Multiple sequence alignment - TraesCS5D01G258200

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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 TraesCS5D01G258200 chr5D 100.000 4570 0 0 1 4570 364736343 364740912 0.000000e+00 8440
1 TraesCS5D01G258200 chr5B 95.983 3610 118 16 574 4161 430732643 430736247 0.000000e+00 5838
2 TraesCS5D01G258200 chr5B 94.767 344 14 3 218 558 430732314 430732656 2.420000e-147 532
3 TraesCS5D01G258200 chr5B 83.133 415 37 15 4176 4570 430736346 430736747 9.410000e-92 348
4 TraesCS5D01G258200 chr5B 100.000 80 0 0 107 186 430732135 430732214 1.020000e-31 148
5 TraesCS5D01G258200 chr5A 94.907 2533 73 23 724 3228 466012904 466015408 0.000000e+00 3912
6 TraesCS5D01G258200 chr5A 93.567 886 45 6 3282 4161 466015575 466016454 0.000000e+00 1310
7 TraesCS5D01G258200 chr5A 95.477 398 16 2 4174 4570 466016534 466016930 6.450000e-178 634


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 TraesCS5D01G258200 chr5D 364736343 364740912 4569 False 8440.0 8440 100.000000 1 4570 1 chr5D.!!$F1 4569
1 TraesCS5D01G258200 chr5B 430732135 430736747 4612 False 1716.5 5838 93.470750 107 4570 4 chr5B.!!$F1 4463
2 TraesCS5D01G258200 chr5A 466012904 466016930 4026 False 1952.0 3912 94.650333 724 4570 3 chr5A.!!$F1 3846

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
690 765 1.142262 CCATGCTCCTGTGATGGATGA 59.858 52.381 0.00 0.0 39.29 2.92 F
821 902 3.054655 GGCCCAATAGAATTATAGCCCGA 60.055 47.826 0.00 0.0 32.93 5.14 F
1641 1742 3.056179 TGACATTGGTGAGCGTAATCTCA 60.056 43.478 0.00 0.0 40.50 3.27 F
2343 2444 0.117340 AGAAGGTACCTGGGAGCAGT 59.883 55.000 17.14 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1742 0.460284 CTCCCAAGTACGCGATTGCT 60.460 55.000 15.93 0.0 39.65 3.91 R
1806 1907 1.068250 GGTATCCACGCTCCTCAGC 59.932 63.158 0.00 0.0 42.96 4.26 R
3192 3300 1.302192 TTGGTCCTGTGGCTTACGC 60.302 57.895 0.00 0.0 0.00 4.42 R
4319 4633 1.901591 ATGGCTCAAACACTCCACAG 58.098 50.000 0.00 0.0 0.00 3.66 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 2.271777 TCGGAAATTGAGGGGTTAGGT 58.728 47.619 0.00 0.00 0.00 3.08
21 22 2.645797 TCGGAAATTGAGGGGTTAGGTT 59.354 45.455 0.00 0.00 0.00 3.50
22 23 3.074836 TCGGAAATTGAGGGGTTAGGTTT 59.925 43.478 0.00 0.00 0.00 3.27
23 24 3.830178 CGGAAATTGAGGGGTTAGGTTTT 59.170 43.478 0.00 0.00 0.00 2.43
24 25 4.321675 CGGAAATTGAGGGGTTAGGTTTTG 60.322 45.833 0.00 0.00 0.00 2.44
25 26 4.836175 GGAAATTGAGGGGTTAGGTTTTGA 59.164 41.667 0.00 0.00 0.00 2.69
26 27 5.305902 GGAAATTGAGGGGTTAGGTTTTGAA 59.694 40.000 0.00 0.00 0.00 2.69
27 28 6.419484 AAATTGAGGGGTTAGGTTTTGAAG 57.581 37.500 0.00 0.00 0.00 3.02
28 29 4.529716 TTGAGGGGTTAGGTTTTGAAGT 57.470 40.909 0.00 0.00 0.00 3.01
29 30 4.529716 TGAGGGGTTAGGTTTTGAAGTT 57.470 40.909 0.00 0.00 0.00 2.66
30 31 4.466827 TGAGGGGTTAGGTTTTGAAGTTC 58.533 43.478 0.00 0.00 0.00 3.01
31 32 3.825014 GAGGGGTTAGGTTTTGAAGTTCC 59.175 47.826 0.00 0.00 0.00 3.62
32 33 3.465966 AGGGGTTAGGTTTTGAAGTTCCT 59.534 43.478 0.00 0.00 0.00 3.36
33 34 4.078805 AGGGGTTAGGTTTTGAAGTTCCTT 60.079 41.667 0.00 0.00 0.00 3.36
34 35 5.134850 AGGGGTTAGGTTTTGAAGTTCCTTA 59.865 40.000 0.00 0.00 0.00 2.69
35 36 6.014647 GGGGTTAGGTTTTGAAGTTCCTTAT 58.985 40.000 0.00 0.00 0.00 1.73
36 37 7.018851 AGGGGTTAGGTTTTGAAGTTCCTTATA 59.981 37.037 0.00 0.00 0.00 0.98
37 38 7.338703 GGGGTTAGGTTTTGAAGTTCCTTATAG 59.661 40.741 0.00 0.00 0.00 1.31
38 39 8.105197 GGGTTAGGTTTTGAAGTTCCTTATAGA 58.895 37.037 0.00 0.00 0.00 1.98
39 40 9.511272 GGTTAGGTTTTGAAGTTCCTTATAGAA 57.489 33.333 0.00 0.00 0.00 2.10
67 68 3.996480 CCCTCGGGTCTCTTTATTCATC 58.004 50.000 0.00 0.00 0.00 2.92
68 69 3.388024 CCCTCGGGTCTCTTTATTCATCA 59.612 47.826 0.00 0.00 0.00 3.07
69 70 4.502259 CCCTCGGGTCTCTTTATTCATCAG 60.502 50.000 0.00 0.00 0.00 2.90
70 71 4.100189 CCTCGGGTCTCTTTATTCATCAGT 59.900 45.833 0.00 0.00 0.00 3.41
71 72 5.011090 TCGGGTCTCTTTATTCATCAGTG 57.989 43.478 0.00 0.00 0.00 3.66
72 73 4.122776 CGGGTCTCTTTATTCATCAGTGG 58.877 47.826 0.00 0.00 0.00 4.00
73 74 4.141937 CGGGTCTCTTTATTCATCAGTGGA 60.142 45.833 0.00 0.00 0.00 4.02
74 75 5.119694 GGGTCTCTTTATTCATCAGTGGAC 58.880 45.833 0.00 0.00 0.00 4.02
75 76 5.338381 GGGTCTCTTTATTCATCAGTGGACA 60.338 44.000 0.00 0.00 0.00 4.02
76 77 6.173339 GGTCTCTTTATTCATCAGTGGACAA 58.827 40.000 0.00 0.00 0.00 3.18
77 78 6.655003 GGTCTCTTTATTCATCAGTGGACAAA 59.345 38.462 0.00 0.00 0.00 2.83
78 79 7.337942 GGTCTCTTTATTCATCAGTGGACAAAT 59.662 37.037 0.00 0.00 0.00 2.32
79 80 8.734386 GTCTCTTTATTCATCAGTGGACAAATT 58.266 33.333 0.00 0.00 0.00 1.82
80 81 8.950210 TCTCTTTATTCATCAGTGGACAAATTC 58.050 33.333 0.00 0.00 0.00 2.17
81 82 8.634335 TCTTTATTCATCAGTGGACAAATTCA 57.366 30.769 0.00 0.00 0.00 2.57
82 83 9.246670 TCTTTATTCATCAGTGGACAAATTCAT 57.753 29.630 0.00 0.00 0.00 2.57
83 84 9.512435 CTTTATTCATCAGTGGACAAATTCATC 57.488 33.333 0.00 0.00 0.00 2.92
84 85 8.578448 TTATTCATCAGTGGACAAATTCATCA 57.422 30.769 0.00 0.00 0.00 3.07
85 86 7.655521 ATTCATCAGTGGACAAATTCATCAT 57.344 32.000 0.00 0.00 0.00 2.45
86 87 8.756486 ATTCATCAGTGGACAAATTCATCATA 57.244 30.769 0.00 0.00 0.00 2.15
87 88 8.756486 TTCATCAGTGGACAAATTCATCATAT 57.244 30.769 0.00 0.00 0.00 1.78
88 89 8.161699 TCATCAGTGGACAAATTCATCATATG 57.838 34.615 0.00 0.00 0.00 1.78
89 90 7.776500 TCATCAGTGGACAAATTCATCATATGT 59.224 33.333 1.90 0.00 0.00 2.29
90 91 7.324354 TCAGTGGACAAATTCATCATATGTG 57.676 36.000 1.90 1.04 0.00 3.21
91 92 7.111466 TCAGTGGACAAATTCATCATATGTGA 58.889 34.615 1.90 3.46 39.04 3.58
92 93 7.776500 TCAGTGGACAAATTCATCATATGTGAT 59.224 33.333 1.90 0.00 45.87 3.06
93 94 8.410912 CAGTGGACAAATTCATCATATGTGATT 58.589 33.333 1.61 0.69 42.37 2.57
94 95 8.974238 AGTGGACAAATTCATCATATGTGATTT 58.026 29.630 1.61 6.21 42.37 2.17
104 105 8.680039 TCATCATATGTGATTTAACATGCTCA 57.320 30.769 1.61 0.00 42.37 4.26
105 106 9.122779 TCATCATATGTGATTTAACATGCTCAA 57.877 29.630 1.61 0.00 42.37 3.02
204 221 5.220381 GTGCTAAAACTGAAGCTTAAACCC 58.780 41.667 0.00 0.00 39.53 4.11
205 222 4.279922 TGCTAAAACTGAAGCTTAAACCCC 59.720 41.667 0.00 0.00 39.53 4.95
206 223 4.321750 GCTAAAACTGAAGCTTAAACCCCC 60.322 45.833 0.00 0.00 35.80 5.40
207 224 1.905637 AACTGAAGCTTAAACCCCCG 58.094 50.000 0.00 0.00 0.00 5.73
269 341 4.711399 TCCATCTCAATCATCACATCCAC 58.289 43.478 0.00 0.00 0.00 4.02
279 351 3.259625 TCATCACATCCACGAACCAGTTA 59.740 43.478 0.00 0.00 0.00 2.24
300 372 8.669243 CAGTTATGAAGGTTATTTGAGGACTTC 58.331 37.037 0.00 0.00 35.96 3.01
437 512 2.392662 TGGGACACATCAAAAGCCAAA 58.607 42.857 0.00 0.00 0.00 3.28
451 526 2.851195 AGCCAAACTCTCGTGTGATTT 58.149 42.857 0.00 0.00 29.31 2.17
557 632 7.547370 GCTAGAGTCAGATACACATGTTTCTTT 59.453 37.037 0.00 0.00 34.80 2.52
558 633 7.897575 AGAGTCAGATACACATGTTTCTTTC 57.102 36.000 0.00 2.68 34.80 2.62
559 634 7.675062 AGAGTCAGATACACATGTTTCTTTCT 58.325 34.615 0.00 4.70 34.80 2.52
560 635 8.153550 AGAGTCAGATACACATGTTTCTTTCTT 58.846 33.333 0.00 0.00 34.80 2.52
561 636 8.682936 AGTCAGATACACATGTTTCTTTCTTT 57.317 30.769 0.00 0.00 34.80 2.52
562 637 9.125026 AGTCAGATACACATGTTTCTTTCTTTT 57.875 29.630 0.00 0.00 34.80 2.27
563 638 9.736023 GTCAGATACACATGTTTCTTTCTTTTT 57.264 29.630 0.00 0.00 34.80 1.94
690 765 1.142262 CCATGCTCCTGTGATGGATGA 59.858 52.381 0.00 0.00 39.29 2.92
697 772 3.899980 CTCCTGTGATGGATGACCTATGA 59.100 47.826 0.00 0.00 35.30 2.15
820 901 3.279434 GGCCCAATAGAATTATAGCCCG 58.721 50.000 0.00 0.00 32.93 6.13
821 902 3.054655 GGCCCAATAGAATTATAGCCCGA 60.055 47.826 0.00 0.00 32.93 5.14
822 903 4.192317 GCCCAATAGAATTATAGCCCGAG 58.808 47.826 0.00 0.00 0.00 4.63
823 904 4.192317 CCCAATAGAATTATAGCCCGAGC 58.808 47.826 0.00 0.00 40.32 5.03
824 905 4.192317 CCAATAGAATTATAGCCCGAGCC 58.808 47.826 0.00 0.00 41.25 4.70
1641 1742 3.056179 TGACATTGGTGAGCGTAATCTCA 60.056 43.478 0.00 0.00 40.50 3.27
1647 1748 3.850657 GTGAGCGTAATCTCAGCAATC 57.149 47.619 0.00 0.00 43.10 2.67
1777 1878 3.312736 AGTGTGGTTTCATTGAGGGTT 57.687 42.857 0.00 0.00 0.00 4.11
1806 1907 2.848887 TGTGTTTGAAAATTCGTGTGCG 59.151 40.909 0.00 0.00 39.92 5.34
1824 1925 1.068250 GCTGAGGAGCGTGGATACC 59.932 63.158 0.00 0.00 34.87 2.73
1881 1982 2.818432 CTGCAGTGAAAGAGCTTTGGAT 59.182 45.455 5.25 0.00 32.11 3.41
1912 2013 3.184628 AGAATGGAGTCATCTGGGTTCA 58.815 45.455 0.00 0.00 32.24 3.18
1962 2063 3.346631 GAATGCTTGCAGCCACGGG 62.347 63.158 0.87 0.00 41.51 5.28
2343 2444 0.117340 AGAAGGTACCTGGGAGCAGT 59.883 55.000 17.14 0.00 0.00 4.40
2563 2664 2.031674 GCTTGCACTTGCCTTTGGGT 62.032 55.000 0.00 0.00 41.18 4.51
2589 2690 2.772191 ACTGCACCTGGGACACCA 60.772 61.111 0.00 0.00 46.94 4.17
2774 2880 1.070134 AGCTGCAGTTCAGTTCCGTTA 59.930 47.619 16.64 0.00 44.66 3.18
2775 2881 1.461127 GCTGCAGTTCAGTTCCGTTAG 59.539 52.381 16.64 0.00 44.66 2.34
2860 2968 9.578439 GTCCATTTGAGAAAGATTTTTAGATGG 57.422 33.333 0.00 0.00 0.00 3.51
2947 3055 2.391926 TGACCACCCTCTTGTGTCTA 57.608 50.000 0.00 0.00 34.35 2.59
2948 3056 1.968493 TGACCACCCTCTTGTGTCTAC 59.032 52.381 0.00 0.00 34.35 2.59
2949 3057 1.968493 GACCACCCTCTTGTGTCTACA 59.032 52.381 0.00 0.00 34.35 2.74
3100 3208 7.127955 AGGGACTAGAAATCATCAATTACCTGT 59.872 37.037 0.00 0.00 36.02 4.00
3194 3302 5.455392 ACTCACATTTGAATGAGAAAAGCG 58.545 37.500 10.48 0.00 44.32 4.68
3237 3370 3.492482 GCCTTCTGCTTTTAGTTTTGGCA 60.492 43.478 0.00 0.00 36.91 4.92
3262 3401 2.528041 ACTGAGACCTTGTCCGTTTC 57.472 50.000 0.00 0.00 32.18 2.78
3280 3419 5.449862 CCGTTTCTTTTTCATCTCACACCAA 60.450 40.000 0.00 0.00 0.00 3.67
3330 3553 5.763204 TCTGCACATGATAGATACGTCTACA 59.237 40.000 0.00 0.00 39.66 2.74
3354 3577 7.562454 ACATTGTAGTAGCCTTGTAGGTACATA 59.438 37.037 0.00 0.00 37.80 2.29
3484 3711 6.037610 GGGCATCAGAAACTCATGTACTAAAG 59.962 42.308 0.00 0.00 0.00 1.85
3744 3973 5.105595 GGATGTAGGAGCTTTGCTTTTGAAT 60.106 40.000 0.00 0.00 39.88 2.57
3854 4083 8.157476 AGTATCACATTCTTGAAGGTGTAGTTT 58.843 33.333 21.91 9.95 33.17 2.66
3997 4226 5.813672 GCATGTGATATTTTGCAAGGACATT 59.186 36.000 0.00 0.00 35.22 2.71
4078 4307 7.167924 TGATGTTTGCCATTGCTTTATAGAA 57.832 32.000 0.00 0.00 38.71 2.10
4161 4390 7.556733 AACAGGACGTTCTAACATTTGTAAA 57.443 32.000 0.00 0.00 29.27 2.01
4164 4393 7.227910 ACAGGACGTTCTAACATTTGTAAACAT 59.772 33.333 0.00 0.00 0.00 2.71
4167 4396 8.898792 GGACGTTCTAACATTTGTAAACATTTC 58.101 33.333 0.00 0.00 0.00 2.17
4168 4397 8.483743 ACGTTCTAACATTTGTAAACATTTCG 57.516 30.769 0.00 0.00 0.00 3.46
4170 4399 9.160576 CGTTCTAACATTTGTAAACATTTCGAA 57.839 29.630 0.00 0.00 0.00 3.71
4185 4498 6.092748 ACATTTCGAATGGTTAGTTGATTGC 58.907 36.000 0.00 0.00 0.00 3.56
4267 4581 0.781278 TTTGGGTGAGGTAAAGGGGG 59.219 55.000 0.00 0.00 0.00 5.40
4307 4621 3.243636 ACCAAAGCTGTCTTTCATGCAAG 60.244 43.478 0.00 0.00 40.35 4.01
4309 4623 0.520404 AGCTGTCTTTCATGCAAGCG 59.480 50.000 0.00 0.00 0.00 4.68
4319 4633 1.005294 CATGCAAGCGACCACTTTGC 61.005 55.000 0.00 1.75 34.28 3.68
4344 4675 5.304101 TGTGGAGTGTTTGAGCCATTATTTT 59.696 36.000 0.00 0.00 32.26 1.82
4381 4712 9.388506 AGATAACATTTTCTCTACCATTGAGTG 57.611 33.333 0.00 0.00 33.59 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.271777 ACCTAACCCCTCAATTTCCGA 58.728 47.619 0.00 0.00 0.00 4.55
1 2 2.801077 ACCTAACCCCTCAATTTCCG 57.199 50.000 0.00 0.00 0.00 4.30
2 3 4.836175 TCAAAACCTAACCCCTCAATTTCC 59.164 41.667 0.00 0.00 0.00 3.13
3 4 6.041637 ACTTCAAAACCTAACCCCTCAATTTC 59.958 38.462 0.00 0.00 0.00 2.17
4 5 5.903010 ACTTCAAAACCTAACCCCTCAATTT 59.097 36.000 0.00 0.00 0.00 1.82
5 6 5.464069 ACTTCAAAACCTAACCCCTCAATT 58.536 37.500 0.00 0.00 0.00 2.32
6 7 5.074746 ACTTCAAAACCTAACCCCTCAAT 57.925 39.130 0.00 0.00 0.00 2.57
7 8 4.529716 ACTTCAAAACCTAACCCCTCAA 57.470 40.909 0.00 0.00 0.00 3.02
8 9 4.466827 GAACTTCAAAACCTAACCCCTCA 58.533 43.478 0.00 0.00 0.00 3.86
9 10 3.825014 GGAACTTCAAAACCTAACCCCTC 59.175 47.826 0.00 0.00 0.00 4.30
10 11 3.465966 AGGAACTTCAAAACCTAACCCCT 59.534 43.478 0.00 0.00 27.25 4.79
11 12 3.840991 AGGAACTTCAAAACCTAACCCC 58.159 45.455 0.00 0.00 27.25 4.95
46 47 3.388024 TGATGAATAAAGAGACCCGAGGG 59.612 47.826 6.63 6.63 42.03 4.30
47 48 4.100189 ACTGATGAATAAAGAGACCCGAGG 59.900 45.833 0.00 0.00 0.00 4.63
48 49 5.046529 CACTGATGAATAAAGAGACCCGAG 58.953 45.833 0.00 0.00 0.00 4.63
49 50 4.141937 CCACTGATGAATAAAGAGACCCGA 60.142 45.833 0.00 0.00 0.00 5.14
50 51 4.122776 CCACTGATGAATAAAGAGACCCG 58.877 47.826 0.00 0.00 0.00 5.28
51 52 5.119694 GTCCACTGATGAATAAAGAGACCC 58.880 45.833 0.00 0.00 0.00 4.46
52 53 5.734720 TGTCCACTGATGAATAAAGAGACC 58.265 41.667 0.00 0.00 0.00 3.85
53 54 7.672983 TTTGTCCACTGATGAATAAAGAGAC 57.327 36.000 0.00 0.00 0.00 3.36
54 55 8.868522 AATTTGTCCACTGATGAATAAAGAGA 57.131 30.769 0.00 0.00 0.00 3.10
55 56 8.733458 TGAATTTGTCCACTGATGAATAAAGAG 58.267 33.333 0.00 0.00 0.00 2.85
56 57 8.634335 TGAATTTGTCCACTGATGAATAAAGA 57.366 30.769 0.00 0.00 0.00 2.52
57 58 9.512435 GATGAATTTGTCCACTGATGAATAAAG 57.488 33.333 0.00 0.00 0.00 1.85
58 59 9.022884 TGATGAATTTGTCCACTGATGAATAAA 57.977 29.630 0.00 0.00 0.00 1.40
59 60 8.578448 TGATGAATTTGTCCACTGATGAATAA 57.422 30.769 0.00 0.00 0.00 1.40
60 61 8.756486 ATGATGAATTTGTCCACTGATGAATA 57.244 30.769 0.00 0.00 0.00 1.75
61 62 7.655521 ATGATGAATTTGTCCACTGATGAAT 57.344 32.000 0.00 0.00 0.00 2.57
62 63 8.626526 CATATGATGAATTTGTCCACTGATGAA 58.373 33.333 0.00 0.00 0.00 2.57
63 64 7.776500 ACATATGATGAATTTGTCCACTGATGA 59.224 33.333 10.38 0.00 0.00 2.92
64 65 7.860872 CACATATGATGAATTTGTCCACTGATG 59.139 37.037 10.38 0.00 29.03 3.07
65 66 7.776500 TCACATATGATGAATTTGTCCACTGAT 59.224 33.333 10.38 0.00 29.03 2.90
66 67 7.111466 TCACATATGATGAATTTGTCCACTGA 58.889 34.615 10.38 0.00 29.03 3.41
67 68 7.324354 TCACATATGATGAATTTGTCCACTG 57.676 36.000 10.38 0.00 29.03 3.66
68 69 8.529424 AATCACATATGATGAATTTGTCCACT 57.471 30.769 10.38 0.00 45.26 4.00
78 79 9.122779 TGAGCATGTTAAATCACATATGATGAA 57.877 29.630 10.38 0.00 45.26 2.57
79 80 8.680039 TGAGCATGTTAAATCACATATGATGA 57.320 30.769 10.38 9.81 45.26 2.92
80 81 9.177304 GTTGAGCATGTTAAATCACATATGATG 57.823 33.333 10.38 4.41 45.26 3.07
82 83 7.338957 TGGTTGAGCATGTTAAATCACATATGA 59.661 33.333 10.38 0.00 35.51 2.15
83 84 7.482474 TGGTTGAGCATGTTAAATCACATATG 58.518 34.615 0.00 0.00 35.51 1.78
84 85 7.557358 TCTGGTTGAGCATGTTAAATCACATAT 59.443 33.333 0.00 0.00 35.51 1.78
85 86 6.883756 TCTGGTTGAGCATGTTAAATCACATA 59.116 34.615 0.00 0.00 35.51 2.29
86 87 5.711506 TCTGGTTGAGCATGTTAAATCACAT 59.288 36.000 0.00 0.00 37.93 3.21
87 88 5.069318 TCTGGTTGAGCATGTTAAATCACA 58.931 37.500 0.00 0.00 0.00 3.58
88 89 5.627499 TCTGGTTGAGCATGTTAAATCAC 57.373 39.130 0.00 0.00 0.00 3.06
89 90 6.839124 AATCTGGTTGAGCATGTTAAATCA 57.161 33.333 0.00 0.00 0.00 2.57
90 91 8.243426 TGTTAATCTGGTTGAGCATGTTAAATC 58.757 33.333 0.00 0.00 0.00 2.17
91 92 8.121305 TGTTAATCTGGTTGAGCATGTTAAAT 57.879 30.769 0.00 0.00 0.00 1.40
92 93 7.309133 CCTGTTAATCTGGTTGAGCATGTTAAA 60.309 37.037 0.00 0.00 0.00 1.52
93 94 6.150976 CCTGTTAATCTGGTTGAGCATGTTAA 59.849 38.462 0.00 0.00 0.00 2.01
94 95 5.647658 CCTGTTAATCTGGTTGAGCATGTTA 59.352 40.000 0.00 0.00 0.00 2.41
95 96 4.460382 CCTGTTAATCTGGTTGAGCATGTT 59.540 41.667 0.00 0.00 0.00 2.71
96 97 4.012374 CCTGTTAATCTGGTTGAGCATGT 58.988 43.478 0.00 0.00 0.00 3.21
97 98 3.379372 CCCTGTTAATCTGGTTGAGCATG 59.621 47.826 0.00 0.00 33.97 4.06
98 99 3.266772 TCCCTGTTAATCTGGTTGAGCAT 59.733 43.478 0.00 0.00 33.97 3.79
99 100 2.642311 TCCCTGTTAATCTGGTTGAGCA 59.358 45.455 0.00 0.00 33.97 4.26
100 101 3.350219 TCCCTGTTAATCTGGTTGAGC 57.650 47.619 0.00 0.00 33.97 4.26
101 102 6.414732 TGTAATCCCTGTTAATCTGGTTGAG 58.585 40.000 0.00 0.00 33.97 3.02
102 103 6.381498 TGTAATCCCTGTTAATCTGGTTGA 57.619 37.500 0.00 0.00 33.97 3.18
103 104 6.828273 TGATGTAATCCCTGTTAATCTGGTTG 59.172 38.462 0.00 0.00 44.73 3.77
104 105 6.969043 TGATGTAATCCCTGTTAATCTGGTT 58.031 36.000 0.00 0.00 44.73 3.67
105 106 6.575244 TGATGTAATCCCTGTTAATCTGGT 57.425 37.500 0.00 0.00 44.73 4.00
252 324 3.310774 GGTTCGTGGATGTGATGATTGAG 59.689 47.826 0.00 0.00 0.00 3.02
269 341 7.372451 TCAAATAACCTTCATAACTGGTTCG 57.628 36.000 0.00 0.00 42.38 3.95
279 351 7.234355 ACTTGAAGTCCTCAAATAACCTTCAT 58.766 34.615 0.00 0.00 43.54 2.57
300 372 2.834549 TCTAGCCCTTCTCCTGAACTTG 59.165 50.000 0.00 0.00 0.00 3.16
339 411 4.201871 CCGCAACAACAAAAACACTCTCTA 60.202 41.667 0.00 0.00 0.00 2.43
349 421 3.040147 TGTTTTCCCGCAACAACAAAA 57.960 38.095 0.00 0.00 31.05 2.44
353 425 1.857837 CACATGTTTTCCCGCAACAAC 59.142 47.619 0.00 0.00 37.67 3.32
415 490 2.607499 TGGCTTTTGATGTGTCCCAAT 58.393 42.857 0.00 0.00 0.00 3.16
428 503 2.639065 TCACACGAGAGTTTGGCTTTT 58.361 42.857 0.00 0.00 46.40 2.27
495 570 9.893305 AACTTCTTTGTACATATTTTCCTTTCG 57.107 29.630 0.00 0.00 0.00 3.46
560 635 6.097554 AGGAAACATGTGTGTACCATCAAAAA 59.902 34.615 0.00 0.00 37.67 1.94
561 636 5.596361 AGGAAACATGTGTGTACCATCAAAA 59.404 36.000 0.00 0.00 37.67 2.44
562 637 5.136828 AGGAAACATGTGTGTACCATCAAA 58.863 37.500 0.00 0.00 37.67 2.69
563 638 4.724399 AGGAAACATGTGTGTACCATCAA 58.276 39.130 0.00 0.00 37.67 2.57
564 639 4.365514 AGGAAACATGTGTGTACCATCA 57.634 40.909 0.00 0.00 37.67 3.07
565 640 5.705609 AAAGGAAACATGTGTGTACCATC 57.294 39.130 0.00 0.00 37.67 3.51
566 641 7.589958 TTAAAAGGAAACATGTGTGTACCAT 57.410 32.000 0.00 0.00 37.67 3.55
567 642 7.589958 ATTAAAAGGAAACATGTGTGTACCA 57.410 32.000 0.00 0.00 37.67 3.25
568 643 9.620660 CTAATTAAAAGGAAACATGTGTGTACC 57.379 33.333 0.00 0.00 37.67 3.34
569 644 9.620660 CCTAATTAAAAGGAAACATGTGTGTAC 57.379 33.333 0.00 0.00 35.16 2.90
570 645 8.798402 CCCTAATTAAAAGGAAACATGTGTGTA 58.202 33.333 0.00 0.00 35.16 2.90
571 646 7.256154 CCCCTAATTAAAAGGAAACATGTGTGT 60.256 37.037 0.00 0.00 36.82 3.72
572 647 7.039363 TCCCCTAATTAAAAGGAAACATGTGTG 60.039 37.037 0.00 0.00 36.08 3.82
573 648 7.013834 TCCCCTAATTAAAAGGAAACATGTGT 58.986 34.615 0.00 0.00 36.08 3.72
574 649 7.475137 TCCCCTAATTAAAAGGAAACATGTG 57.525 36.000 0.00 0.00 36.08 3.21
575 650 7.953493 TCTTCCCCTAATTAAAAGGAAACATGT 59.047 33.333 8.46 0.00 36.22 3.21
576 651 8.361169 TCTTCCCCTAATTAAAAGGAAACATG 57.639 34.615 8.46 0.00 36.22 3.21
577 652 9.201989 GATCTTCCCCTAATTAAAAGGAAACAT 57.798 33.333 8.46 6.74 36.22 2.71
578 653 8.398743 AGATCTTCCCCTAATTAAAAGGAAACA 58.601 33.333 8.46 3.44 36.22 2.83
579 654 8.824756 AGATCTTCCCCTAATTAAAAGGAAAC 57.175 34.615 8.46 6.60 36.22 2.78
580 655 8.059461 GGAGATCTTCCCCTAATTAAAAGGAAA 58.941 37.037 0.00 3.12 40.37 3.13
581 656 7.185671 TGGAGATCTTCCCCTAATTAAAAGGAA 59.814 37.037 0.00 9.16 46.19 3.36
582 657 6.681093 TGGAGATCTTCCCCTAATTAAAAGGA 59.319 38.462 0.00 0.00 46.19 3.36
583 658 6.911308 TGGAGATCTTCCCCTAATTAAAAGG 58.089 40.000 0.00 1.08 46.19 3.11
584 659 8.001292 ACATGGAGATCTTCCCCTAATTAAAAG 58.999 37.037 0.00 0.00 46.19 2.27
585 660 7.882755 ACATGGAGATCTTCCCCTAATTAAAA 58.117 34.615 0.00 0.00 46.19 1.52
631 706 7.787623 AAACATGGGAATCTCTTCTCAAAAT 57.212 32.000 0.00 0.00 44.87 1.82
690 765 4.227197 CTGGGTCTTACTGGATCATAGGT 58.773 47.826 0.00 0.00 0.00 3.08
697 772 3.256704 TCCAAACTGGGTCTTACTGGAT 58.743 45.455 0.00 0.00 38.32 3.41
773 849 6.320494 ACAGTACTGAGAGACAAGTAGTTG 57.680 41.667 29.30 8.81 39.82 3.16
820 901 1.669795 CGTGCAATCCCTTTTTGGCTC 60.670 52.381 0.00 0.00 0.00 4.70
821 902 0.318120 CGTGCAATCCCTTTTTGGCT 59.682 50.000 0.00 0.00 0.00 4.75
822 903 0.670239 CCGTGCAATCCCTTTTTGGC 60.670 55.000 0.00 0.00 0.00 4.52
823 904 0.037419 CCCGTGCAATCCCTTTTTGG 60.037 55.000 0.00 0.00 0.00 3.28
824 905 0.670239 GCCCGTGCAATCCCTTTTTG 60.670 55.000 0.00 0.00 37.47 2.44
911 994 1.377202 TGAAGACGATGGCAAGGGC 60.377 57.895 0.00 0.00 40.13 5.19
1452 1553 3.695606 GCTCCTGCGTCCCTGACA 61.696 66.667 0.00 0.00 32.09 3.58
1454 1555 3.695606 GTGCTCCTGCGTCCCTGA 61.696 66.667 0.00 0.00 43.34 3.86
1641 1742 0.460284 CTCCCAAGTACGCGATTGCT 60.460 55.000 15.93 0.00 39.65 3.91
1647 1748 1.374252 AAGTGCTCCCAAGTACGCG 60.374 57.895 3.53 3.53 42.38 6.01
1777 1878 7.971168 ACACGAATTTTCAAACACATAAACTGA 59.029 29.630 0.00 0.00 0.00 3.41
1806 1907 1.068250 GGTATCCACGCTCCTCAGC 59.932 63.158 0.00 0.00 42.96 4.26
1824 1925 1.600957 CCAGCTAACATCGCATTCCAG 59.399 52.381 0.00 0.00 0.00 3.86
1881 1982 6.596888 CAGATGACTCCATTCTAGCAAAAAGA 59.403 38.462 0.00 0.00 32.09 2.52
1888 1989 2.703007 ACCCAGATGACTCCATTCTAGC 59.297 50.000 0.00 0.00 32.09 3.42
1912 2013 8.354426 ACTGTTAAACGTAATTTTGTTAGGCAT 58.646 29.630 0.00 0.00 0.00 4.40
1962 2063 2.963599 TACCTTCCTCAACAAACCCC 57.036 50.000 0.00 0.00 0.00 4.95
2208 2309 1.493950 GATCATTCGGTGCAGCCTCG 61.494 60.000 10.90 1.24 34.25 4.63
2343 2444 9.513906 TGAATAACACCATCAAGTTCTATTGAA 57.486 29.630 0.00 0.00 42.21 2.69
2563 2664 1.614051 CCCAGGTGCAGTGCTAATCAA 60.614 52.381 17.60 0.00 0.00 2.57
2860 2968 1.377536 GAGTCAAGAGCTTCATGGCC 58.622 55.000 0.00 0.00 0.00 5.36
2947 3055 8.357402 GGACAATAATTAGGTTTCAAGTTGTGT 58.643 33.333 2.11 0.00 0.00 3.72
2948 3056 8.576442 AGGACAATAATTAGGTTTCAAGTTGTG 58.424 33.333 2.11 0.00 0.00 3.33
2949 3057 8.706322 AGGACAATAATTAGGTTTCAAGTTGT 57.294 30.769 2.11 0.00 0.00 3.32
3192 3300 1.302192 TTGGTCCTGTGGCTTACGC 60.302 57.895 0.00 0.00 0.00 4.42
3194 3302 2.354805 CCTAGTTGGTCCTGTGGCTTAC 60.355 54.545 0.00 0.00 0.00 2.34
3237 3370 2.289072 CGGACAAGGTCTCAGTTCACAT 60.289 50.000 0.00 0.00 32.47 3.21
3262 3401 7.965107 GCTAATACTTGGTGTGAGATGAAAAAG 59.035 37.037 0.00 0.00 0.00 2.27
3307 3529 6.002062 TGTAGACGTATCTATCATGTGCAG 57.998 41.667 0.00 0.00 39.66 4.41
3330 3553 8.722622 ATATGTACCTACAAGGCTACTACAAT 57.277 34.615 0.00 0.00 39.63 2.71
3354 3577 9.092338 TGGCTTATGGAAAATCTGCAAATATAT 57.908 29.630 0.00 0.00 0.00 0.86
3484 3711 5.819825 CTGCTATCCCAGGAGTTAAAAAC 57.180 43.478 0.00 0.00 37.90 2.43
3744 3973 2.040145 TGCATCATCCACTGTCCTTTCA 59.960 45.455 0.00 0.00 0.00 2.69
3854 4083 3.066064 TGCAAAGTTTCGCTAGCAAAGAA 59.934 39.130 16.45 7.49 36.07 2.52
3974 4203 7.837202 AAATGTCCTTGCAAAATATCACATG 57.163 32.000 0.00 0.00 0.00 3.21
3997 4226 9.973661 TTTACATCCTTCCTCTTTATCATGAAA 57.026 29.630 0.00 0.00 0.00 2.69
4078 4307 3.509575 CAGTCTCTCTAAGTCTGGTGCTT 59.490 47.826 0.00 0.00 37.46 3.91
4161 4390 6.071952 AGCAATCAACTAACCATTCGAAATGT 60.072 34.615 0.00 0.00 0.00 2.71
4164 4393 5.957842 AGCAATCAACTAACCATTCGAAA 57.042 34.783 0.00 0.00 0.00 3.46
4167 4396 6.019075 TCGATTAGCAATCAACTAACCATTCG 60.019 38.462 8.81 0.00 37.78 3.34
4168 4397 7.246674 TCGATTAGCAATCAACTAACCATTC 57.753 36.000 8.81 0.00 37.78 2.67
4170 4399 6.238103 CGTTCGATTAGCAATCAACTAACCAT 60.238 38.462 8.81 0.00 37.78 3.55
4172 4401 5.490213 CGTTCGATTAGCAATCAACTAACC 58.510 41.667 8.81 0.00 37.78 2.85
4185 4498 3.728076 TGGAGATTCCCGTTCGATTAG 57.272 47.619 0.00 0.00 35.03 1.73
4267 4581 3.551846 TGGTTTGTCTTTGGAGTTCTCC 58.448 45.455 11.53 11.53 0.00 3.71
4288 4602 2.606308 CGCTTGCATGAAAGACAGCTTT 60.606 45.455 18.26 0.00 46.62 3.51
4319 4633 1.901591 ATGGCTCAAACACTCCACAG 58.098 50.000 0.00 0.00 0.00 3.66
4373 4704 3.162202 TGCAAAACACACCACTCAATG 57.838 42.857 0.00 0.00 0.00 2.82
4380 4711 2.697229 TGGATGAATGCAAAACACACCA 59.303 40.909 0.00 2.99 0.00 4.17
4381 4712 3.383620 TGGATGAATGCAAAACACACC 57.616 42.857 0.00 0.40 0.00 4.16
4439 4773 7.104290 GGTGCCTAAGGGAACATATAATAGTC 58.896 42.308 0.00 0.00 43.07 2.59
4529 4863 3.244009 TGCCTTGTGTGAAGAGAGAGAAG 60.244 47.826 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.