Multiple sequence alignment - TraesCS3A01G402300

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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 TraesCS3A01G402300 chr3A 100.000 2893 0 0 1 2893 647756611 647753719 0.000000e+00 5343
1 TraesCS3A01G402300 chr3A 82.895 304 48 4 1100 1401 59532234 59532535 1.320000e-68 270
2 TraesCS3A01G402300 chr3D 93.292 1938 76 21 973 2893 511726823 511724923 0.000000e+00 2809
3 TraesCS3A01G402300 chr3D 91.785 913 46 18 78 978 511727807 511726912 0.000000e+00 1243
4 TraesCS3A01G402300 chr3D 82.895 304 48 4 1100 1401 47493584 47493885 1.320000e-68 270
5 TraesCS3A01G402300 chr3B 95.055 1092 44 8 973 2058 674063510 674062423 0.000000e+00 1709
6 TraesCS3A01G402300 chr3B 90.781 922 36 20 78 979 674064484 674063592 0.000000e+00 1186
7 TraesCS3A01G402300 chr3B 90.657 578 29 11 2082 2653 674062433 674061875 0.000000e+00 745
8 TraesCS3A01G402300 chr3B 89.960 249 15 3 2651 2893 674061793 674061549 2.160000e-81 313
9 TraesCS3A01G402300 chr3B 82.566 304 49 4 1100 1401 74294229 74294530 6.150000e-67 265
10 TraesCS3A01G402300 chr1B 89.394 396 33 7 1039 1428 475470184 475469792 9.320000e-135 490
11 TraesCS3A01G402300 chr1D 89.141 396 34 7 1039 1428 353557759 353557367 4.330000e-133 484
12 TraesCS3A01G402300 chr1A 88.889 396 35 7 1039 1428 453523585 453523193 2.020000e-131 479
13 TraesCS3A01G402300 chr4B 93.776 241 12 1 1543 1783 37400109 37399872 2.740000e-95 359
14 TraesCS3A01G402300 chr4B 84.351 262 37 3 1109 1368 77651297 77651556 1.330000e-63 254
15 TraesCS3A01G402300 chr2B 97.037 135 4 0 1649 1783 728932995 728933129 8.060000e-56 228


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 TraesCS3A01G402300 chr3A 647753719 647756611 2892 True 5343.00 5343 100.00000 1 2893 1 chr3A.!!$R1 2892
1 TraesCS3A01G402300 chr3D 511724923 511727807 2884 True 2026.00 2809 92.53850 78 2893 2 chr3D.!!$R1 2815
2 TraesCS3A01G402300 chr3B 674061549 674064484 2935 True 988.25 1709 91.61325 78 2893 4 chr3B.!!$R1 2815

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
446 451 0.105709 CTCCCTCTCCCTCTCCTTCC 60.106 65.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2212 0.999406 GCGCACACGTAACAGATCAT 59.001 50.0 0.3 0.0 42.83 2.45 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
41 42 8.779354 AAGTTAAACTATTTTTGGTTTGCACA 57.221 26.923 0.00 0.00 37.01 4.57
42 43 8.419076 AGTTAAACTATTTTTGGTTTGCACAG 57.581 30.769 0.00 0.00 37.01 3.66
43 44 8.038351 AGTTAAACTATTTTTGGTTTGCACAGT 58.962 29.630 0.00 0.00 37.01 3.55
44 45 8.661257 GTTAAACTATTTTTGGTTTGCACAGTT 58.339 29.630 0.00 0.00 37.01 3.16
45 46 7.680442 AAACTATTTTTGGTTTGCACAGTTT 57.320 28.000 0.00 0.00 34.83 2.66
46 47 7.680442 AACTATTTTTGGTTTGCACAGTTTT 57.320 28.000 0.00 0.00 0.00 2.43
47 48 7.680442 ACTATTTTTGGTTTGCACAGTTTTT 57.320 28.000 0.00 0.00 0.00 1.94
48 49 8.779354 ACTATTTTTGGTTTGCACAGTTTTTA 57.221 26.923 0.00 0.00 0.00 1.52
49 50 9.220767 ACTATTTTTGGTTTGCACAGTTTTTAA 57.779 25.926 0.00 0.00 0.00 1.52
50 51 9.484326 CTATTTTTGGTTTGCACAGTTTTTAAC 57.516 29.630 0.00 0.00 0.00 2.01
51 52 6.861065 TTTTGGTTTGCACAGTTTTTAACA 57.139 29.167 0.00 0.00 0.00 2.41
52 53 7.440523 TTTTGGTTTGCACAGTTTTTAACAT 57.559 28.000 0.00 0.00 0.00 2.71
53 54 7.440523 TTTGGTTTGCACAGTTTTTAACATT 57.559 28.000 0.00 0.00 0.00 2.71
54 55 7.440523 TTGGTTTGCACAGTTTTTAACATTT 57.559 28.000 0.00 0.00 0.00 2.32
55 56 7.440523 TGGTTTGCACAGTTTTTAACATTTT 57.559 28.000 0.00 0.00 0.00 1.82
56 57 8.547967 TGGTTTGCACAGTTTTTAACATTTTA 57.452 26.923 0.00 0.00 0.00 1.52
57 58 8.443937 TGGTTTGCACAGTTTTTAACATTTTAC 58.556 29.630 0.00 0.00 0.00 2.01
58 59 8.443937 GGTTTGCACAGTTTTTAACATTTTACA 58.556 29.630 0.00 0.00 0.00 2.41
59 60 9.256715 GTTTGCACAGTTTTTAACATTTTACAC 57.743 29.630 0.00 0.00 0.00 2.90
60 61 8.764524 TTGCACAGTTTTTAACATTTTACACT 57.235 26.923 0.00 0.00 0.00 3.55
61 62 9.856488 TTGCACAGTTTTTAACATTTTACACTA 57.144 25.926 0.00 0.00 0.00 2.74
62 63 9.856488 TGCACAGTTTTTAACATTTTACACTAA 57.144 25.926 0.00 0.00 0.00 2.24
150 151 7.766283 TGATCATGGATACGATTGAGTAGATC 58.234 38.462 0.00 0.00 42.51 2.75
157 158 7.177392 TGGATACGATTGAGTAGATCATCACAT 59.823 37.037 0.00 0.00 37.25 3.21
168 169 3.645212 AGATCATCACATTGACCTCGGAT 59.355 43.478 0.00 0.00 0.00 4.18
204 205 7.627298 ATTCTTTCATTCCATTCTCTCACAG 57.373 36.000 0.00 0.00 0.00 3.66
245 247 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
246 248 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
328 330 0.251916 CTCCGTCCCAAGCCAACATA 59.748 55.000 0.00 0.00 0.00 2.29
423 428 1.751924 CCTAACCTCCTCACTTCTCCG 59.248 57.143 0.00 0.00 0.00 4.63
424 429 1.135333 CTAACCTCCTCACTTCTCCGC 59.865 57.143 0.00 0.00 0.00 5.54
425 430 0.543174 AACCTCCTCACTTCTCCGCT 60.543 55.000 0.00 0.00 0.00 5.52
440 445 1.076339 CGCTTCTCCCTCTCCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
441 446 1.106944 CGCTTCTCCCTCTCCCTCTC 61.107 65.000 0.00 0.00 0.00 3.20
442 447 0.759060 GCTTCTCCCTCTCCCTCTCC 60.759 65.000 0.00 0.00 0.00 3.71
443 448 0.933700 CTTCTCCCTCTCCCTCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
444 449 1.290732 CTTCTCCCTCTCCCTCTCCTT 59.709 57.143 0.00 0.00 0.00 3.36
446 451 0.105709 CTCCCTCTCCCTCTCCTTCC 60.106 65.000 0.00 0.00 0.00 3.46
447 452 0.855855 TCCCTCTCCCTCTCCTTCCA 60.856 60.000 0.00 0.00 0.00 3.53
504 511 0.108756 GCTCGCTCCGTCTAAAAGGT 60.109 55.000 0.00 0.00 0.00 3.50
510 517 0.669318 TCCGTCTAAAAGGTGCAGCG 60.669 55.000 10.78 0.00 0.00 5.18
620 627 1.465777 GCAAAAAGGGTACGTGCGTAT 59.534 47.619 7.72 0.00 32.82 3.06
624 631 3.591196 AAAGGGTACGTGCGTATGTAA 57.409 42.857 7.17 0.00 32.82 2.41
685 693 9.719355 AACTTCTCTTCCTTTCTTTTATCTCTC 57.281 33.333 0.00 0.00 0.00 3.20
686 694 9.100197 ACTTCTCTTCCTTTCTTTTATCTCTCT 57.900 33.333 0.00 0.00 0.00 3.10
687 695 9.586435 CTTCTCTTCCTTTCTTTTATCTCTCTC 57.414 37.037 0.00 0.00 0.00 3.20
688 696 8.073467 TCTCTTCCTTTCTTTTATCTCTCTCC 57.927 38.462 0.00 0.00 0.00 3.71
748 766 1.203052 TCCCAGTTAACTACGCTTCCG 59.797 52.381 8.04 0.00 41.14 4.30
819 837 4.929808 TGCTCAGAAGGAAACGAATTCTAC 59.070 41.667 3.52 0.00 38.18 2.59
830 848 7.547370 AGGAAACGAATTCTACTCTGATTTCTG 59.453 37.037 3.52 0.00 38.18 3.02
831 849 6.654793 AACGAATTCTACTCTGATTTCTGC 57.345 37.500 3.52 0.00 0.00 4.26
854 873 7.406916 TGCCCAGTATTTGTTTCCTTCTAATA 58.593 34.615 0.00 0.00 0.00 0.98
868 887 7.825331 TCCTTCTAATATATAGGAGATGCGG 57.175 40.000 0.00 0.00 33.08 5.69
890 909 6.386654 CGGGTGCATATTTGGTATATTTTCC 58.613 40.000 0.00 0.00 0.00 3.13
915 934 3.161306 GCTTTTTAGGCATCGTTCGTTC 58.839 45.455 0.00 0.00 0.00 3.95
917 936 4.638963 CTTTTTAGGCATCGTTCGTTCTC 58.361 43.478 0.00 0.00 0.00 2.87
920 939 0.389948 AGGCATCGTTCGTTCTCCAC 60.390 55.000 0.00 0.00 0.00 4.02
949 968 9.247861 AGTATTTGGCAAGAGAATAAAATCACT 57.752 29.630 0.00 0.00 0.00 3.41
961 980 9.500864 GAGAATAAAATCACTGATTCTTTCTGC 57.499 33.333 18.96 11.86 38.46 4.26
968 987 9.453572 AAATCACTGATTCTTTCTGCTTATACA 57.546 29.630 4.70 0.00 30.29 2.29
970 989 7.386059 TCACTGATTCTTTCTGCTTATACACA 58.614 34.615 0.00 0.00 0.00 3.72
971 990 8.043113 TCACTGATTCTTTCTGCTTATACACAT 58.957 33.333 0.00 0.00 0.00 3.21
981 1096 6.577103 TCTGCTTATACACATCTTCCTCTTG 58.423 40.000 0.00 0.00 0.00 3.02
988 1103 3.817647 ACACATCTTCCTCTTGTTTCAGC 59.182 43.478 0.00 0.00 0.00 4.26
994 1109 0.886490 CCTCTTGTTTCAGCAGGCGT 60.886 55.000 0.00 0.00 0.00 5.68
1419 1534 1.737363 GCCAAGTACGAGCTCTCCAAG 60.737 57.143 12.85 0.00 0.00 3.61
1432 1547 1.149288 TCTCCAAGTACCAGGTGAGGT 59.851 52.381 0.76 0.00 45.72 3.85
1436 1551 2.372172 CCAAGTACCAGGTGAGGTTTCT 59.628 50.000 0.76 0.00 43.08 2.52
1439 1554 4.790718 AGTACCAGGTGAGGTTTCTTTT 57.209 40.909 0.76 0.00 43.08 2.27
1440 1555 5.899631 AGTACCAGGTGAGGTTTCTTTTA 57.100 39.130 0.76 0.00 43.08 1.52
1533 1650 3.214328 GGTGTTTGACTGTGATCCTTGT 58.786 45.455 0.00 0.00 0.00 3.16
1625 1742 0.602638 TGGCGAGCTTCATCAACGTT 60.603 50.000 0.00 0.00 0.00 3.99
1691 1808 0.674895 GGCAAGACCATCAGTTCGCT 60.675 55.000 0.00 0.00 38.86 4.93
1937 2057 4.319133 CCAGGTGCGGCATTAACT 57.681 55.556 5.72 0.00 0.00 2.24
1939 2059 1.014352 CCAGGTGCGGCATTAACTAC 58.986 55.000 5.72 0.00 0.00 2.73
1940 2060 1.406887 CCAGGTGCGGCATTAACTACT 60.407 52.381 5.72 0.00 0.00 2.57
1941 2061 1.933853 CAGGTGCGGCATTAACTACTC 59.066 52.381 5.72 0.00 0.00 2.59
1950 2070 4.443621 GGCATTAACTACTCCACTCTTCC 58.556 47.826 0.00 0.00 0.00 3.46
1973 2093 1.338200 CCGGTCTTCCTCTTCCACTTG 60.338 57.143 0.00 0.00 0.00 3.16
2067 2187 0.742505 ATGTTGATGATTGGCTGCCG 59.257 50.000 14.98 0.00 0.00 5.69
2073 2193 0.748450 ATGATTGGCTGCCGGATTTG 59.252 50.000 14.98 0.00 0.00 2.32
2074 2194 1.227060 GATTGGCTGCCGGATTTGC 60.227 57.895 14.98 2.26 0.00 3.68
2080 2200 0.525761 GCTGCCGGATTTGCTTGTAA 59.474 50.000 5.05 0.00 0.00 2.41
2084 2208 4.676723 GCTGCCGGATTTGCTTGTAAAATA 60.677 41.667 5.05 0.00 0.00 1.40
2085 2209 5.590530 TGCCGGATTTGCTTGTAAAATAT 57.409 34.783 5.05 0.00 0.00 1.28
2088 2212 6.039616 GCCGGATTTGCTTGTAAAATATTGA 58.960 36.000 5.05 0.00 0.00 2.57
2157 2285 9.350951 ACTGTTTAGCTTTTACTCTGGTTATTT 57.649 29.630 0.00 0.00 0.00 1.40
2225 2353 3.129988 GGTTAGTAGGAGTACATGCACGT 59.870 47.826 0.00 0.00 0.00 4.49
2389 2518 4.630940 GCTATAGCTAGTGGAGTACCGTAG 59.369 50.000 17.75 0.00 37.22 3.51
2390 2519 4.703379 ATAGCTAGTGGAGTACCGTAGT 57.297 45.455 0.00 0.00 39.42 2.73
2391 2520 5.815233 ATAGCTAGTGGAGTACCGTAGTA 57.185 43.478 0.00 0.00 39.42 1.82
2403 2532 5.246307 AGTACCGTAGTAACTCGTAAGGTT 58.754 41.667 0.00 0.00 35.45 3.50
2441 2570 2.795291 TGGCCTCATGGGTACTATCT 57.205 50.000 3.32 0.00 37.43 1.98
2442 2571 3.915346 TGGCCTCATGGGTACTATCTA 57.085 47.619 3.32 0.00 37.43 1.98
2443 2572 4.419984 TGGCCTCATGGGTACTATCTAT 57.580 45.455 3.32 0.00 37.43 1.98
2444 2573 4.353777 TGGCCTCATGGGTACTATCTATC 58.646 47.826 3.32 0.00 37.43 2.08
2565 2694 5.685511 GCGTGCATCTCTTTTTCAAGTTAAA 59.314 36.000 0.00 0.00 0.00 1.52
2626 2761 5.912955 AGCTAAAATGGCGCGAATAATAAAC 59.087 36.000 12.10 0.00 34.52 2.01
2638 2774 7.939386 GCGCGAATAATAAACAAATTAGCATTC 59.061 33.333 12.10 0.00 32.74 2.67
2750 2970 2.110990 CAGTTGCGTTGTGTTGTCATG 58.889 47.619 0.00 0.00 0.00 3.07
2789 3009 4.178545 CCAATTTCAGCAGTTTGGGTAG 57.821 45.455 0.00 0.00 35.93 3.18
2869 3095 9.638300 CATTCTCTGTATAAACTTATCAAACGC 57.362 33.333 0.00 0.00 0.00 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.220767 TGTGCAAACCAAAAATAGTTTAACTTT 57.779 25.926 1.94 0.00 34.52 2.66
16 17 8.779354 TGTGCAAACCAAAAATAGTTTAACTT 57.221 26.923 1.94 0.00 34.52 2.66
17 18 8.038351 ACTGTGCAAACCAAAAATAGTTTAACT 58.962 29.630 2.32 2.32 34.52 2.24
18 19 8.192068 ACTGTGCAAACCAAAAATAGTTTAAC 57.808 30.769 0.00 0.00 34.52 2.01
19 20 8.779354 AACTGTGCAAACCAAAAATAGTTTAA 57.221 26.923 0.00 0.00 34.52 1.52
20 21 8.779354 AAACTGTGCAAACCAAAAATAGTTTA 57.221 26.923 0.00 0.00 35.00 2.01
21 22 7.680442 AAACTGTGCAAACCAAAAATAGTTT 57.320 28.000 0.00 0.00 36.65 2.66
22 23 7.680442 AAAACTGTGCAAACCAAAAATAGTT 57.320 28.000 0.00 0.00 0.00 2.24
23 24 7.680442 AAAAACTGTGCAAACCAAAAATAGT 57.320 28.000 0.00 0.00 0.00 2.12
24 25 9.484326 GTTAAAAACTGTGCAAACCAAAAATAG 57.516 29.630 0.00 0.00 0.00 1.73
25 26 8.999431 TGTTAAAAACTGTGCAAACCAAAAATA 58.001 25.926 0.00 0.00 0.00 1.40
26 27 7.875971 TGTTAAAAACTGTGCAAACCAAAAAT 58.124 26.923 0.00 0.00 0.00 1.82
27 28 7.259290 TGTTAAAAACTGTGCAAACCAAAAA 57.741 28.000 0.00 0.00 0.00 1.94
28 29 6.861065 TGTTAAAAACTGTGCAAACCAAAA 57.139 29.167 0.00 0.00 0.00 2.44
29 30 7.440523 AATGTTAAAAACTGTGCAAACCAAA 57.559 28.000 0.00 0.00 0.00 3.28
30 31 7.440523 AAATGTTAAAAACTGTGCAAACCAA 57.559 28.000 0.00 0.00 0.00 3.67
31 32 7.440523 AAAATGTTAAAAACTGTGCAAACCA 57.559 28.000 0.00 0.00 0.00 3.67
32 33 8.443937 TGTAAAATGTTAAAAACTGTGCAAACC 58.556 29.630 0.00 0.00 0.00 3.27
33 34 9.256715 GTGTAAAATGTTAAAAACTGTGCAAAC 57.743 29.630 0.00 0.00 0.00 2.93
34 35 9.209175 AGTGTAAAATGTTAAAAACTGTGCAAA 57.791 25.926 0.00 0.00 0.00 3.68
35 36 8.764524 AGTGTAAAATGTTAAAAACTGTGCAA 57.235 26.923 0.00 0.00 0.00 4.08
36 37 9.856488 TTAGTGTAAAATGTTAAAAACTGTGCA 57.144 25.926 0.00 0.00 0.00 4.57
63 64 9.875691 ACATCGATGTGCAATATATATGTACTT 57.124 29.630 29.49 0.00 40.03 2.24
70 71 9.325198 GGGAAATACATCGATGTGCAATATATA 57.675 33.333 35.46 16.48 41.89 0.86
71 72 7.828717 TGGGAAATACATCGATGTGCAATATAT 59.171 33.333 35.46 19.24 41.89 0.86
72 73 7.164803 TGGGAAATACATCGATGTGCAATATA 58.835 34.615 35.46 17.88 41.89 0.86
73 74 6.003326 TGGGAAATACATCGATGTGCAATAT 58.997 36.000 35.46 20.58 41.89 1.28
74 75 5.372373 TGGGAAATACATCGATGTGCAATA 58.628 37.500 35.46 19.28 41.89 1.90
75 76 4.206375 TGGGAAATACATCGATGTGCAAT 58.794 39.130 35.46 21.27 41.89 3.56
76 77 3.615155 TGGGAAATACATCGATGTGCAA 58.385 40.909 35.46 20.00 41.89 4.08
85 86 9.657419 AAAATTTCAGTTCATGGGAAATACATC 57.343 29.630 12.56 0.00 39.58 3.06
150 151 2.868583 GACATCCGAGGTCAATGTGATG 59.131 50.000 8.30 0.00 33.91 3.07
157 158 1.905894 TGATTGGACATCCGAGGTCAA 59.094 47.619 14.70 0.46 39.43 3.18
168 169 7.174413 TGGAATGAAAGAATACTGATTGGACA 58.826 34.615 0.00 0.00 0.00 4.02
204 205 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
245 247 7.676043 TGGATGGGTAGATATTAAGGAAGAGAG 59.324 40.741 0.00 0.00 0.00 3.20
246 248 7.544650 TGGATGGGTAGATATTAAGGAAGAGA 58.455 38.462 0.00 0.00 0.00 3.10
309 311 0.251916 TATGTTGGCTTGGGACGGAG 59.748 55.000 0.00 0.00 0.00 4.63
310 312 0.035820 GTATGTTGGCTTGGGACGGA 60.036 55.000 0.00 0.00 0.00 4.69
423 428 0.759060 GGAGAGGGAGAGGGAGAAGC 60.759 65.000 0.00 0.00 0.00 3.86
424 429 0.933700 AGGAGAGGGAGAGGGAGAAG 59.066 60.000 0.00 0.00 0.00 2.85
425 430 1.289530 GAAGGAGAGGGAGAGGGAGAA 59.710 57.143 0.00 0.00 0.00 2.87
440 445 1.133809 CCCTGTGGAGGTTGGAAGGA 61.134 60.000 0.00 0.00 37.73 3.36
441 446 1.380302 CCCTGTGGAGGTTGGAAGG 59.620 63.158 0.00 0.00 37.73 3.46
442 447 1.358152 TACCCTGTGGAGGTTGGAAG 58.642 55.000 0.00 0.00 38.89 3.46
443 448 1.822425 TTACCCTGTGGAGGTTGGAA 58.178 50.000 0.00 0.00 38.89 3.53
444 449 1.822425 TTTACCCTGTGGAGGTTGGA 58.178 50.000 0.00 0.00 38.89 3.53
446 451 2.723273 GGATTTACCCTGTGGAGGTTG 58.277 52.381 0.00 0.00 38.89 3.77
447 452 1.280998 CGGATTTACCCTGTGGAGGTT 59.719 52.381 0.00 0.00 38.89 3.50
577 584 3.243569 ACGATCCTTTTCCGCTATCTCTG 60.244 47.826 0.00 0.00 0.00 3.35
581 588 1.527311 GCACGATCCTTTTCCGCTATC 59.473 52.381 0.00 0.00 0.00 2.08
583 590 0.248012 TGCACGATCCTTTTCCGCTA 59.752 50.000 0.00 0.00 0.00 4.26
584 591 0.605319 TTGCACGATCCTTTTCCGCT 60.605 50.000 0.00 0.00 0.00 5.52
586 593 2.697431 TTTTGCACGATCCTTTTCCG 57.303 45.000 0.00 0.00 0.00 4.30
587 594 3.317150 CCTTTTTGCACGATCCTTTTCC 58.683 45.455 0.00 0.00 0.00 3.13
592 599 2.433436 GTACCCTTTTTGCACGATCCT 58.567 47.619 0.00 0.00 0.00 3.24
593 600 1.129811 CGTACCCTTTTTGCACGATCC 59.870 52.381 0.00 0.00 34.66 3.36
620 627 0.323629 GTGGTGGCTGCCTACTTACA 59.676 55.000 21.03 6.82 0.00 2.41
624 631 3.706373 CGGTGGTGGCTGCCTACT 61.706 66.667 21.03 0.00 0.00 2.57
748 766 1.137675 GCCTTTCTTGGATCAATGGCC 59.862 52.381 0.00 0.00 33.66 5.36
802 820 7.835634 AATCAGAGTAGAATTCGTTTCCTTC 57.164 36.000 0.00 0.00 34.67 3.46
819 837 4.946157 ACAAATACTGGGCAGAAATCAGAG 59.054 41.667 0.00 0.00 33.19 3.35
830 848 6.775594 ATTAGAAGGAAACAAATACTGGGC 57.224 37.500 0.00 0.00 0.00 5.36
854 873 1.644509 TGCACCCGCATCTCCTATAT 58.355 50.000 0.00 0.00 45.36 0.86
868 887 7.867403 CACAGGAAAATATACCAAATATGCACC 59.133 37.037 0.00 0.00 0.00 5.01
890 909 3.492313 GAACGATGCCTAAAAAGCACAG 58.508 45.455 0.00 0.00 44.40 3.66
915 934 2.009774 CTTGCCAAATACTCCGTGGAG 58.990 52.381 14.35 14.35 46.91 3.86
917 936 2.009774 CTCTTGCCAAATACTCCGTGG 58.990 52.381 0.00 0.00 35.39 4.94
920 939 6.677781 TTTATTCTCTTGCCAAATACTCCG 57.322 37.500 0.00 0.00 0.00 4.63
949 968 9.102757 GAAGATGTGTATAAGCAGAAAGAATCA 57.897 33.333 0.00 0.00 0.00 2.57
961 980 8.777865 TGAAACAAGAGGAAGATGTGTATAAG 57.222 34.615 0.00 0.00 0.00 1.73
968 987 4.070716 CTGCTGAAACAAGAGGAAGATGT 58.929 43.478 0.00 0.00 0.00 3.06
970 989 3.683802 CCTGCTGAAACAAGAGGAAGAT 58.316 45.455 0.00 0.00 0.00 2.40
971 990 2.811873 GCCTGCTGAAACAAGAGGAAGA 60.812 50.000 0.00 0.00 0.00 2.87
981 1096 0.884704 TCCTTCACGCCTGCTGAAAC 60.885 55.000 0.00 0.00 0.00 2.78
988 1103 2.825836 GGCCATCCTTCACGCCTG 60.826 66.667 0.00 0.00 38.41 4.85
994 1109 1.945354 GACGACGAGGCCATCCTTCA 61.945 60.000 5.01 0.00 44.46 3.02
1419 1534 6.569801 GCAATAAAAGAAACCTCACCTGGTAC 60.570 42.308 0.00 0.00 39.83 3.34
1432 1547 6.312399 ACGAGTGTGATGCAATAAAAGAAA 57.688 33.333 0.00 0.00 0.00 2.52
1436 1551 3.991121 TCGACGAGTGTGATGCAATAAAA 59.009 39.130 0.00 0.00 0.00 1.52
1439 1554 2.931512 TCGACGAGTGTGATGCAATA 57.068 45.000 0.00 0.00 0.00 1.90
1440 1555 2.159184 AGATCGACGAGTGTGATGCAAT 60.159 45.455 3.01 0.00 0.00 3.56
1691 1808 2.743538 GACAGCATCTGCACGGCA 60.744 61.111 4.79 0.00 45.16 5.69
1748 1865 4.124351 TCGTAGCCGCCGTTCAGG 62.124 66.667 0.00 0.00 44.97 3.86
1811 1928 3.842923 CCGAGCATGCCGAGACCT 61.843 66.667 24.22 1.64 0.00 3.85
1937 2057 2.050350 CGGCCGGAAGAGTGGAGTA 61.050 63.158 20.10 0.00 0.00 2.59
1939 2059 4.148825 CCGGCCGGAAGAGTGGAG 62.149 72.222 41.82 7.45 37.50 3.86
1950 2070 2.184579 GAAGAGGAAGACCGGCCG 59.815 66.667 21.04 21.04 41.83 6.13
1973 2093 7.194607 ACCGTGATGATTTATTCATGATCAC 57.805 36.000 0.00 10.44 45.29 3.06
2080 2200 7.409697 GCACACGTAACAGATCATCAATATTT 58.590 34.615 0.00 0.00 0.00 1.40
2084 2208 3.306973 CGCACACGTAACAGATCATCAAT 59.693 43.478 0.00 0.00 33.53 2.57
2085 2209 2.666022 CGCACACGTAACAGATCATCAA 59.334 45.455 0.00 0.00 33.53 2.57
2088 2212 0.999406 GCGCACACGTAACAGATCAT 59.001 50.000 0.30 0.00 42.83 2.45
2093 2217 2.170985 GCTGCGCACACGTAACAG 59.829 61.111 5.66 0.00 42.83 3.16
2094 2218 3.342627 GGCTGCGCACACGTAACA 61.343 61.111 5.66 0.00 42.83 2.41
2260 2388 3.252215 TGTTTCCACATTGATCGACCAAC 59.748 43.478 0.00 0.00 0.00 3.77
2297 2425 3.194062 GAGCACTATCAAGAGGTCAAGC 58.806 50.000 0.00 0.00 39.66 4.01
2330 2458 5.619981 GCATGGCACCTAAGTTGAAACTAAG 60.620 44.000 0.00 0.00 38.57 2.18
2403 2532 7.888021 TGAGGCCATGACTTAGAAATTTAGAAA 59.112 33.333 5.01 0.00 0.00 2.52
2441 2570 3.517296 AGCTAGCTCTACCTGCTGATA 57.483 47.619 12.68 0.00 41.32 2.15
2442 2571 2.380064 AGCTAGCTCTACCTGCTGAT 57.620 50.000 12.68 0.00 41.32 2.90
2443 2572 3.073798 AGATAGCTAGCTCTACCTGCTGA 59.926 47.826 23.26 0.00 41.32 4.26
2444 2573 3.420893 AGATAGCTAGCTCTACCTGCTG 58.579 50.000 23.26 0.00 41.32 4.41
2474 2603 2.390306 TTTAGGTCGCAGTGGCAGCA 62.390 55.000 0.00 0.00 41.24 4.41
2565 2694 7.625606 GCGCTTAATTTGTCTTACCACTTACAT 60.626 37.037 0.00 0.00 0.00 2.29
2626 2761 7.318141 ACACTGGAAAGATGAATGCTAATTTG 58.682 34.615 0.00 0.00 0.00 2.32
2638 2774 3.849911 TCGAAGCTACACTGGAAAGATG 58.150 45.455 0.00 0.00 0.00 2.90
2750 2970 0.598065 GGGGTGCATCACTGTTGAAC 59.402 55.000 0.00 0.00 34.61 3.18
2869 3095 1.271379 TGCCCAACTGTACGTAGTCAG 59.729 52.381 10.71 10.71 43.93 3.51


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

AutoCloner maintained by Alex Coulton.