Multiple sequence alignment - TraesCS6D01G219100

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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 TraesCS6D01G219100 chr6D 100.000 3749 0 0 1 3749 309036879 309040627 0.000000e+00 6924.0
1 TraesCS6D01G219100 chr6A 94.168 1989 93 7 834 2822 445762494 445764459 0.000000e+00 3009.0
2 TraesCS6D01G219100 chr6A 89.468 921 70 11 2820 3734 445772748 445773647 0.000000e+00 1138.0
3 TraesCS6D01G219100 chr6A 87.004 454 32 9 320 769 445762046 445762476 1.570000e-133 486.0
4 TraesCS6D01G219100 chr6B 93.827 891 44 5 796 1676 476696765 476697654 0.000000e+00 1330.0
5 TraesCS6D01G219100 chr6B 89.387 848 65 15 2903 3749 476712967 476713790 0.000000e+00 1044.0
6 TraesCS6D01G219100 chr6B 88.830 752 79 5 1 752 476696021 476696767 0.000000e+00 918.0
7 TraesCS6D01G219100 chr6B 94.549 532 29 0 1866 2397 476707752 476708283 0.000000e+00 822.0
8 TraesCS6D01G219100 chr6B 92.321 560 30 7 2360 2911 476708317 476708871 0.000000e+00 784.0
9 TraesCS6D01G219100 chr6B 86.977 215 7 4 1670 1866 476705598 476705809 4.870000e-54 222.0
10 TraesCS6D01G219100 chr3D 78.125 288 46 13 3440 3716 42845413 42845694 2.320000e-37 167.0
11 TraesCS6D01G219100 chr3D 82.099 162 16 5 2965 3125 178651985 178651836 3.930000e-25 126.0
12 TraesCS6D01G219100 chr3B 77.241 290 50 11 3438 3716 66701992 66702276 5.010000e-34 156.0
13 TraesCS6D01G219100 chr3B 81.481 162 17 5 2965 3125 257099115 257098966 1.830000e-23 121.0
14 TraesCS6D01G219100 chr3A 80.864 162 18 5 2965 3125 221275149 221275000 8.510000e-22 115.0
15 TraesCS6D01G219100 chr7A 94.286 70 4 0 2965 3034 428820259 428820190 1.420000e-19 108.0
16 TraesCS6D01G219100 chr7B 80.576 139 26 1 3510 3647 12530758 12530620 5.120000e-19 106.0
17 TraesCS6D01G219100 chr7B 92.958 71 5 0 2964 3034 375201206 375201136 1.840000e-18 104.0
18 TraesCS6D01G219100 chr7D 80.000 155 18 4 2965 3119 562189214 562189355 6.620000e-18 102.0
19 TraesCS6D01G219100 chr7D 91.429 70 6 0 2965 3034 380190670 380190601 3.080000e-16 97.1
20 TraesCS6D01G219100 chr2D 92.647 68 4 1 2967 3034 263511876 263511810 3.080000e-16 97.1
21 TraesCS6D01G219100 chr1D 81.513 119 19 3 3511 3627 16831256 16831373 1.110000e-15 95.3
22 TraesCS6D01G219100 chr1A 80.833 120 18 5 3511 3627 17820216 17820333 5.160000e-14 89.8
23 TraesCS6D01G219100 chr2B 97.297 37 1 0 3044 3080 367708148 367708112 3.130000e-06 63.9


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 TraesCS6D01G219100 chr6D 309036879 309040627 3748 False 6924.000000 6924 100.000000 1 3749 1 chr6D.!!$F1 3748
1 TraesCS6D01G219100 chr6A 445762046 445764459 2413 False 1747.500000 3009 90.586000 320 2822 2 chr6A.!!$F2 2502
2 TraesCS6D01G219100 chr6A 445772748 445773647 899 False 1138.000000 1138 89.468000 2820 3734 1 chr6A.!!$F1 914
3 TraesCS6D01G219100 chr6B 476696021 476697654 1633 False 1124.000000 1330 91.328500 1 1676 2 chr6B.!!$F2 1675
4 TraesCS6D01G219100 chr6B 476712967 476713790 823 False 1044.000000 1044 89.387000 2903 3749 1 chr6B.!!$F1 846
5 TraesCS6D01G219100 chr6B 476705598 476708871 3273 False 609.333333 822 91.282333 1670 2911 3 chr6B.!!$F3 1241

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
204 205 0.721718 CGCGTCTCCAACATTTCCTC 59.278 55.0 0.00 0.0 0.0 3.71 F
1668 1682 0.179258 GCGACCATGACGAACGAAAC 60.179 55.0 14.41 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1721 0.173481 CGTCTTCTTCCATCGCCTCA 59.827 55.0 0.00 0.00 0.00 3.86 R
3201 5266 0.248336 TATCCTCAACAGCGCGTACG 60.248 55.0 11.84 11.84 44.07 3.67 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
23 24 1.069090 GCCAATCCGACGCATCCTA 59.931 57.895 0.00 0.00 0.00 2.94
33 34 2.030457 CGACGCATCCTAACCAATTGTC 59.970 50.000 4.43 0.00 0.00 3.18
34 35 3.006940 GACGCATCCTAACCAATTGTCA 58.993 45.455 4.43 0.00 0.00 3.58
45 46 3.897239 ACCAATTGTCAAAGTCACCTCA 58.103 40.909 4.43 0.00 0.00 3.86
50 51 1.416401 TGTCAAAGTCACCTCAGGACC 59.584 52.381 0.00 0.00 35.89 4.46
68 69 4.528596 AGGACCATCCTTATCCACGATAAG 59.471 45.833 12.51 12.51 46.91 1.73
72 73 5.542635 ACCATCCTTATCCACGATAAGCTTA 59.457 40.000 8.99 8.99 45.80 3.09
73 74 6.042781 ACCATCCTTATCCACGATAAGCTTAA 59.957 38.462 10.85 0.00 45.80 1.85
74 75 6.934645 CCATCCTTATCCACGATAAGCTTAAA 59.065 38.462 10.85 0.00 45.80 1.52
78 79 7.069578 TCCTTATCCACGATAAGCTTAAAGACT 59.930 37.037 10.85 0.00 45.80 3.24
82 83 5.046878 TCCACGATAAGCTTAAAGACTGGAA 60.047 40.000 10.85 1.44 0.00 3.53
118 119 4.813766 AGAGAGGGGCTCCCATATCTCTT 61.814 52.174 21.34 11.85 43.77 2.85
183 184 1.296392 CTGCCTCGATGGTTGGTGA 59.704 57.895 0.00 0.00 38.35 4.02
204 205 0.721718 CGCGTCTCCAACATTTCCTC 59.278 55.000 0.00 0.00 0.00 3.71
205 206 1.673033 CGCGTCTCCAACATTTCCTCT 60.673 52.381 0.00 0.00 0.00 3.69
218 219 3.269592 TTTCCTCTAGACCTCCACCAA 57.730 47.619 0.00 0.00 0.00 3.67
219 220 2.233305 TCCTCTAGACCTCCACCAAC 57.767 55.000 0.00 0.00 0.00 3.77
295 296 0.981277 TTACTGGAGCTAGGGGGTGC 60.981 60.000 0.00 0.00 0.00 5.01
311 312 1.755395 TGCTGCCTCCATGGATTGC 60.755 57.895 23.11 23.11 38.35 3.56
318 319 1.779025 CTCCATGGATTGCCGAAGCG 61.779 60.000 16.63 0.00 44.31 4.68
329 330 1.145803 GCCGAAGCGAAACTTACTGT 58.854 50.000 0.00 0.00 39.29 3.55
373 374 2.279173 ACCTTGGAGCATTAGGAAGGT 58.721 47.619 0.00 0.00 41.29 3.50
544 547 7.979444 TCAAGACTACTTCTGTTAAAATGGG 57.021 36.000 0.00 0.00 33.46 4.00
583 586 6.712241 CATGAACATCTTTCTAGTTCGTGT 57.288 37.500 15.05 0.00 46.45 4.49
588 591 8.085909 TGAACATCTTTCTAGTTCGTGTTCATA 58.914 33.333 19.39 7.45 45.00 2.15
641 646 7.497773 ACTAAATAGAACCTCTTTACAGGCT 57.502 36.000 0.00 0.00 36.98 4.58
744 749 5.897377 ACCCGGAATATTTCACTCAAAAG 57.103 39.130 0.73 0.00 0.00 2.27
751 756 9.463443 CGGAATATTTCACTCAAAAGAAAAACT 57.537 29.630 0.00 0.00 37.30 2.66
757 762 9.803315 ATTTCACTCAAAAGAAAAACTAACTCC 57.197 29.630 0.00 0.00 37.30 3.85
758 763 7.011828 TCACTCAAAAGAAAAACTAACTCCG 57.988 36.000 0.00 0.00 0.00 4.63
759 764 6.819649 TCACTCAAAAGAAAAACTAACTCCGA 59.180 34.615 0.00 0.00 0.00 4.55
760 765 7.334921 TCACTCAAAAGAAAAACTAACTCCGAA 59.665 33.333 0.00 0.00 0.00 4.30
761 766 8.129211 CACTCAAAAGAAAAACTAACTCCGAAT 58.871 33.333 0.00 0.00 0.00 3.34
762 767 9.333724 ACTCAAAAGAAAAACTAACTCCGAATA 57.666 29.630 0.00 0.00 0.00 1.75
769 774 9.939802 AGAAAAACTAACTCCGAATATTACTGT 57.060 29.630 0.00 0.00 0.00 3.55
831 836 1.861542 TTGCGCCAACAGGAAATCCG 61.862 55.000 4.18 0.00 42.08 4.18
857 862 2.039818 AGATCTGCGACCGTCTTCTA 57.960 50.000 0.00 0.00 0.00 2.10
860 865 1.531423 TCTGCGACCGTCTTCTACTT 58.469 50.000 0.00 0.00 0.00 2.24
861 866 1.199327 TCTGCGACCGTCTTCTACTTG 59.801 52.381 0.00 0.00 0.00 3.16
878 883 4.208686 GTACTCGGCCTCGGCAGG 62.209 72.222 10.51 1.08 44.11 4.85
901 906 3.857665 TCGATCGCGATCAATATAAAGGC 59.142 43.478 39.26 16.09 42.51 4.35
905 910 2.416547 CGCGATCAATATAAAGGCAGGG 59.583 50.000 0.00 0.00 0.00 4.45
908 913 3.438087 CGATCAATATAAAGGCAGGGCTG 59.562 47.826 0.00 0.00 0.00 4.85
1062 1076 4.803426 GAGGTCACGGCCTGCGAG 62.803 72.222 0.00 0.00 39.34 5.03
1073 1087 4.498520 CTGCGAGTCACGGGCGAT 62.499 66.667 0.00 0.00 42.83 4.58
1074 1088 4.492160 TGCGAGTCACGGGCGATC 62.492 66.667 0.00 0.00 42.83 3.69
1096 1110 1.301716 GAGCGTCACCTTGCTTCCA 60.302 57.895 0.00 0.00 42.60 3.53
1145 1159 2.125673 CTACTTCACCACCGGCGG 60.126 66.667 27.06 27.06 0.00 6.13
1205 1219 0.713883 GAAACGATGCACGACGACAT 59.286 50.000 14.18 4.71 45.77 3.06
1222 1236 3.105686 ATGGTGCGCGATCCCATCA 62.106 57.895 12.10 4.78 33.73 3.07
1369 1383 3.168271 CGGCGCCGATGGAATATG 58.832 61.111 44.86 10.04 42.83 1.78
1542 1556 1.153549 GCCGTCTCCATGGTCTGTC 60.154 63.158 12.58 0.97 0.00 3.51
1664 1678 0.802222 ATGAGCGACCATGACGAACG 60.802 55.000 14.41 0.00 0.00 3.95
1667 1681 0.319211 AGCGACCATGACGAACGAAA 60.319 50.000 14.41 0.00 0.00 3.46
1668 1682 0.179258 GCGACCATGACGAACGAAAC 60.179 55.000 14.41 0.00 0.00 2.78
1686 1700 0.472471 ACAAGGTGGCCGAAGAAGAA 59.528 50.000 0.00 0.00 0.00 2.52
1687 1701 1.160137 CAAGGTGGCCGAAGAAGAAG 58.840 55.000 0.00 0.00 0.00 2.85
1688 1702 1.056660 AAGGTGGCCGAAGAAGAAGA 58.943 50.000 0.00 0.00 0.00 2.87
1703 1717 6.306643 AGAAGAAGATAACAGGAAAGAGGG 57.693 41.667 0.00 0.00 0.00 4.30
1707 1721 4.870021 AGATAACAGGAAAGAGGGCAAT 57.130 40.909 0.00 0.00 0.00 3.56
1725 1739 2.611225 ATGAGGCGATGGAAGAAGAC 57.389 50.000 0.00 0.00 0.00 3.01
1726 1740 0.173481 TGAGGCGATGGAAGAAGACG 59.827 55.000 0.00 0.00 0.00 4.18
1730 1744 1.140407 GCGATGGAAGAAGACGACGG 61.140 60.000 0.00 0.00 0.00 4.79
1782 1796 2.488820 GGCACGGAGTCGGAGTAC 59.511 66.667 4.48 0.00 41.61 2.73
1783 1797 2.045131 GGCACGGAGTCGGAGTACT 61.045 63.158 4.48 0.00 41.61 2.73
1784 1798 0.745845 GGCACGGAGTCGGAGTACTA 60.746 60.000 4.48 0.00 41.61 1.82
1785 1799 0.376502 GCACGGAGTCGGAGTACTAC 59.623 60.000 4.48 0.00 41.61 2.73
1786 1800 1.730501 CACGGAGTCGGAGTACTACA 58.269 55.000 5.80 0.00 41.61 2.74
1787 1801 1.664659 CACGGAGTCGGAGTACTACAG 59.335 57.143 5.80 0.00 41.61 2.74
1875 3859 2.983592 CAACCGGGCCAGACCAAC 60.984 66.667 6.32 0.00 42.05 3.77
2025 4009 3.276091 TCGCAGCAACACAACCGG 61.276 61.111 0.00 0.00 0.00 5.28
2104 4088 3.984186 CTGGAGAAGAGGGGGCGGA 62.984 68.421 0.00 0.00 0.00 5.54
2235 4219 2.743928 CTTGTCCAGCAGCCCGAC 60.744 66.667 2.99 2.99 0.00 4.79
2265 4249 2.806608 CAAGCATTGGCAAGTTCACT 57.193 45.000 5.96 0.00 43.94 3.41
2407 4463 4.988598 CACAACCTGCTCCGGCGT 62.989 66.667 6.01 0.00 42.25 5.68
2518 4574 2.159819 GACGGTCTGCAAGCTGAGGA 62.160 60.000 0.00 0.00 0.00 3.71
2573 4629 0.308376 TTTGGCAGTACGCGGAAAAC 59.692 50.000 12.47 2.77 43.84 2.43
2619 4675 5.985530 CAGATCAGTTGTACTTGAACAGACA 59.014 40.000 0.00 0.00 0.00 3.41
2657 4713 1.897615 GGATCATGAGGCTGGCTGC 60.898 63.158 9.06 7.96 41.94 5.25
2663 4719 2.436292 GAGGCTGGCTGCACAGAG 60.436 66.667 18.32 3.27 45.15 3.35
2713 4769 4.855388 CCTCGTTTGATGATTTGAAGCTTG 59.145 41.667 2.10 0.00 0.00 4.01
2715 4771 5.451908 TCGTTTGATGATTTGAAGCTTGAC 58.548 37.500 2.10 0.00 0.00 3.18
2730 4786 1.338337 CTTGACCGCGATACCATCTCT 59.662 52.381 8.23 0.00 0.00 3.10
2755 4816 6.373495 TGTCGTGCTAGATACTTGAGTCTTTA 59.627 38.462 0.00 0.00 0.00 1.85
2756 4817 6.908284 GTCGTGCTAGATACTTGAGTCTTTAG 59.092 42.308 0.00 0.00 0.00 1.85
2892 4956 6.374333 TGTTCTAGTTTCAACTTTCAAGCACT 59.626 34.615 0.00 0.00 40.37 4.40
2948 5013 3.498777 GTCCAGAGTCAAACCTGTTTAGC 59.501 47.826 0.00 0.00 0.00 3.09
2950 5015 4.591498 TCCAGAGTCAAACCTGTTTAGCTA 59.409 41.667 0.00 0.00 0.00 3.32
2951 5016 4.932200 CCAGAGTCAAACCTGTTTAGCTAG 59.068 45.833 0.00 0.00 0.00 3.42
2952 5017 4.932200 CAGAGTCAAACCTGTTTAGCTAGG 59.068 45.833 0.00 0.00 40.01 3.02
2953 5018 4.020128 AGAGTCAAACCTGTTTAGCTAGGG 60.020 45.833 5.27 4.34 38.42 3.53
3066 5131 9.338291 GCATTTGATGTTGTAGATATTAGCATG 57.662 33.333 0.00 0.00 0.00 4.06
3127 5192 7.559897 TGACTTTGGAGAAACCTAAAACTTGAT 59.440 33.333 0.00 0.00 39.86 2.57
3128 5193 8.990163 ACTTTGGAGAAACCTAAAACTTGATA 57.010 30.769 0.00 0.00 39.86 2.15
3201 5266 1.838846 TCATCTCGGATGCCTCCCC 60.839 63.158 2.04 0.00 38.45 4.81
3203 5268 3.758133 ATCTCGGATGCCTCCCCGT 62.758 63.158 2.04 0.00 45.48 5.28
3207 5272 4.603946 GGATGCCTCCCCGTACGC 62.604 72.222 10.49 0.00 35.28 4.42
3242 5307 7.148340 GGATAAGATCCTCTTTGTGTTGTTCTG 60.148 40.741 0.00 0.00 46.19 3.02
3251 5316 6.582636 TCTTTGTGTTGTTCTGTCTCACTAT 58.417 36.000 0.00 0.00 0.00 2.12
3254 5319 5.912892 TGTGTTGTTCTGTCTCACTATCAA 58.087 37.500 0.00 0.00 0.00 2.57
3264 5329 3.987868 GTCTCACTATCAACAGTTTGCGA 59.012 43.478 0.00 0.00 32.17 5.10
3286 5351 1.604378 CCCTTCCTGGCTTCATCGT 59.396 57.895 0.00 0.00 0.00 3.73
3293 5358 1.134580 CCTGGCTTCATCGTCTCACAT 60.135 52.381 0.00 0.00 0.00 3.21
3335 5401 6.095440 GGTAGCATGGTTCTCATAATTGTTGT 59.905 38.462 1.12 0.00 34.12 3.32
3338 5404 6.015180 AGCATGGTTCTCATAATTGTTGTTGT 60.015 34.615 0.00 0.00 34.12 3.32
3716 5783 2.974623 GTGGGCCCACATGATGAAA 58.025 52.632 43.88 8.74 45.53 2.69
3728 5795 3.181469 ACATGATGAAATTGAGGCCATGC 60.181 43.478 5.01 0.00 34.84 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.006888 ACAATTGGTTAGGATGCGTCG 58.993 47.619 10.83 0.00 0.00 5.12
15 16 4.082787 ACTTTGACAATTGGTTAGGATGCG 60.083 41.667 10.83 0.00 0.00 4.73
23 24 4.277476 TGAGGTGACTTTGACAATTGGTT 58.723 39.130 10.83 0.00 44.43 3.67
33 34 2.616510 GGATGGTCCTGAGGTGACTTTG 60.617 54.545 0.00 0.00 35.07 2.77
34 35 1.630878 GGATGGTCCTGAGGTGACTTT 59.369 52.381 0.00 0.00 35.07 2.66
50 51 7.872993 TCTTTAAGCTTATCGTGGATAAGGATG 59.127 37.037 20.83 3.74 46.65 3.51
68 69 1.468914 CGCCCTTTCCAGTCTTTAAGC 59.531 52.381 0.00 0.00 0.00 3.09
72 73 0.606673 GCTCGCCCTTTCCAGTCTTT 60.607 55.000 0.00 0.00 0.00 2.52
73 74 1.003233 GCTCGCCCTTTCCAGTCTT 60.003 57.895 0.00 0.00 0.00 3.01
74 75 2.665603 GCTCGCCCTTTCCAGTCT 59.334 61.111 0.00 0.00 0.00 3.24
93 94 0.787084 TATGGGAGCCCCTCTCTAGG 59.213 60.000 11.10 0.00 45.70 3.02
98 99 1.175262 AGAGATATGGGAGCCCCTCT 58.825 55.000 11.10 4.78 45.70 3.69
118 119 0.030092 CCCCTCCTCCACTAATCCCA 60.030 60.000 0.00 0.00 0.00 4.37
124 125 2.040606 GTGGCCCCTCCTCCACTA 59.959 66.667 0.00 0.00 46.90 2.74
166 167 1.003839 GTCACCAACCATCGAGGCA 60.004 57.895 0.00 0.00 43.14 4.75
183 184 0.953960 GGAAATGTTGGAGACGCGGT 60.954 55.000 12.47 0.00 0.00 5.68
195 196 3.108376 GGTGGAGGTCTAGAGGAAATGT 58.892 50.000 0.00 0.00 0.00 2.71
204 205 1.205893 GAGCTGTTGGTGGAGGTCTAG 59.794 57.143 0.00 0.00 34.52 2.43
205 206 1.267121 GAGCTGTTGGTGGAGGTCTA 58.733 55.000 0.00 0.00 34.52 2.59
218 219 4.335647 CAAGGTGGGGCGAGCTGT 62.336 66.667 0.00 0.00 0.00 4.40
250 251 7.773690 ACCAACACCATAACATTAGATAAGGAC 59.226 37.037 0.00 0.00 0.00 3.85
258 259 6.882140 TCCAGTAACCAACACCATAACATTAG 59.118 38.462 0.00 0.00 0.00 1.73
295 296 2.191513 CGGCAATCCATGGAGGCAG 61.192 63.158 31.05 26.18 37.29 4.85
305 306 0.521735 AAGTTTCGCTTCGGCAATCC 59.478 50.000 0.00 0.00 41.88 3.01
311 312 3.057734 AGAACAGTAAGTTTCGCTTCGG 58.942 45.455 0.00 0.00 41.51 4.30
318 319 8.426881 AGAGTTTGAAGAGAACAGTAAGTTTC 57.573 34.615 0.00 0.00 41.51 2.78
329 330 8.095169 GGTTGGTCTATAAGAGTTTGAAGAGAA 58.905 37.037 0.00 0.00 0.00 2.87
615 620 6.476053 GCCTGTAAAGAGGTTCTATTTAGTCG 59.524 42.308 0.00 0.00 35.29 4.18
616 621 7.492994 CAGCCTGTAAAGAGGTTCTATTTAGTC 59.507 40.741 0.00 0.00 35.29 2.59
619 624 6.352737 CCCAGCCTGTAAAGAGGTTCTATTTA 60.353 42.308 0.00 0.00 35.29 1.40
627 632 1.208165 CCCCCAGCCTGTAAAGAGGT 61.208 60.000 0.00 0.00 35.29 3.85
641 646 0.544357 CAGACTATATCGGGCCCCCA 60.544 60.000 18.66 2.53 35.37 4.96
702 707 0.391228 TAGTTTGTGCTGGCGTGAGA 59.609 50.000 0.00 0.00 0.00 3.27
774 779 9.550406 CCCAGTAATATTCGGAGTTATGTTAAA 57.450 33.333 0.00 0.00 0.00 1.52
775 780 8.926374 TCCCAGTAATATTCGGAGTTATGTTAA 58.074 33.333 0.00 0.00 0.00 2.01
776 781 8.481492 TCCCAGTAATATTCGGAGTTATGTTA 57.519 34.615 0.00 0.00 0.00 2.41
777 782 7.369551 TCCCAGTAATATTCGGAGTTATGTT 57.630 36.000 0.00 0.00 0.00 2.71
778 783 6.014499 CCTCCCAGTAATATTCGGAGTTATGT 60.014 42.308 14.77 0.00 38.79 2.29
779 784 6.398918 CCTCCCAGTAATATTCGGAGTTATG 58.601 44.000 14.77 2.58 38.79 1.90
780 785 5.484290 CCCTCCCAGTAATATTCGGAGTTAT 59.516 44.000 14.77 0.00 38.79 1.89
831 836 2.586357 GTCGCAGATCTTCCGCCC 60.586 66.667 7.49 0.00 40.67 6.13
857 862 3.003113 GCCGAGGCCGAGTACAAGT 62.003 63.158 1.97 0.00 38.22 3.16
860 865 3.449227 CTGCCGAGGCCGAGTACA 61.449 66.667 12.05 0.00 41.09 2.90
861 866 4.208686 CCTGCCGAGGCCGAGTAC 62.209 72.222 12.05 0.00 41.09 2.73
908 913 1.200839 GTATACCGTGATTGCGCGC 59.799 57.895 27.26 27.26 46.11 6.86
957 971 1.689273 GGTTCTCCGGCAGATGACTAT 59.311 52.381 0.00 0.00 0.00 2.12
1096 1110 2.433446 CTCCAGTTGCCAGCCACT 59.567 61.111 0.00 0.00 0.00 4.00
1205 1219 3.780173 TGATGGGATCGCGCACCA 61.780 61.111 19.44 17.99 39.97 4.17
1297 1311 2.421739 GGCGCTCCATATGGACGT 59.578 61.111 30.13 0.00 39.78 4.34
1322 1336 2.285368 ACCAGGGAGATGGCCGAA 60.285 61.111 0.00 0.00 44.80 4.30
1527 1541 1.268794 CGATCGACAGACCATGGAGAC 60.269 57.143 21.47 9.43 0.00 3.36
1664 1678 1.266989 CTTCTTCGGCCACCTTGTTTC 59.733 52.381 2.24 0.00 0.00 2.78
1667 1681 0.472471 TTCTTCTTCGGCCACCTTGT 59.528 50.000 2.24 0.00 0.00 3.16
1668 1682 1.160137 CTTCTTCTTCGGCCACCTTG 58.840 55.000 2.24 0.00 0.00 3.61
1686 1700 4.228210 TCATTGCCCTCTTTCCTGTTATCT 59.772 41.667 0.00 0.00 0.00 1.98
1687 1701 4.526970 TCATTGCCCTCTTTCCTGTTATC 58.473 43.478 0.00 0.00 0.00 1.75
1688 1702 4.530875 CTCATTGCCCTCTTTCCTGTTAT 58.469 43.478 0.00 0.00 0.00 1.89
1703 1717 1.332997 CTTCTTCCATCGCCTCATTGC 59.667 52.381 0.00 0.00 0.00 3.56
1707 1721 0.173481 CGTCTTCTTCCATCGCCTCA 59.827 55.000 0.00 0.00 0.00 3.86
1725 1739 1.515519 CATGTCACCGTACCCGTCG 60.516 63.158 0.00 0.00 0.00 5.12
1726 1740 1.808390 GCATGTCACCGTACCCGTC 60.808 63.158 0.00 0.00 0.00 4.79
1730 1744 2.106683 GCCTGCATGTCACCGTACC 61.107 63.158 0.00 0.00 0.00 3.34
1779 1793 1.582168 GCCGTCGTCGCTGTAGTAC 60.582 63.158 0.00 0.00 35.54 2.73
1780 1794 2.787249 GCCGTCGTCGCTGTAGTA 59.213 61.111 0.00 0.00 35.54 1.82
1781 1795 4.456253 CGCCGTCGTCGCTGTAGT 62.456 66.667 0.00 0.00 35.54 2.73
1873 3857 2.919971 GCTCTTCCAGCGTCTTGTT 58.080 52.632 0.00 0.00 38.76 2.83
1968 3952 0.955919 GTAGGTTCACCAGCAGCCAC 60.956 60.000 0.00 0.00 38.89 5.01
2104 4088 4.083862 GAGCCCCTCGTCGCCTTT 62.084 66.667 0.00 0.00 0.00 3.11
2235 4219 2.733227 GCCAATGCTTGTCAGGAAATCG 60.733 50.000 0.00 0.00 33.53 3.34
2265 4249 1.004560 CAAGCTGGGCTTCGACTCA 60.005 57.895 1.50 0.00 46.77 3.41
2407 4463 1.472878 CTCGATCTCGTCAACCTTGGA 59.527 52.381 0.00 0.00 40.80 3.53
2608 4664 0.679505 TCCGTCCCTGTCTGTTCAAG 59.320 55.000 0.00 0.00 0.00 3.02
2663 4719 1.079543 TCGAGCAGCTCCTCAAAGC 60.080 57.895 17.16 0.00 42.82 3.51
2713 4769 0.669077 ACAGAGATGGTATCGCGGTC 59.331 55.000 6.13 0.00 32.89 4.79
2715 4771 0.386100 CGACAGAGATGGTATCGCGG 60.386 60.000 6.13 0.00 34.06 6.46
2730 4786 4.262617 AGACTCAAGTATCTAGCACGACA 58.737 43.478 0.00 0.00 0.00 4.35
2948 5013 6.238648 AGATGTTAAACTTGGTCAACCCTAG 58.761 40.000 0.00 0.00 41.35 3.02
2950 5015 5.061721 AGATGTTAAACTTGGTCAACCCT 57.938 39.130 0.00 0.00 34.29 4.34
2951 5016 6.235664 TCTAGATGTTAAACTTGGTCAACCC 58.764 40.000 0.00 0.00 34.29 4.11
2952 5017 7.227910 TGTTCTAGATGTTAAACTTGGTCAACC 59.772 37.037 0.00 0.00 0.00 3.77
2953 5018 8.149973 TGTTCTAGATGTTAAACTTGGTCAAC 57.850 34.615 0.00 0.00 0.00 3.18
3127 5192 0.892755 CCGGCGCCTAGTATTGGATA 59.107 55.000 26.68 0.00 0.00 2.59
3128 5193 1.671742 CCGGCGCCTAGTATTGGAT 59.328 57.895 26.68 0.00 0.00 3.41
3150 5215 2.938086 GCCCAAATTTTCGGCCGGT 61.938 57.895 27.83 6.35 36.63 5.28
3201 5266 0.248336 TATCCTCAACAGCGCGTACG 60.248 55.000 11.84 11.84 44.07 3.67
3203 5268 1.746787 TCTTATCCTCAACAGCGCGTA 59.253 47.619 8.43 0.00 0.00 4.42
3229 5294 6.345298 TGATAGTGAGACAGAACAACACAAA 58.655 36.000 0.00 0.00 34.47 2.83
3233 5298 5.912892 TGTTGATAGTGAGACAGAACAACA 58.087 37.500 0.00 0.00 42.08 3.33
3242 5307 3.987868 TCGCAAACTGTTGATAGTGAGAC 59.012 43.478 0.00 0.00 36.83 3.36
3251 5316 0.884704 GGGCTCTCGCAAACTGTTGA 60.885 55.000 0.00 0.00 36.83 3.18
3254 5319 0.603975 GAAGGGCTCTCGCAAACTGT 60.604 55.000 0.00 0.00 38.10 3.55
3272 5337 0.532573 GTGAGACGATGAAGCCAGGA 59.467 55.000 0.00 0.00 0.00 3.86
3274 5339 2.306341 ATGTGAGACGATGAAGCCAG 57.694 50.000 0.00 0.00 0.00 4.85
3335 5401 7.196637 ACCCCCAAGTTAATTTAAAACACAA 57.803 32.000 0.00 0.00 0.00 3.33
3338 5404 8.722622 TGATACCCCCAAGTTAATTTAAAACA 57.277 30.769 0.00 0.00 0.00 2.83
3467 5533 6.988522 ACAGTTTAACCCCAAATACACATTC 58.011 36.000 0.00 0.00 0.00 2.67
3471 5537 7.013559 ACACTTACAGTTTAACCCCAAATACAC 59.986 37.037 0.00 0.00 0.00 2.90
3568 5634 4.083110 ACATGGTGAAATCTCTTGAAAGCG 60.083 41.667 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.