Multiple sequence alignment - TraesCS5B01G049200

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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 TraesCS5B01G049200 chr5B 100.000 2669 0 0 1 2669 55027382 55030050 0.000000e+00 4929
1 TraesCS5B01G049200 chr5B 85.915 1065 95 28 530 1571 54859684 54860716 0.000000e+00 1085
2 TraesCS5B01G049200 chr5B 85.837 812 66 22 699 1481 54549063 54549854 0.000000e+00 817
3 TraesCS5B01G049200 chr5B 79.354 867 100 48 734 1543 54830706 54831550 1.090000e-148 536
4 TraesCS5B01G049200 chr5B 77.922 385 37 14 698 1035 54845106 54845489 2.100000e-46 196
5 TraesCS5B01G049200 chr5B 87.821 156 15 4 1027 1181 54847650 54847802 2.110000e-41 180
6 TraesCS5B01G049200 chr5D 92.399 1855 120 11 1 1845 51891872 51893715 0.000000e+00 2625
7 TraesCS5B01G049200 chr5D 82.984 1669 188 52 1 1627 51859896 51861510 0.000000e+00 1421
8 TraesCS5B01G049200 chr5D 86.203 906 74 22 698 1566 51851867 51852758 0.000000e+00 933
9 TraesCS5B01G049200 chr5D 86.391 845 71 28 1843 2660 51893796 51894623 0.000000e+00 883
10 TraesCS5B01G049200 chr5D 85.820 811 69 20 699 1481 51674860 51675652 0.000000e+00 819
11 TraesCS5B01G049200 chr5D 78.261 207 39 6 37 240 58937910 58937707 7.760000e-26 128
12 TraesCS5B01G049200 chr5A 90.534 1067 78 12 1 1063 41045184 41046231 0.000000e+00 1389
13 TraesCS5B01G049200 chr5A 82.247 1673 194 52 1 1628 40933687 40935301 0.000000e+00 1349
14 TraesCS5B01G049200 chr5A 82.247 1673 194 52 1 1628 40967570 40969184 0.000000e+00 1349
15 TraesCS5B01G049200 chr5A 82.128 1673 196 52 1 1628 41004452 41006066 0.000000e+00 1338
16 TraesCS5B01G049200 chr5A 84.316 797 72 25 699 1461 40684276 40685053 0.000000e+00 730
17 TraesCS5B01G049200 chr5A 90.088 565 52 3 1 565 41083722 41084282 0.000000e+00 730
18 TraesCS5B01G049200 chr5A 87.407 540 49 11 1096 1628 41046228 41046755 1.060000e-168 603
19 TraesCS5B01G049200 chr5A 89.277 401 28 3 559 952 41087147 41087539 3.090000e-134 488
20 TraesCS5B01G049200 chr5A 86.154 325 24 11 758 1063 40925041 40925363 5.510000e-87 331
21 TraesCS5B01G049200 chr5A 92.308 143 10 1 949 1091 41087713 41087854 4.510000e-48 202
22 TraesCS5B01G049200 chr5A 87.023 131 10 6 1834 1960 40629563 40629690 9.960000e-30 141
23 TraesCS5B01G049200 chr2D 87.261 157 20 0 1685 1841 512769192 512769348 2.110000e-41 180
24 TraesCS5B01G049200 chr2B 85.821 134 15 4 1685 1816 479013955 479014086 3.580000e-29 139
25 TraesCS5B01G049200 chr1B 86.260 131 14 4 1704 1832 57068262 57068134 3.580000e-29 139
26 TraesCS5B01G049200 chr1B 82.877 146 25 0 1691 1836 491242171 491242026 6.000000e-27 132
27 TraesCS5B01G049200 chr1B 81.818 154 27 1 1685 1837 328643677 328643830 7.760000e-26 128
28 TraesCS5B01G049200 chr4B 78.027 223 41 7 19 237 136262438 136262656 1.670000e-27 134
29 TraesCS5B01G049200 chr4B 84.173 139 18 3 1700 1837 182672265 182672400 6.000000e-27 132
30 TraesCS5B01G049200 chr1D 82.468 154 26 1 1685 1837 366243681 366243834 1.670000e-27 134
31 TraesCS5B01G049200 chr1D 77.833 203 41 4 37 237 273646135 273646335 3.610000e-24 122
32 TraesCS5B01G049200 chr3D 76.786 224 48 4 19 240 261588559 261588780 3.610000e-24 122
33 TraesCS5B01G049200 chr7A 84.298 121 15 4 1700 1818 495571563 495571681 6.040000e-22 115
34 TraesCS5B01G049200 chr7A 76.364 220 47 5 24 241 335927287 335927503 2.170000e-21 113


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 TraesCS5B01G049200 chr5B 55027382 55030050 2668 False 4929.000000 4929 100.000000 1 2669 1 chr5B.!!$F4 2668
1 TraesCS5B01G049200 chr5B 54859684 54860716 1032 False 1085.000000 1085 85.915000 530 1571 1 chr5B.!!$F3 1041
2 TraesCS5B01G049200 chr5B 54549063 54549854 791 False 817.000000 817 85.837000 699 1481 1 chr5B.!!$F1 782
3 TraesCS5B01G049200 chr5B 54830706 54831550 844 False 536.000000 536 79.354000 734 1543 1 chr5B.!!$F2 809
4 TraesCS5B01G049200 chr5D 51891872 51894623 2751 False 1754.000000 2625 89.395000 1 2660 2 chr5D.!!$F4 2659
5 TraesCS5B01G049200 chr5D 51859896 51861510 1614 False 1421.000000 1421 82.984000 1 1627 1 chr5D.!!$F3 1626
6 TraesCS5B01G049200 chr5D 51851867 51852758 891 False 933.000000 933 86.203000 698 1566 1 chr5D.!!$F2 868
7 TraesCS5B01G049200 chr5D 51674860 51675652 792 False 819.000000 819 85.820000 699 1481 1 chr5D.!!$F1 782
8 TraesCS5B01G049200 chr5A 40933687 40935301 1614 False 1349.000000 1349 82.247000 1 1628 1 chr5A.!!$F4 1627
9 TraesCS5B01G049200 chr5A 40967570 40969184 1614 False 1349.000000 1349 82.247000 1 1628 1 chr5A.!!$F5 1627
10 TraesCS5B01G049200 chr5A 41004452 41006066 1614 False 1338.000000 1338 82.128000 1 1628 1 chr5A.!!$F6 1627
11 TraesCS5B01G049200 chr5A 41045184 41046755 1571 False 996.000000 1389 88.970500 1 1628 2 chr5A.!!$F7 1627
12 TraesCS5B01G049200 chr5A 40684276 40685053 777 False 730.000000 730 84.316000 699 1461 1 chr5A.!!$F2 762
13 TraesCS5B01G049200 chr5A 41083722 41087854 4132 False 473.333333 730 90.557667 1 1091 3 chr5A.!!$F8 1090

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
797 3707 1.098869 TGCTAGAAGTCAGAGCTCCG 58.901 55.0 10.93 0.0 37.12 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 5198 0.468226 ACCACCATTCACGACACTGT 59.532 50.0 0.0 0.0 0.0 3.55 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
81 83 3.200825 TGGATTTCTCTAAGAGGCCCTTG 59.799 47.826 14.65 6.82 36.34 3.61
112 114 3.221771 TGTTTGCCTGCAAAGACTACAT 58.778 40.909 16.98 0.00 45.16 2.29
202 204 2.710377 AGCACATCGTAGAAATTGCCA 58.290 42.857 0.00 0.00 43.58 4.92
215 217 6.966435 AGAAATTGCCAATGTAAAATTCGG 57.034 33.333 0.00 0.00 0.00 4.30
230 232 4.931661 AATTCGGTAAAGATCGCCTCTA 57.068 40.909 0.00 0.00 32.41 2.43
243 253 1.341209 CGCCTCTATGGTGCATGACTA 59.659 52.381 0.00 0.00 39.73 2.59
247 257 4.021104 GCCTCTATGGTGCATGACTACATA 60.021 45.833 0.00 0.00 38.35 2.29
253 263 5.612725 TGGTGCATGACTACATATGAAGA 57.387 39.130 10.38 0.00 35.09 2.87
301 314 3.004419 TCTGTGAAGACTAACCACGACAG 59.996 47.826 0.00 0.00 33.78 3.51
322 335 2.029020 GGGCCACTCAAAATTCTTCACC 60.029 50.000 4.39 0.00 0.00 4.02
401 414 6.423182 TCGTCATTTTCTATGATTTTCCCCT 58.577 36.000 0.00 0.00 0.00 4.79
444 457 6.315714 TCTCGAGGATAATTCTAGAACCCAT 58.684 40.000 13.56 1.15 0.00 4.00
473 486 2.955660 TCAAACATTTCGCCAAGAAGGT 59.044 40.909 0.00 0.00 40.40 3.50
476 489 2.863809 ACATTTCGCCAAGAAGGTTCT 58.136 42.857 0.00 0.00 40.40 3.01
477 490 2.554032 ACATTTCGCCAAGAAGGTTCTG 59.446 45.455 0.00 0.00 40.40 3.02
642 3539 8.844244 AGAATCAGATGCTCATTAAAATGGTAC 58.156 33.333 3.00 0.00 37.03 3.34
664 3573 7.117812 GGTACGCATCATGCTTAATAAGTACAT 59.882 37.037 17.90 0.00 42.25 2.29
669 3578 7.573843 GCATCATGCTTAATAAGTACATGACCC 60.574 40.741 18.73 12.21 46.99 4.46
779 3688 7.600752 GTCGAATAGGGGATAGAAGAGAATTTG 59.399 40.741 0.00 0.00 0.00 2.32
783 3693 6.432403 AGGGGATAGAAGAGAATTTGCTAG 57.568 41.667 0.00 0.00 0.00 3.42
797 3707 1.098869 TGCTAGAAGTCAGAGCTCCG 58.901 55.000 10.93 0.00 37.12 4.63
835 3748 8.373981 CAATATAATCCATTGTATTTTGGCCCA 58.626 33.333 0.00 0.00 33.58 5.36
896 3814 2.509166 TCGATACTCCACAGTCCACT 57.491 50.000 0.00 0.00 33.62 4.00
929 3887 1.377202 GGAGCTCGGCATTTGTCCA 60.377 57.895 7.83 0.00 0.00 4.02
962 4103 4.519540 ATCACCTTTTTCCGGTCAAATG 57.480 40.909 0.00 4.72 30.82 2.32
1042 4191 1.808411 CCCAACTCTAAGCAAGCGAA 58.192 50.000 0.00 0.00 0.00 4.70
1080 4229 3.166489 AGCCTCGTATACAAGAGCAAC 57.834 47.619 3.32 0.00 33.39 4.17
1128 4339 0.250858 TACACTGAAGACCGGGTCGA 60.251 55.000 20.87 8.71 37.67 4.20
1192 4403 0.826062 TGATCTTCGGCATGAGCTCA 59.174 50.000 20.79 20.79 41.70 4.26
1267 4478 1.448497 GGTGGTGGAACTGGACGAA 59.552 57.895 0.00 0.00 36.74 3.85
1298 4509 0.827368 GAAGGAGATGGAGAAGGCGT 59.173 55.000 0.00 0.00 0.00 5.68
1502 4726 7.650504 TGCAGAGAATAATGTAATACACGTACC 59.349 37.037 0.00 0.00 0.00 3.34
1697 4922 4.602340 ATGAACAGTACTCACTCCGTTT 57.398 40.909 0.00 0.00 30.46 3.60
1754 4979 9.537192 AATCGGATGAATATAGACACGTTTTAA 57.463 29.630 0.00 0.00 0.00 1.52
1773 4998 8.259194 CGTTTTAATGTGTTTGTTCACTCATTC 58.741 33.333 4.80 0.00 40.01 2.67
1779 5004 4.576463 GTGTTTGTTCACTCATTCCAGTCT 59.424 41.667 0.00 0.00 35.68 3.24
1783 5008 5.745312 TGTTCACTCATTCCAGTCTGTAT 57.255 39.130 0.00 0.00 0.00 2.29
1791 5016 4.649674 TCATTCCAGTCTGTATGTAGTCCC 59.350 45.833 0.00 0.00 0.00 4.46
1792 5017 4.332683 TTCCAGTCTGTATGTAGTCCCT 57.667 45.455 0.00 0.00 0.00 4.20
1796 5021 5.546499 TCCAGTCTGTATGTAGTCCCTTTTT 59.454 40.000 0.00 0.00 0.00 1.94
1897 5206 9.723447 GGATCTAATGATACATATACAGTGTCG 57.277 37.037 0.00 0.00 33.72 4.35
1907 5216 2.448926 TACAGTGTCGTGAATGGTGG 57.551 50.000 0.00 0.00 0.00 4.61
1938 5247 4.816385 TCTGTAACCTTGCTCAAACTTCAG 59.184 41.667 0.00 0.00 0.00 3.02
1948 5257 7.540055 CCTTGCTCAAACTTCAGAAATATTGAC 59.460 37.037 0.00 0.00 0.00 3.18
1950 5259 8.846943 TGCTCAAACTTCAGAAATATTGACTA 57.153 30.769 0.00 0.00 0.00 2.59
2013 5323 8.045176 TCTTTTCTTTTGAGAATAAGCTAGGC 57.955 34.615 0.00 0.00 0.00 3.93
2022 5332 6.040878 TGAGAATAAGCTAGGCGAAGTAAAC 58.959 40.000 0.00 0.00 0.00 2.01
2025 5335 7.779073 AGAATAAGCTAGGCGAAGTAAACTTA 58.221 34.615 0.00 0.00 36.11 2.24
2031 5341 6.368243 AGCTAGGCGAAGTAAACTTAAACTTC 59.632 38.462 7.44 7.44 45.26 3.01
2033 5343 5.370679 AGGCGAAGTAAACTTAAACTTCCA 58.629 37.500 10.68 0.00 45.72 3.53
2034 5344 5.824097 AGGCGAAGTAAACTTAAACTTCCAA 59.176 36.000 10.68 0.00 45.72 3.53
2037 5347 7.650504 GGCGAAGTAAACTTAAACTTCCAAAAT 59.349 33.333 10.68 0.00 45.72 1.82
2102 5412 7.549615 TTCAAAATTGTGATGAATGTTGCAA 57.450 28.000 0.00 0.00 32.55 4.08
2109 5419 7.789273 TTGTGATGAATGTTGCAAAGAAAAT 57.211 28.000 0.00 0.00 0.00 1.82
2111 5421 8.883954 TGTGATGAATGTTGCAAAGAAAATAA 57.116 26.923 0.00 0.00 0.00 1.40
2112 5422 9.322773 TGTGATGAATGTTGCAAAGAAAATAAA 57.677 25.926 0.00 0.00 0.00 1.40
2154 5464 2.046285 GGCCCCACCATGAAACTCG 61.046 63.158 0.00 0.00 38.86 4.18
2162 5472 4.062293 CCACCATGAAACTCGTCTTTGTA 58.938 43.478 0.00 0.00 0.00 2.41
2163 5473 4.084013 CCACCATGAAACTCGTCTTTGTAC 60.084 45.833 0.00 0.00 0.00 2.90
2178 5488 1.857965 TGTACTCATGCAGCTCCTCT 58.142 50.000 0.00 0.00 0.00 3.69
2189 5503 2.936912 GCTCCTCTGACGTGTGGCT 61.937 63.158 0.00 0.00 0.00 4.75
2194 5508 4.320456 CTGACGTGTGGCTGCCCT 62.320 66.667 17.53 0.00 0.00 5.19
2196 5510 2.244117 CTGACGTGTGGCTGCCCTAT 62.244 60.000 17.53 0.00 0.00 2.57
2203 5517 1.694150 TGTGGCTGCCCTATATGAGTC 59.306 52.381 17.53 0.00 0.00 3.36
2214 5543 1.645710 ATATGAGTCATCCCCCGACC 58.354 55.000 9.42 0.00 33.70 4.79
2223 5552 4.778143 CCCCCGACCGGCTGAAAG 62.778 72.222 0.00 0.00 0.00 2.62
2235 5564 1.648467 GCTGAAAGTAAGCCCCTGCG 61.648 60.000 0.00 0.00 38.57 5.18
2236 5565 1.648467 CTGAAAGTAAGCCCCTGCGC 61.648 60.000 0.00 0.00 44.33 6.09
2250 5579 2.888534 GCGCGCGATGAACCCTTA 60.889 61.111 37.18 0.00 0.00 2.69
2251 5580 3.003478 CGCGCGATGAACCCTTAC 58.997 61.111 28.94 0.00 0.00 2.34
2263 5594 2.284493 CCTTACGGAGGCCCCCTA 59.716 66.667 0.11 0.00 39.09 3.53
2279 5610 1.000163 CCCTATACGTCGCTCATTGCT 60.000 52.381 0.00 0.00 40.11 3.91
2281 5612 3.305131 CCCTATACGTCGCTCATTGCTAA 60.305 47.826 0.00 0.00 40.11 3.09
2292 5623 3.612479 GCTCATTGCTAATTATTGGCGGG 60.612 47.826 8.66 1.37 40.39 6.13
2293 5624 2.295909 TCATTGCTAATTATTGGCGGGC 59.704 45.455 8.66 0.00 40.39 6.13
2294 5625 1.769026 TTGCTAATTATTGGCGGGCA 58.231 45.000 8.66 0.00 40.39 5.36
2298 5629 1.680735 CTAATTATTGGCGGGCAAGCA 59.319 47.619 21.74 11.33 39.27 3.91
2301 5632 1.181741 TTATTGGCGGGCAAGCACAA 61.182 50.000 21.74 10.39 39.27 3.33
2307 5638 4.362476 GGGCAAGCACAAAGGGCG 62.362 66.667 0.00 0.00 36.08 6.13
2310 5641 1.657556 GCAAGCACAAAGGGCGTAA 59.342 52.632 0.00 0.00 36.08 3.18
2321 5652 3.637184 GGGCGTAACTTCCCTTTCA 57.363 52.632 0.00 0.00 39.46 2.69
2322 5653 2.124277 GGGCGTAACTTCCCTTTCAT 57.876 50.000 0.00 0.00 39.46 2.57
2329 5660 5.390991 GCGTAACTTCCCTTTCATTCTTCTG 60.391 44.000 0.00 0.00 0.00 3.02
2485 5818 8.739039 CCTGAATTCAAGTATGTTCACCAATTA 58.261 33.333 9.88 0.00 0.00 1.40
2541 5875 9.588774 CATGTGTTTCAAAAATGTTCATGAATC 57.411 29.630 12.12 6.28 34.14 2.52
2617 5951 7.781324 ATGATTTCTAAAAGAGGCAAAGGAA 57.219 32.000 0.00 0.00 0.00 3.36
2660 5994 3.749226 AGGCAGCCTAAAATAGAGATGC 58.251 45.455 14.18 0.00 37.53 3.91
2661 5995 3.393941 AGGCAGCCTAAAATAGAGATGCT 59.606 43.478 14.18 0.00 37.99 3.79
2662 5996 4.594920 AGGCAGCCTAAAATAGAGATGCTA 59.405 41.667 14.18 0.00 37.99 3.49
2663 5997 5.250313 AGGCAGCCTAAAATAGAGATGCTAT 59.750 40.000 14.18 0.00 37.99 2.97
2664 5998 5.353678 GGCAGCCTAAAATAGAGATGCTATG 59.646 44.000 3.29 0.00 39.73 2.23
2665 5999 6.169094 GCAGCCTAAAATAGAGATGCTATGA 58.831 40.000 0.00 0.00 39.73 2.15
2666 6000 6.652481 GCAGCCTAAAATAGAGATGCTATGAA 59.348 38.462 0.00 0.00 39.73 2.57
2667 6001 7.173907 GCAGCCTAAAATAGAGATGCTATGAAA 59.826 37.037 0.00 0.00 39.73 2.69
2668 6002 9.060347 CAGCCTAAAATAGAGATGCTATGAAAA 57.940 33.333 0.00 0.00 39.73 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.056050 TCTAACACCTTCGAAGACAAAGC 58.944 43.478 26.61 0.00 34.32 3.51
73 75 1.710809 ACAAGTGATAACCAAGGGCCT 59.289 47.619 0.00 0.00 0.00 5.19
75 77 3.860754 GCAAACAAGTGATAACCAAGGGC 60.861 47.826 0.00 0.00 0.00 5.19
81 83 2.295909 TGCAGGCAAACAAGTGATAACC 59.704 45.455 0.00 0.00 0.00 2.85
112 114 0.179004 CAGTGCCACAACCAACCCTA 60.179 55.000 0.00 0.00 0.00 3.53
162 164 3.430790 GCTTTTTCTTCACCAAAGCCTGT 60.431 43.478 4.80 0.00 44.43 4.00
202 204 6.317893 AGGCGATCTTTACCGAATTTTACATT 59.682 34.615 0.00 0.00 0.00 2.71
215 217 3.060602 GCACCATAGAGGCGATCTTTAC 58.939 50.000 0.00 0.00 43.14 2.01
230 232 6.178607 TCTTCATATGTAGTCATGCACCAT 57.821 37.500 8.95 0.00 35.70 3.55
243 253 4.807834 CACGAGCTTGTCATCTTCATATGT 59.192 41.667 2.72 0.00 0.00 2.29
247 257 3.599730 TCACGAGCTTGTCATCTTCAT 57.400 42.857 2.72 0.00 0.00 2.57
253 263 3.369147 CGATTTCTTCACGAGCTTGTCAT 59.631 43.478 2.72 0.00 0.00 3.06
301 314 2.029020 GGTGAAGAATTTTGAGTGGCCC 60.029 50.000 0.00 0.00 0.00 5.80
322 335 2.819595 CGGGCCGAACATGTCCAG 60.820 66.667 24.41 0.00 0.00 3.86
444 457 6.536582 TCTTGGCGAAATGTTTGAAAATTTCA 59.463 30.769 15.85 4.03 41.02 2.69
556 582 2.872038 GCGAAGAACTTCTGGGTGATGT 60.872 50.000 11.85 0.00 37.44 3.06
566 3463 4.504826 GGAGTATAAGCTGCGAAGAACTTC 59.495 45.833 0.00 4.67 36.29 3.01
664 3573 2.855209 CCAAAATTGCATTGGGGTCA 57.145 45.000 9.35 0.00 42.95 4.02
669 3578 0.036577 TCCGCCCAAAATTGCATTGG 60.037 50.000 10.13 10.13 45.62 3.16
779 3688 1.099689 ACGGAGCTCTGACTTCTAGC 58.900 55.000 29.29 0.00 36.48 3.42
783 3693 1.446966 GGCACGGAGCTCTGACTTC 60.447 63.158 29.29 13.27 44.79 3.01
797 3707 7.944729 ATGGATTATATTGTGGATAAGGCAC 57.055 36.000 0.00 0.00 0.00 5.01
835 3748 1.102978 GCGGTTACCTGATGCCAAAT 58.897 50.000 0.00 0.00 0.00 2.32
849 3767 3.825611 GGCAATGGCGATGCGGTT 61.826 61.111 8.02 0.00 44.75 4.44
896 3814 1.597854 CTCCTTTGCGCCACTCACA 60.598 57.895 4.18 0.00 0.00 3.58
929 3887 1.665137 AAGGTGATACGGGAGGGTTT 58.335 50.000 0.00 0.00 0.00 3.27
962 4103 0.602372 GGCAGGATGATCTTCGAGCC 60.602 60.000 19.91 19.91 39.69 4.70
1042 4191 3.763897 AGGCTTTGACTTTTGAGTTGTGT 59.236 39.130 0.00 0.00 0.00 3.72
1192 4403 2.967397 GTGTGGCACATGCAGCAT 59.033 55.556 24.95 0.52 44.52 3.79
1502 4726 4.111375 AGGATAACAGAGCAACGTACAG 57.889 45.455 0.00 0.00 0.00 2.74
1509 4733 6.946340 TGATACAGAAAGGATAACAGAGCAA 58.054 36.000 0.00 0.00 0.00 3.91
1547 4772 1.479323 CACCTGCATGATTTCCTTGGG 59.521 52.381 0.00 0.00 0.00 4.12
1578 4803 5.729718 ACAGGTATTCCCAGGTACAGTTTAT 59.270 40.000 0.00 0.00 34.66 1.40
1588 4813 1.486726 GACAGGACAGGTATTCCCAGG 59.513 57.143 0.00 0.00 33.01 4.45
1595 4820 4.706842 AACACTTTGACAGGACAGGTAT 57.293 40.909 0.00 0.00 0.00 2.73
1725 4950 6.745116 ACGTGTCTATATTCATCCGATTCAA 58.255 36.000 0.00 0.00 0.00 2.69
1747 4972 7.678194 ATGAGTGAACAAACACATTAAAACG 57.322 32.000 0.00 0.00 42.45 3.60
1754 4979 4.889409 ACTGGAATGAGTGAACAAACACAT 59.111 37.500 0.00 0.00 42.45 3.21
1767 4992 5.221342 GGGACTACATACAGACTGGAATGAG 60.221 48.000 20.71 16.09 0.00 2.90
1773 4998 5.422214 AAAAGGGACTACATACAGACTGG 57.578 43.478 7.51 0.00 38.49 4.00
1889 5198 0.468226 ACCACCATTCACGACACTGT 59.532 50.000 0.00 0.00 0.00 3.55
1891 5200 3.695830 AATACCACCATTCACGACACT 57.304 42.857 0.00 0.00 0.00 3.55
1959 5268 5.297527 ACCTCGGTTTTGTTTACTTAACCTG 59.702 40.000 0.00 0.00 38.27 4.00
1989 5298 6.963805 CGCCTAGCTTATTCTCAAAAGAAAAG 59.036 38.462 0.00 0.56 44.49 2.27
2004 5314 7.381323 AGTTTAAGTTTACTTCGCCTAGCTTA 58.619 34.615 0.00 0.00 37.40 3.09
2007 5317 6.477669 AAGTTTAAGTTTACTTCGCCTAGC 57.522 37.500 0.00 0.00 37.40 3.42
2082 5392 7.789273 TTCTTTGCAACATTCATCACAATTT 57.211 28.000 0.00 0.00 0.00 1.82
2111 5421 9.111613 CCCACACATGCAAAATTTTCATATATT 57.888 29.630 0.00 0.00 0.00 1.28
2112 5422 7.227116 GCCCACACATGCAAAATTTTCATATAT 59.773 33.333 0.00 0.00 0.00 0.86
2113 5423 6.538021 GCCCACACATGCAAAATTTTCATATA 59.462 34.615 0.00 0.00 0.00 0.86
2122 5432 1.678724 GGGCCCACACATGCAAAAT 59.321 52.632 19.95 0.00 0.00 1.82
2154 5464 2.675348 GGAGCTGCATGAGTACAAAGAC 59.325 50.000 0.00 0.00 0.00 3.01
2162 5472 0.536260 GTCAGAGGAGCTGCATGAGT 59.464 55.000 8.35 0.00 44.52 3.41
2163 5473 0.528033 CGTCAGAGGAGCTGCATGAG 60.528 60.000 8.35 2.40 44.52 2.90
2178 5488 0.973496 TATAGGGCAGCCACACGTCA 60.973 55.000 15.19 0.00 0.00 4.35
2189 5503 2.551270 GGGGATGACTCATATAGGGCA 58.449 52.381 0.00 0.00 0.00 5.36
2194 5508 2.816411 GGTCGGGGGATGACTCATATA 58.184 52.381 0.00 0.00 36.58 0.86
2196 5510 0.826256 CGGTCGGGGGATGACTCATA 60.826 60.000 0.00 0.00 36.58 2.15
2218 5547 1.674322 GCGCAGGGGCTTACTTTCA 60.674 57.895 0.30 0.00 38.10 2.69
2232 5561 3.650907 TAAGGGTTCATCGCGCGCA 62.651 57.895 32.61 18.69 0.00 6.09
2235 5564 3.003478 CGTAAGGGTTCATCGCGC 58.997 61.111 0.00 0.00 0.00 6.86
2248 5577 0.540365 CGTATAGGGGGCCTCCGTAA 60.540 60.000 18.50 6.41 39.10 3.18
2249 5578 1.075482 CGTATAGGGGGCCTCCGTA 59.925 63.158 18.50 15.09 39.84 4.02
2250 5579 2.203596 CGTATAGGGGGCCTCCGT 60.204 66.667 18.50 12.41 34.61 4.69
2251 5580 2.203596 ACGTATAGGGGGCCTCCG 60.204 66.667 18.50 6.30 34.61 4.63
2279 5610 1.407258 GTGCTTGCCCGCCAATAATTA 59.593 47.619 0.00 0.00 31.91 1.40
2281 5612 0.969917 TGTGCTTGCCCGCCAATAAT 60.970 50.000 0.00 0.00 31.91 1.28
2292 5623 0.663269 GTTACGCCCTTTGTGCTTGC 60.663 55.000 0.00 0.00 0.00 4.01
2293 5624 0.951558 AGTTACGCCCTTTGTGCTTG 59.048 50.000 0.00 0.00 0.00 4.01
2294 5625 1.607148 GAAGTTACGCCCTTTGTGCTT 59.393 47.619 0.00 0.00 0.00 3.91
2298 5629 3.334413 GGGAAGTTACGCCCTTTGT 57.666 52.632 8.69 0.00 41.31 2.83
2307 5638 6.004574 ACCAGAAGAATGAAAGGGAAGTTAC 58.995 40.000 0.00 0.00 0.00 2.50
2310 5641 4.731313 ACCAGAAGAATGAAAGGGAAGT 57.269 40.909 0.00 0.00 0.00 3.01
2321 5652 5.485209 ACCGACTAGAAAACCAGAAGAAT 57.515 39.130 0.00 0.00 0.00 2.40
2322 5653 4.950205 ACCGACTAGAAAACCAGAAGAA 57.050 40.909 0.00 0.00 0.00 2.52
2329 5660 4.301628 TCGAGAAAACCGACTAGAAAACC 58.698 43.478 0.00 0.00 0.00 3.27
2358 5689 7.560991 TGACATGAATAATTCCATAGTTGCCTT 59.439 33.333 0.00 0.00 0.00 4.35
2359 5690 7.062322 TGACATGAATAATTCCATAGTTGCCT 58.938 34.615 0.00 0.00 0.00 4.75
2397 5728 9.620259 TTCTTGGGCATTTTTAAAACATTAAGT 57.380 25.926 0.00 0.00 0.00 2.24
2403 5734 7.148018 TGCAAATTCTTGGGCATTTTTAAAACA 60.148 29.630 0.00 0.00 32.76 2.83
2404 5735 7.199078 TGCAAATTCTTGGGCATTTTTAAAAC 58.801 30.769 0.00 0.00 32.76 2.43
2436 5767 8.199449 CAGGAGTATATTTAAAGTACCCGAACA 58.801 37.037 8.95 0.00 0.00 3.18
2437 5768 8.416329 TCAGGAGTATATTTAAAGTACCCGAAC 58.584 37.037 8.95 0.00 0.00 3.95
2438 5769 8.537728 TCAGGAGTATATTTAAAGTACCCGAA 57.462 34.615 8.95 3.96 0.00 4.30
2440 5771 9.774413 AATTCAGGAGTATATTTAAAGTACCCG 57.226 33.333 8.95 7.52 0.00 5.28
2456 5789 5.940470 GGTGAACATACTTGAATTCAGGAGT 59.060 40.000 23.00 18.82 31.94 3.85
2512 5845 8.196103 TCATGAACATTTTTGAAACACATGAGA 58.804 29.630 0.00 0.00 37.34 3.27
2516 5849 9.550406 AGATTCATGAACATTTTTGAAACACAT 57.450 25.926 11.07 0.00 32.35 3.21
2632 5966 6.948309 TCTCTATTTTAGGCTGCCTTTCTTTT 59.052 34.615 28.55 9.84 34.61 2.27
2641 5975 6.169094 TCATAGCATCTCTATTTTAGGCTGC 58.831 40.000 0.00 0.00 35.86 5.25


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

AutoCloner maintained by Alex Coulton.