TraesCS1D01G069100 chr1D 85.725 2718 339 32 1063 3748 49973246 49975946 0.000000e+00 2824.0
2 TraesCS1D01G069100 chr1D 84.998 2733 352 26 974 3681 49956206 49958905 0.000000e+00 2723.0
3 TraesCS1D01G069100 chr1D 86.843 2455 283 23 1063 3492 50022600 50025039 0.000000e+00 2708.0
4 TraesCS1D01G069100 chr1D 85.817 2510 321 24 1064 3552 50059241 50061736 0.000000e+00 2630.0
5 TraesCS1D01G069100 chr1D 89.871 1777 175 3 1717 3492 50008022 50009794 0.000000e+00 2279.0
6 TraesCS1D01G069100 chr1D 100.000 803 0 0 4606 5408 50112150 50112952 0.000000e+00 1483.0
7 TraesCS1D01G069100 chr1D 89.366 1072 85 13 2913 3968 80651710 80652768 0.000000e+00 1321.0
8 TraesCS1D01G069100 chr1D 96.631 653 22 0 1 653 50087108 50087760 0.000000e+00 1085.0
9 TraesCS1D01G069100 chr1D 95.712 653 28 0 1 653 359780932 359781584 0.000000e+00 1051.0
10 TraesCS1D01G069100 chr1D 92.614 704 39 5 945 1635 50007332 50008035 0.000000e+00 1000.0
11 TraesCS1D01G069100 chr1D 85.947 491 36 16 4767 5246 80656066 80656534 1.350000e-135 494.0
12 TraesCS1D01G069100 chr1D 89.239 381 34 6 4001 4379 80652770 80653145 2.280000e-128 470.0
13 TraesCS1D01G069100 chr1D 80.364 494 69 13 3782 4268 49959721 49960193 3.100000e-92 350.0
14 TraesCS1D01G069100 chr1D 93.023 43 2 1 5287 5329 50063804 50063845 1.630000e-05 62.1
15 TraesCS1D01G069100 chr1A 95.288 3523 112 12 927 4407 49354667 49358177 0.000000e+00 5537.0
16 TraesCS1D01G069100 chr1A 86.467 2845 322 39 942 3748 49346660 49349479 0.000000e+00 3062.0
17 TraesCS1D01G069100 chr1A 84.949 2724 337 35 974 3660 49293321 49296008 0.000000e+00 2691.0
18 TraesCS1D01G069100 chr1A 85.422 830 78 27 4610 5408 49358195 49359012 0.000000e+00 822.0
19 TraesCS1D01G069100 chr1A 80.624 929 139 29 1054 1953 48999711 48998795 0.000000e+00 680.0
20 TraesCS1D01G069100 chr1A 86.759 506 42 15 4820 5308 99155571 99156068 1.710000e-149 540.0
21 TraesCS1D01G069100 chr1B 97.009 2608 63 5 1810 4407 70694934 70697536 0.000000e+00 4370.0
22 TraesCS1D01G069100 chr1B 84.705 2759 354 39 941 3660 70333674 70336403 0.000000e+00 2695.0
23 TraesCS1D01G069100 chr1B 82.871 2598 400 30 996 3558 70169714 70172301 0.000000e+00 2290.0
24 TraesCS1D01G069100 chr1B 90.050 1206 71 18 654 1824 70689512 70690703 0.000000e+00 1517.0
25 TraesCS1D01G069100 chr1B 85.383 1252 143 14 2516 3743 70497481 70498716 0.000000e+00 1262.0
26 TraesCS1D01G069100 chr1B 93.393 333 20 2 4690 5021 70697683 70698014 4.870000e-135 492.0
27 TraesCS1D01G069100 chr1B 88.696 230 19 3 5080 5309 70703265 70703487 1.920000e-69 274.0
28 TraesCS1D01G069100 chr1B 84.211 95 8 3 5018 5106 70702775 70702868 9.650000e-13 86.1
29 TraesCS1D01G069100 chr5D 96.018 653 26 0 1 653 376886003 376886655 0.000000e+00 1062.0
30 TraesCS1D01G069100 chr5D 95.865 653 26 1 1 653 455628245 455627594 0.000000e+00 1055.0
31 TraesCS1D01G069100 chr5D 95.719 654 27 1 1 653 312385569 312384916 0.000000e+00 1051.0
32 TraesCS1D01G069100 chr5D 83.146 89 15 0 4060 4148 527152522 527152610 1.250000e-11 82.4
33 TraesCS1D01G069100 chr7D 95.865 653 27 0 1 653 169400086 169400738 0.000000e+00 1057.0
34 TraesCS1D01G069100 chr6D 95.865 653 27 0 1 653 15511089 15510437 0.000000e+00 1057.0
35 TraesCS1D01G069100 chr6D 95.865 653 27 0 1 653 429882739 429882087 0.000000e+00 1057.0
36 TraesCS1D01G069100 chr3D 96.000 650 26 0 4 653 502898864 502898215 0.000000e+00 1057.0
37 TraesCS1D01G069100 chr3A 83.146 89 15 0 4060 4148 667699972 667700060 1.250000e-11 82.4
38 TraesCS1D01G069100 chr5B 86.364 66 9 0 4060 4125 663224660 663224725 7.510000e-09 73.1
39 TraesCS1D01G069100 chr5A 80.899 89 17 0 4060 4148 654153102 654153190 2.700000e-08 71.3


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 TraesCS1D01G069100 chr1D 50107545 50112952 5407 False 4811.000000 8139 100.0000 1 5408 2 chr1D.!!$F8 5407
1 TraesCS1D01G069100 chr1D 49973246 49975946 2700 False 2824.000000 2824 85.7250 1063 3748 1 chr1D.!!$F1 2685
2 TraesCS1D01G069100 chr1D 50022600 50025039 2439 False 2708.000000 2708 86.8430 1063 3492 1 chr1D.!!$F2 2429
3 TraesCS1D01G069100 chr1D 50007332 50009794 2462 False 1639.500000 2279 91.2425 945 3492 2 chr1D.!!$F6 2547
4 TraesCS1D01G069100 chr1D 49956206 49960193 3987 False 1536.500000 2723 82.6810 974 4268 2 chr1D.!!$F5 3294
5 TraesCS1D01G069100 chr1D 50059241 50063845 4604 False 1346.050000 2630 89.4200 1064 5329 2 chr1D.!!$F7 4265
6 TraesCS1D01G069100 chr1D 50087108 50087760 652 False 1085.000000 1085 96.6310 1 653 1 chr1D.!!$F3 652
7 TraesCS1D01G069100 chr1D 359780932 359781584 652 False 1051.000000 1051 95.7120 1 653 1 chr1D.!!$F4 652
8 TraesCS1D01G069100 chr1D 80651710 80656534 4824 False 761.666667 1321 88.1840 2913 5246 3 chr1D.!!$F9 2333
9 TraesCS1D01G069100 chr1A 49354667 49359012 4345 False 3179.500000 5537 90.3550 927 5408 2 chr1A.!!$F4 4481
10 TraesCS1D01G069100 chr1A 49346660 49349479 2819 False 3062.000000 3062 86.4670 942 3748 1 chr1A.!!$F2 2806
11 TraesCS1D01G069100 chr1A 49293321 49296008 2687 False 2691.000000 2691 84.9490 974 3660 1 chr1A.!!$F1 2686
12 TraesCS1D01G069100 chr1A 48998795 48999711 916 True 680.000000 680 80.6240 1054 1953 1 chr1A.!!$R1 899
13 TraesCS1D01G069100 chr1B 70333674 70336403 2729 False 2695.000000 2695 84.7050 941 3660 1 chr1B.!!$F2 2719
14 TraesCS1D01G069100 chr1B 70694934 70698014 3080 False 2431.000000 4370 95.2010 1810 5021 2 chr1B.!!$F5 3211
15 TraesCS1D01G069100 chr1B 70169714 70172301 2587 False 2290.000000 2290 82.8710 996 3558 1 chr1B.!!$F1 2562
16 TraesCS1D01G069100 chr1B 70689512 70690703 1191 False 1517.000000 1517 90.0500 654 1824 1 chr1B.!!$F4 1170
17 TraesCS1D01G069100 chr1B 70497481 70498716 1235 False 1262.000000 1262 85.3830 2516 3743 1 chr1B.!!$F3 1227
18 TraesCS1D01G069100 chr5D 376886003 376886655 652 False 1062.000000 1062 96.0180 1 653 1 chr5D.!!$F1 652
19 TraesCS1D01G069100 chr5D 455627594 455628245 651 True 1055.000000 1055 95.8650 1 653 1 chr5D.!!$R2 652
20 TraesCS1D01G069100 chr5D 312384916 312385569 653 True 1051.000000 1051 95.7190 1 653 1 chr5D.!!$R1 652
21 TraesCS1D01G069100 chr7D 169400086 169400738 652 False 1057.000000 1057 95.8650 1 653 1 chr7D.!!$F1 652
22 TraesCS1D01G069100 chr6D 15510437 15511089 652 True 1057.000000 1057 95.8650 1 653 1 chr6D.!!$R1 652
23 TraesCS1D01G069100 chr6D 429882087 429882739 652 True 1057.000000 1057 95.8650 1 653 1 chr6D.!!$R2 652
24 TraesCS1D01G069100 chr3D 502898215 502898864 649 True 1057.000000 1057 96.0000 4 653 1 chr3D.!!$R1 649

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
681 683 0.519519 CGTTATGCTCCCGTTTGCAA 59.480 50.000 0.00 0.0 42.74 4.08 F
1024 1042 0.103937 GCTCCTCCTCTTCATCACGG 59.896 60.000 0.00 0.0 0.00 4.94 F
1868 2096 1.462731 AAGCCGGAGCAATGCACAAA 61.463 50.000 5.05 0.0 43.56 2.83 F
2451 2679 0.756903 AGTACAGCCGGACACAGTTT 59.243 50.000 5.05 0.0 0.00 2.66 F
2825 3053 3.071023 GTGGAAGGATCGATGATGGGTTA 59.929 47.826 0.54 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1697 2.473816 TCACACAAGCTCTTCAGAACG 58.526 47.619 0.00 0.0 0.00 3.95 R
2022 2250 2.933906 TGAACGAGTTCCAAGTGACAAC 59.066 45.455 12.76 0.0 38.77 3.32 R
3786 4758 5.809562 TGTCCAAAAATGCAAACACTGTTAG 59.190 36.000 0.00 0.0 0.00 2.34 R
4230 6483 0.468226 AAGGTTTCGTCCTGCACAGA 59.532 50.000 0.00 0.0 37.93 3.41 R
4608 8264 0.682292 TCGGTTGGCACACTGTATCA 59.318 50.000 0.00 0.0 39.29 2.15 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
218 219 2.258726 GCCAACTCCACGAACACCC 61.259 63.158 0.00 0.00 0.00 4.61
287 288 4.036262 TGATGTTTGGTAGCACACAAAGTC 59.964 41.667 17.00 11.13 37.27 3.01
293 294 3.118038 TGGTAGCACACAAAGTCTTCCTT 60.118 43.478 0.00 0.00 33.79 3.36
427 428 9.551734 CAAGTCAATCACATCATTCTCCTAATA 57.448 33.333 0.00 0.00 0.00 0.98
514 516 1.003331 CGAGCTAGTCAAGTAGAGGCG 60.003 57.143 0.00 0.00 0.00 5.52
516 518 1.746220 AGCTAGTCAAGTAGAGGCGTG 59.254 52.381 0.00 0.00 0.00 5.34
517 519 1.743958 GCTAGTCAAGTAGAGGCGTGA 59.256 52.381 0.00 0.00 0.00 4.35
530 532 4.715713 AGAGGCGTGATAGTGACACTATA 58.284 43.478 24.72 12.53 41.21 1.31
662 664 0.853530 AGGGCATATTCAACCTCCCC 59.146 55.000 0.00 0.00 34.34 4.81
663 665 0.537371 GGGCATATTCAACCTCCCCG 60.537 60.000 0.00 0.00 0.00 5.73
666 668 2.158726 GGCATATTCAACCTCCCCGTTA 60.159 50.000 0.00 0.00 0.00 3.18
668 670 3.502211 GCATATTCAACCTCCCCGTTATG 59.498 47.826 0.00 0.00 0.00 1.90
673 675 1.632965 AACCTCCCCGTTATGCTCCC 61.633 60.000 0.00 0.00 0.00 4.30
681 683 0.519519 CGTTATGCTCCCGTTTGCAA 59.480 50.000 0.00 0.00 42.74 4.08
693 695 1.063469 CGTTTGCAACCTCTTTGACGT 59.937 47.619 0.00 0.00 37.39 4.34
712 714 2.414559 CGTCGGTTTGTGTACGTCCTAT 60.415 50.000 0.00 0.00 0.00 2.57
728 730 2.849943 TCCTATAGGGTTGCACCATGTT 59.150 45.455 18.97 0.00 41.02 2.71
763 766 5.303078 ACCTATGAGTGAAATGATACGCTCT 59.697 40.000 0.00 0.00 42.06 4.09
769 772 7.739295 TGAGTGAAATGATACGCTCTAAAAAC 58.261 34.615 0.00 0.00 42.06 2.43
770 773 7.602644 TGAGTGAAATGATACGCTCTAAAAACT 59.397 33.333 0.00 0.00 42.06 2.66
772 775 9.431887 AGTGAAATGATACGCTCTAAAAACTTA 57.568 29.630 0.00 0.00 0.00 2.24
774 777 9.210329 TGAAATGATACGCTCTAAAAACTTACA 57.790 29.630 0.00 0.00 0.00 2.41
840 844 9.539825 AAAACAAAAACAAGATGTGCATATACA 57.460 25.926 0.00 0.00 34.63 2.29
865 869 1.003118 TGTCCATTTAACGGCTCAGCT 59.997 47.619 0.00 0.00 0.00 4.24
869 873 1.061131 CATTTAACGGCTCAGCTCACG 59.939 52.381 0.00 0.00 0.00 4.35
971 981 1.700368 CTCACCCTCCTCCTCCTCA 59.300 63.158 0.00 0.00 0.00 3.86
972 982 0.686112 CTCACCCTCCTCCTCCTCAC 60.686 65.000 0.00 0.00 0.00 3.51
1024 1042 0.103937 GCTCCTCCTCTTCATCACGG 59.896 60.000 0.00 0.00 0.00 4.94
1047 1065 2.284625 TCCAGCATCCACCTCCGT 60.285 61.111 0.00 0.00 0.00 4.69
1247 1304 1.745087 CGTATTGTTTCAGCAGGCCAT 59.255 47.619 5.01 0.00 0.00 4.40
1629 1697 3.609853 TGATGCCTTCTCATACAACACC 58.390 45.455 0.00 0.00 0.00 4.16
1868 2096 1.462731 AAGCCGGAGCAATGCACAAA 61.463 50.000 5.05 0.00 43.56 2.83
2004 2232 6.645790 AAATGTTCAGAGAAATGACAAGCT 57.354 33.333 0.00 0.00 0.00 3.74
2451 2679 0.756903 AGTACAGCCGGACACAGTTT 59.243 50.000 5.05 0.00 0.00 2.66
2825 3053 3.071023 GTGGAAGGATCGATGATGGGTTA 59.929 47.826 0.54 0.00 0.00 2.85
2979 3210 5.359009 AGTGGAATAATGGTGAGCATTTCTG 59.641 40.000 15.51 0.00 0.00 3.02
3063 3295 5.643379 ATTCCAGAAATTACGTGCAATGT 57.357 34.783 0.00 0.00 40.66 2.71
3786 4758 3.119101 TCCCTGAGTTAATCGAGCTGAAC 60.119 47.826 0.00 0.00 0.00 3.18
4230 6483 3.146847 GACCTGACTTCGTTTTCCCAAT 58.853 45.455 0.00 0.00 0.00 3.16
4239 6492 1.068333 CGTTTTCCCAATCTGTGCAGG 60.068 52.381 0.00 0.00 0.00 4.85
4300 6556 5.765182 AGGTTGATTCGTCAAGAAAACATCT 59.235 36.000 0.00 0.00 42.91 2.90
4318 6574 3.726557 TCTGTTGATGAATCAGGGCTT 57.273 42.857 0.00 0.00 38.19 4.35
4327 6583 2.097825 GAATCAGGGCTTGTTGCTGAT 58.902 47.619 0.00 0.00 37.93 2.90
4332 6588 2.939103 CAGGGCTTGTTGCTGATACTAC 59.061 50.000 0.00 0.00 42.39 2.73
4399 8055 7.970102 AGGCAATGGATAGCATTAAATGATTT 58.030 30.769 0.00 0.00 0.00 2.17
4863 9857 2.292267 CAAGGTAGCGGCTTCATGAAT 58.708 47.619 8.26 0.00 0.00 2.57
5004 10005 4.826733 AGACAATCAAACAAGTATGGTGCA 59.173 37.500 0.00 0.00 0.00 4.57
5016 10017 6.435277 ACAAGTATGGTGCATTTTTCTGAGAT 59.565 34.615 0.00 0.00 0.00 2.75
5169 10189 1.133790 GTGTCTCCATTTGGCAGCATC 59.866 52.381 0.00 0.00 34.44 3.91
5174 10194 3.393609 TCTCCATTTGGCAGCATCTATCT 59.606 43.478 0.00 0.00 34.44 1.98
5210 10230 2.388347 GGAGAGAATCCGTTGCAGC 58.612 57.895 0.00 0.00 38.67 5.25
5222 10242 1.679977 TTGCAGCTGCCATCCTTCC 60.680 57.895 34.64 5.72 41.18 3.46
5280 10307 3.343941 TTTGCGGGAACAATAGCTAGT 57.656 42.857 0.00 0.00 0.00 2.57
5369 10397 1.302033 CACACGAGCCTCTTTGCCT 60.302 57.895 0.00 0.00 0.00 4.75
5370 10398 0.886490 CACACGAGCCTCTTTGCCTT 60.886 55.000 0.00 0.00 0.00 4.35
5371 10399 0.886490 ACACGAGCCTCTTTGCCTTG 60.886 55.000 0.00 0.00 0.00 3.61
5374 10402 2.674380 AGCCTCTTTGCCTTGCCG 60.674 61.111 0.00 0.00 0.00 5.69
5375 10403 2.672996 GCCTCTTTGCCTTGCCGA 60.673 61.111 0.00 0.00 0.00 5.54
5376 10404 2.048603 GCCTCTTTGCCTTGCCGAT 61.049 57.895 0.00 0.00 0.00 4.18
5377 10405 1.997928 GCCTCTTTGCCTTGCCGATC 61.998 60.000 0.00 0.00 0.00 3.69
5378 10406 1.379642 CCTCTTTGCCTTGCCGATCC 61.380 60.000 0.00 0.00 0.00 3.36
5379 10407 1.378514 TCTTTGCCTTGCCGATCCC 60.379 57.895 0.00 0.00 0.00 3.85
5381 10409 1.378514 TTTGCCTTGCCGATCCCTC 60.379 57.895 0.00 0.00 0.00 4.30
5382 10410 2.135903 TTTGCCTTGCCGATCCCTCA 62.136 55.000 0.00 0.00 0.00 3.86
5384 10412 1.378514 GCCTTGCCGATCCCTCAAA 60.379 57.895 0.00 0.00 0.00 2.69
5401 10429 8.262601 TCCCTCAAATGTAGCAAATATCTCTA 57.737 34.615 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 0.736053 GCTCTACAGGTGTCTCCGAG 59.264 60.000 0.00 0.00 41.99 4.63
287 288 4.035675 GCAATTCCCGAATACTGAAGGAAG 59.964 45.833 0.00 0.00 39.83 3.46
293 294 6.533730 AGATTATGCAATTCCCGAATACTGA 58.466 36.000 0.00 0.00 0.00 3.41
339 340 5.353678 ACTGCTATTGCTTTCTTCATGACTC 59.646 40.000 0.00 0.00 40.48 3.36
427 428 6.376864 TGTCATTTGATTAACGGGATCACATT 59.623 34.615 0.00 0.00 33.51 2.71
634 636 3.492102 TGAATATGCCCTAGAGCCAAC 57.508 47.619 0.00 0.00 0.00 3.77
638 640 3.558109 GGAGGTTGAATATGCCCTAGAGC 60.558 52.174 0.00 0.00 0.00 4.09
662 664 0.519519 TTGCAAACGGGAGCATAACG 59.480 50.000 0.00 0.00 40.94 3.18
663 665 1.977188 GTTGCAAACGGGAGCATAAC 58.023 50.000 0.00 0.00 40.94 1.89
681 683 1.134610 ACAAACCGACGTCAAAGAGGT 60.135 47.619 17.16 11.27 36.66 3.85
693 695 3.378112 CCTATAGGACGTACACAAACCGA 59.622 47.826 14.11 0.00 37.39 4.69
737 739 5.069119 AGCGTATCATTTCACTCATAGGTGA 59.931 40.000 0.00 0.00 43.41 4.02
740 742 5.777802 AGAGCGTATCATTTCACTCATAGG 58.222 41.667 0.00 0.00 0.00 2.57
741 743 8.803201 TTTAGAGCGTATCATTTCACTCATAG 57.197 34.615 0.00 0.00 0.00 2.23
742 744 9.594478 TTTTTAGAGCGTATCATTTCACTCATA 57.406 29.630 0.00 0.00 0.00 2.15
744 746 7.602644 AGTTTTTAGAGCGTATCATTTCACTCA 59.397 33.333 0.00 0.00 0.00 3.41
747 749 9.474249 GTAAGTTTTTAGAGCGTATCATTTCAC 57.526 33.333 0.00 0.00 0.00 3.18
815 819 9.709495 ATGTATATGCACATCTTGTTTTTGTTT 57.291 25.926 0.00 0.00 33.89 2.83
816 820 9.142515 CATGTATATGCACATCTTGTTTTTGTT 57.857 29.630 0.00 0.00 37.02 2.83
817 821 8.692110 CATGTATATGCACATCTTGTTTTTGT 57.308 30.769 0.00 0.00 37.02 2.83
840 844 0.450184 GCCGTTAAATGGACACGCAT 59.550 50.000 0.00 0.00 32.43 4.73
848 852 1.398390 GTGAGCTGAGCCGTTAAATGG 59.602 52.381 0.00 0.00 0.00 3.16
971 981 1.153005 CGTCGGCTAGGTAGAGGGT 60.153 63.158 0.00 0.00 0.00 4.34
972 982 1.153005 ACGTCGGCTAGGTAGAGGG 60.153 63.158 0.00 0.00 0.00 4.30
1047 1065 0.909133 TGGGCATAGTGGAGCAGTGA 60.909 55.000 0.00 0.00 0.00 3.41
1191 1248 3.378602 TCTTGCGGGCTGAGCGTA 61.379 61.111 0.00 0.00 37.44 4.42
1629 1697 2.473816 TCACACAAGCTCTTCAGAACG 58.526 47.619 0.00 0.00 0.00 3.95
2022 2250 2.933906 TGAACGAGTTCCAAGTGACAAC 59.066 45.455 12.76 0.00 38.77 3.32
2451 2679 7.554959 AGAACTGAACTAGGGAGTGATAAAA 57.445 36.000 0.00 0.00 35.52 1.52
2825 3053 5.904941 TGCAACATTTGTCTGAACAGAATT 58.095 33.333 6.08 0.00 39.48 2.17
3063 3295 8.846943 AGTGTTGTGATATTGAACTTCACATA 57.153 30.769 11.35 3.90 46.46 2.29
3786 4758 5.809562 TGTCCAAAAATGCAAACACTGTTAG 59.190 36.000 0.00 0.00 0.00 2.34
3937 5804 8.989653 TGTTCGAATAAGTCACACACATATTA 57.010 30.769 0.00 0.00 30.59 0.98
4200 6452 2.368875 ACGAAGTCAGGTCAGGATTGTT 59.631 45.455 0.00 0.00 29.74 2.83
4230 6483 0.468226 AAGGTTTCGTCCTGCACAGA 59.532 50.000 0.00 0.00 37.93 3.41
4270 6526 4.447290 TCTTGACGAATCAACCTTGACAA 58.553 39.130 0.00 0.00 40.01 3.18
4278 6534 6.430451 ACAGATGTTTTCTTGACGAATCAAC 58.570 36.000 0.00 0.00 40.01 3.18
4300 6556 3.159213 ACAAGCCCTGATTCATCAACA 57.841 42.857 0.00 0.00 36.18 3.33
4318 6574 2.739913 GCAAACCGTAGTATCAGCAACA 59.260 45.455 0.00 0.00 0.00 3.33
4327 6583 2.934886 AAAGGGTGCAAACCGTAGTA 57.065 45.000 3.26 0.00 0.00 1.82
4605 8261 2.226330 GGTTGGCACACTGTATCAACA 58.774 47.619 19.72 0.21 39.29 3.33
4606 8262 1.196808 CGGTTGGCACACTGTATCAAC 59.803 52.381 13.99 13.99 39.29 3.18
4607 8263 1.070914 TCGGTTGGCACACTGTATCAA 59.929 47.619 0.00 0.00 39.29 2.57
4608 8264 0.682292 TCGGTTGGCACACTGTATCA 59.318 50.000 0.00 0.00 39.29 2.15
4614 8270 1.600636 CCATGTCGGTTGGCACACT 60.601 57.895 0.00 0.00 39.29 3.55
4669 8325 7.745022 ACAAAAATTGAGATTGCATGATACG 57.255 32.000 0.00 0.00 0.00 3.06
4736 8440 4.101585 TCATAAAGAGATGGCCAGGTACAG 59.898 45.833 13.05 0.00 0.00 2.74
4999 9995 7.861372 CAGATGATAATCTCAGAAAAATGCACC 59.139 37.037 0.00 0.00 37.28 5.01
5004 10005 9.388506 ACGAACAGATGATAATCTCAGAAAAAT 57.611 29.630 0.00 0.00 37.28 1.82
5016 10017 7.201741 CCTTACTCTCAGACGAACAGATGATAA 60.202 40.741 0.00 0.00 0.00 1.75
5169 10189 3.189287 GCAGGGTTGTCAAACACAGATAG 59.811 47.826 2.42 0.00 42.60 2.08
5174 10194 2.102554 CGCAGGGTTGTCAAACACA 58.897 52.632 2.42 0.00 42.60 3.72
5210 10230 3.701664 AGGTAAAAAGGAAGGATGGCAG 58.298 45.455 0.00 0.00 0.00 4.85
5257 10284 3.782889 AGCTATTGTTCCCGCAAATTC 57.217 42.857 0.00 0.00 31.63 2.17
5258 10285 4.270008 ACTAGCTATTGTTCCCGCAAATT 58.730 39.130 0.00 0.00 31.63 1.82
5259 10286 3.886123 ACTAGCTATTGTTCCCGCAAAT 58.114 40.909 0.00 0.00 31.63 2.32
5275 10302 6.806249 TGCTGCAATAAACAAACAATACTAGC 59.194 34.615 0.00 0.00 0.00 3.42
5280 10307 8.774890 ATCAATGCTGCAATAAACAAACAATA 57.225 26.923 6.36 0.00 0.00 1.90
5342 10370 2.868253 GGCTCGTGTGCCCTAATTT 58.132 52.632 1.51 0.00 46.82 1.82
5343 10371 4.637771 GGCTCGTGTGCCCTAATT 57.362 55.556 1.51 0.00 46.82 1.40
5351 10379 3.257933 GGCAAAGAGGCTCGTGTG 58.742 61.111 18.48 14.29 40.24 3.82
5369 10397 2.917933 CTACATTTGAGGGATCGGCAA 58.082 47.619 0.00 0.00 0.00 4.52
5370 10398 1.475034 GCTACATTTGAGGGATCGGCA 60.475 52.381 0.00 0.00 0.00 5.69
5371 10399 1.230324 GCTACATTTGAGGGATCGGC 58.770 55.000 0.00 0.00 0.00 5.54
5374 10402 7.882271 AGAGATATTTGCTACATTTGAGGGATC 59.118 37.037 0.00 0.00 0.00 3.36
5375 10403 7.753630 AGAGATATTTGCTACATTTGAGGGAT 58.246 34.615 0.00 0.00 0.00 3.85
5376 10404 7.141758 AGAGATATTTGCTACATTTGAGGGA 57.858 36.000 0.00 0.00 0.00 4.20
5377 10405 7.933577 TGTAGAGATATTTGCTACATTTGAGGG 59.066 37.037 0.00 0.00 39.46 4.30
5378 10406 8.893219 TGTAGAGATATTTGCTACATTTGAGG 57.107 34.615 0.00 0.00 39.46 3.86


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

AutoCloner maintained by Alex Coulton.