Multiple sequence alignment - TraesCS2D01G261800

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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 TraesCS2D01G261800 chr2D 100.000 4212 0 0 1 4212 318322200 318326411 0.000000e+00 7779.0
1 TraesCS2D01G261800 chr2B 93.582 2088 80 17 1637 3677 386286574 386288654 0.000000e+00 3064.0
2 TraesCS2D01G261800 chr2B 90.579 1624 94 24 1 1605 386284988 386286571 0.000000e+00 2097.0
3 TraesCS2D01G261800 chr2A 92.652 1674 62 19 2056 3677 413337863 413336199 0.000000e+00 2353.0
4 TraesCS2D01G261800 chr2A 91.376 916 46 16 469 1365 413339518 413338617 0.000000e+00 1223.0
5 TraesCS2D01G261800 chr2A 91.743 654 27 4 1406 2057 413338614 413337986 0.000000e+00 883.0
6 TraesCS2D01G261800 chr2A 87.580 467 55 3 1 465 413341263 413340798 4.790000e-149 538.0
7 TraesCS2D01G261800 chr2A 85.856 403 42 7 3814 4212 413335953 413335562 8.430000e-112 414.0
8 TraesCS2D01G261800 chr2A 88.060 67 3 2 3726 3792 413336136 413336075 1.620000e-09 75.0
9 TraesCS2D01G261800 chr7A 96.226 53 0 2 1364 1414 613630016 613629964 7.500000e-13 86.1
10 TraesCS2D01G261800 chr7A 92.982 57 2 2 1360 1414 581850997 581850941 9.710000e-12 82.4
11 TraesCS2D01G261800 chr5B 93.220 59 2 2 1358 1414 411034771 411034829 7.500000e-13 86.1
12 TraesCS2D01G261800 chr7B 93.103 58 2 2 1359 1414 741811871 741811928 2.700000e-12 84.2
13 TraesCS2D01G261800 chr7B 93.103 58 2 2 1359 1414 741844197 741844254 2.700000e-12 84.2
14 TraesCS2D01G261800 chr3B 91.803 61 2 3 1356 1414 256200750 256200691 9.710000e-12 82.4
15 TraesCS2D01G261800 chr3A 91.803 61 2 3 1356 1414 217822271 217822212 9.710000e-12 82.4
16 TraesCS2D01G261800 chr3D 90.476 63 3 3 1355 1414 100550558 100550620 3.490000e-11 80.5


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 TraesCS2D01G261800 chr2D 318322200 318326411 4211 False 7779.000000 7779 100.0000 1 4212 1 chr2D.!!$F1 4211
1 TraesCS2D01G261800 chr2B 386284988 386288654 3666 False 2580.500000 3064 92.0805 1 3677 2 chr2B.!!$F1 3676
2 TraesCS2D01G261800 chr2A 413335562 413341263 5701 True 914.333333 2353 89.5445 1 4212 6 chr2A.!!$R1 4211

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
493 1772 0.037512 CAGCAGGGAGGATATCAGCG 60.038 60.000 4.83 0.0 0.00 5.18 F
610 1889 0.462047 ATTTTGAGTCGGCCGCTAGG 60.462 55.000 23.51 0.0 41.62 3.02 F
1606 2906 0.402121 ACTGTGAGGCTCCCCTTTTC 59.598 55.000 12.86 0.0 43.12 2.29 F
1611 2911 1.209504 TGAGGCTCCCCTTTTCGTATG 59.790 52.381 12.86 0.0 43.12 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 2894 0.107165 AGCATACGAAAAGGGGAGCC 60.107 55.000 0.0 0.0 0.00 4.70 R
2304 3733 0.668706 CTGACGAACCAGTGCTCCAG 60.669 60.000 0.0 0.0 0.00 3.86 R
2790 4261 0.807667 CCACATGACAGCTAGGACGC 60.808 60.000 0.0 0.0 0.00 5.19 R
3500 4983 1.202405 CCACAGTTGGTTTTGCAGGAC 60.202 52.381 0.0 0.0 38.23 3.85 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
104 105 2.432874 TCATCGAACATATTGGGGACGT 59.567 45.455 0.00 0.00 0.00 4.34
109 110 3.340034 GAACATATTGGGGACGTTGACA 58.660 45.455 0.00 0.00 0.00 3.58
130 131 0.943835 TTGTGGCGACGAGTGATGTG 60.944 55.000 0.00 0.00 0.00 3.21
132 133 1.372872 TGGCGACGAGTGATGTGTG 60.373 57.895 0.00 0.00 0.00 3.82
147 148 2.046892 GTGCTGGTCCTCATGCGT 60.047 61.111 0.00 0.00 0.00 5.24
183 184 2.514458 AGGTCCTAAGCATTGTTGGG 57.486 50.000 0.00 0.00 0.00 4.12
191 192 0.901580 AGCATTGTTGGGGGAGCAAG 60.902 55.000 0.00 0.00 0.00 4.01
229 230 1.600957 TCGACAACGACGAGAAAGTCT 59.399 47.619 0.00 0.00 43.81 3.24
231 232 2.349627 CGACAACGACGAGAAAGTCTCT 60.350 50.000 0.00 0.00 40.47 3.10
265 266 2.443957 CTTCTTCGCACGGGCAACAC 62.444 60.000 11.77 0.00 41.24 3.32
315 317 0.538977 TCCCGACGACCTTCTTCACT 60.539 55.000 0.00 0.00 0.00 3.41
360 363 1.146263 GGTCCTTAGGTGCATCCCG 59.854 63.158 0.00 0.00 36.75 5.14
466 469 1.305802 AGGGACGACTATGGGTGCA 60.306 57.895 0.00 0.00 0.00 4.57
486 1765 2.771762 GGGAGCAGCAGGGAGGAT 60.772 66.667 0.00 0.00 0.00 3.24
491 1770 1.275856 GAGCAGCAGGGAGGATATCAG 59.724 57.143 4.83 0.00 0.00 2.90
493 1772 0.037512 CAGCAGGGAGGATATCAGCG 60.038 60.000 4.83 0.00 0.00 5.18
557 1836 1.670674 CGGCAGCGGTTGTAGTAGAAA 60.671 52.381 0.00 0.00 0.00 2.52
610 1889 0.462047 ATTTTGAGTCGGCCGCTAGG 60.462 55.000 23.51 0.00 41.62 3.02
703 1982 1.595311 TAGGCTGTCATTGGGGACAT 58.405 50.000 0.00 0.00 45.97 3.06
717 1996 2.038295 GGGGACATGCATTTTTGTTGGA 59.962 45.455 0.00 0.00 0.00 3.53
733 2012 1.338890 TGGACCAAGTGACCGAACCA 61.339 55.000 0.00 0.00 0.00 3.67
759 2039 7.721409 TTTTTAGGGTTAGTGTTGGAGTTTT 57.279 32.000 0.00 0.00 0.00 2.43
851 2134 1.858458 GCGCGTGTTGATAGAGCAATA 59.142 47.619 8.43 0.00 0.00 1.90
852 2135 2.476619 GCGCGTGTTGATAGAGCAATAT 59.523 45.455 8.43 0.00 0.00 1.28
919 2206 1.945354 GCTACGCACTAGGCTGTGGA 61.945 60.000 15.54 0.00 41.67 4.02
1088 2381 2.156098 TGGCCACCTAATCGTTGTTTC 58.844 47.619 0.00 0.00 0.00 2.78
1215 2509 1.227147 AACGATCGCACCGGGTATG 60.227 57.895 16.60 0.00 0.00 2.39
1235 2529 1.725164 GTTTTCTACGCTGACTTCCCG 59.275 52.381 0.00 0.00 0.00 5.14
1299 2599 3.982576 ACGCGATTTGTCTTTCCTTTT 57.017 38.095 15.93 0.00 0.00 2.27
1301 2601 4.287720 ACGCGATTTGTCTTTCCTTTTTC 58.712 39.130 15.93 0.00 0.00 2.29
1305 2605 3.446310 TTTGTCTTTCCTTTTTCCCGC 57.554 42.857 0.00 0.00 0.00 6.13
1443 2743 0.976073 GGACTGGATTCTCCGTGGGA 60.976 60.000 0.00 0.00 40.17 4.37
1534 2834 0.865769 CCAACAGTACGCTGGTTCAC 59.134 55.000 0.00 0.00 40.28 3.18
1594 2894 3.364366 GCACGATTTGGAAGAACTGTGAG 60.364 47.826 0.00 0.00 0.00 3.51
1595 2895 3.187227 CACGATTTGGAAGAACTGTGAGG 59.813 47.826 0.00 0.00 0.00 3.86
1606 2906 0.402121 ACTGTGAGGCTCCCCTTTTC 59.598 55.000 12.86 0.00 43.12 2.29
1611 2911 1.209504 TGAGGCTCCCCTTTTCGTATG 59.790 52.381 12.86 0.00 43.12 2.39
1834 3138 7.028962 TGAATCTGAATAAAAGCATGTTTCGG 58.971 34.615 0.00 0.00 0.00 4.30
1838 3142 8.275015 TCTGAATAAAAGCATGTTTCGGATAA 57.725 30.769 0.00 0.00 29.20 1.75
1841 3145 8.300286 TGAATAAAAGCATGTTTCGGATAAACA 58.700 29.630 5.84 5.84 43.33 2.83
1883 3187 6.751514 TCTTTGCAAGAAGTTTAGTCAACA 57.248 33.333 0.00 0.00 33.17 3.33
1885 3189 7.771183 TCTTTGCAAGAAGTTTAGTCAACAAT 58.229 30.769 0.00 0.00 33.17 2.71
2098 3527 7.386025 AGCTCAATTTGTTAGATTTCAAAAGCC 59.614 33.333 0.00 0.00 36.46 4.35
2266 3695 4.083110 TGCTAGCTTGCATTCTTCAGAAAC 60.083 41.667 19.10 0.00 38.12 2.78
2304 3733 4.590850 AGTTCCTTTGGTTTGCTCAATC 57.409 40.909 0.00 0.00 0.00 2.67
2318 3747 2.354259 CTCAATCTGGAGCACTGGTTC 58.646 52.381 0.00 0.00 0.00 3.62
2570 4019 7.016563 TGCAATCTCTAGTATTGGTGTGGATAT 59.983 37.037 16.85 0.00 35.34 1.63
2722 4171 8.195436 CAGACTTCGACAATATTAAGAAGGGTA 58.805 37.037 20.88 0.00 41.67 3.69
2739 4188 5.019785 AGGGTAAACTTAATAGCCGTCTG 57.980 43.478 0.00 0.00 43.93 3.51
2745 4216 6.663944 AAACTTAATAGCCGTCTGATTGTC 57.336 37.500 0.00 0.00 0.00 3.18
2790 4261 2.737252 GGAAACTCGTGAGGTAAAGCTG 59.263 50.000 1.43 0.00 0.00 4.24
2829 4300 5.244851 TGTGGAAATTACAAAGCCAGCATTA 59.755 36.000 0.00 0.00 0.00 1.90
2846 4317 6.317140 CCAGCATTAGTTTCTGCTTTCTGATA 59.683 38.462 0.00 0.00 46.22 2.15
2905 4385 4.504461 CGATTGTCTGTATACCAGCAGTTC 59.496 45.833 0.00 0.00 41.25 3.01
2938 4419 5.350365 TGTCTTTCGAATTTCCAATACCTCG 59.650 40.000 0.00 0.00 0.00 4.63
2955 4436 2.749076 CCTCGTCCATGCTTTCATTTGA 59.251 45.455 0.00 0.00 0.00 2.69
2995 4476 8.752766 GTGTAACAACTGCTGATTAGTACTTA 57.247 34.615 0.00 0.00 36.32 2.24
3020 4501 8.873215 ACTATTTACATAGAGATGGTTTGTCG 57.127 34.615 2.88 0.00 36.58 4.35
3096 4579 9.528018 CGGTATTTGTTAATAATGCATCCTTTT 57.472 29.630 0.00 0.00 0.00 2.27
3166 4649 2.672996 CGGTTGAGCCCTTGGGTG 60.673 66.667 7.61 0.00 31.55 4.61
3371 4854 1.065491 TGATACCGAGCATGCAGGTTT 60.065 47.619 32.87 27.12 39.31 3.27
3456 4939 5.629079 GCTAGGTGCAAGAAGTTAACAAT 57.371 39.130 8.61 0.00 42.31 2.71
3500 4983 5.255710 TGTTGTGTAGAATGTTGTTTGGG 57.744 39.130 0.00 0.00 0.00 4.12
3515 4998 0.827368 TTGGGTCCTGCAAAACCAAC 59.173 50.000 13.00 1.44 36.37 3.77
3621 5105 4.692625 ACATTCTTGTGAACTCGAATGGAG 59.307 41.667 19.62 0.00 44.19 3.86
3710 5222 2.270923 TGCGATCTTCAATTGAGTCCG 58.729 47.619 8.41 11.62 0.00 4.79
3711 5223 2.094234 TGCGATCTTCAATTGAGTCCGA 60.094 45.455 18.83 11.34 0.00 4.55
3712 5224 2.930040 GCGATCTTCAATTGAGTCCGAA 59.070 45.455 18.83 1.59 0.00 4.30
3713 5225 3.242123 GCGATCTTCAATTGAGTCCGAAC 60.242 47.826 18.83 9.48 0.00 3.95
3714 5226 4.177026 CGATCTTCAATTGAGTCCGAACT 58.823 43.478 8.41 0.00 38.88 3.01
3715 5227 4.627467 CGATCTTCAATTGAGTCCGAACTT 59.373 41.667 8.41 0.00 35.28 2.66
3716 5228 5.445142 CGATCTTCAATTGAGTCCGAACTTG 60.445 44.000 8.41 0.00 35.28 3.16
3717 5229 4.065088 TCTTCAATTGAGTCCGAACTTGG 58.935 43.478 8.41 0.00 35.28 3.61
3718 5230 3.762407 TCAATTGAGTCCGAACTTGGA 57.238 42.857 3.38 0.00 35.28 3.53
3719 5231 4.079980 TCAATTGAGTCCGAACTTGGAA 57.920 40.909 3.38 0.00 40.44 3.53
3720 5232 3.813166 TCAATTGAGTCCGAACTTGGAAC 59.187 43.478 3.38 0.00 40.44 3.62
3721 5233 3.771577 ATTGAGTCCGAACTTGGAACT 57.228 42.857 0.00 0.00 40.44 3.01
3722 5234 3.553828 TTGAGTCCGAACTTGGAACTT 57.446 42.857 0.00 0.00 40.44 2.66
3723 5235 2.833794 TGAGTCCGAACTTGGAACTTG 58.166 47.619 0.00 0.00 40.44 3.16
3724 5236 2.143925 GAGTCCGAACTTGGAACTTGG 58.856 52.381 0.00 0.00 40.44 3.61
3743 5255 2.232941 TGGAACTTGGACCATCTACGAC 59.767 50.000 0.00 0.00 0.00 4.34
3765 5277 2.569853 TGGACGCCTCAAATTCCTCTTA 59.430 45.455 0.00 0.00 0.00 2.10
3766 5278 3.199946 TGGACGCCTCAAATTCCTCTTAT 59.800 43.478 0.00 0.00 0.00 1.73
3767 5279 4.407621 TGGACGCCTCAAATTCCTCTTATA 59.592 41.667 0.00 0.00 0.00 0.98
3768 5280 5.071788 TGGACGCCTCAAATTCCTCTTATAT 59.928 40.000 0.00 0.00 0.00 0.86
3769 5281 5.409826 GGACGCCTCAAATTCCTCTTATATG 59.590 44.000 0.00 0.00 0.00 1.78
3772 5284 5.409826 CGCCTCAAATTCCTCTTATATGTCC 59.590 44.000 0.00 0.00 0.00 4.02
3792 5304 4.351938 CACGGGCGGACGACTTGA 62.352 66.667 0.00 0.00 37.61 3.02
3793 5305 3.608662 ACGGGCGGACGACTTGAA 61.609 61.111 0.00 0.00 37.61 2.69
3794 5306 2.356553 CGGGCGGACGACTTGAAA 60.357 61.111 0.00 0.00 35.47 2.69
3795 5307 1.740296 CGGGCGGACGACTTGAAAT 60.740 57.895 0.00 0.00 35.47 2.17
3796 5308 1.296056 CGGGCGGACGACTTGAAATT 61.296 55.000 0.00 0.00 35.47 1.82
3797 5309 0.446616 GGGCGGACGACTTGAAATTC 59.553 55.000 0.00 0.00 0.00 2.17
3798 5310 0.446616 GGCGGACGACTTGAAATTCC 59.553 55.000 0.00 0.00 0.00 3.01
3799 5311 1.439679 GCGGACGACTTGAAATTCCT 58.560 50.000 0.00 0.00 0.00 3.36
3800 5312 1.393883 GCGGACGACTTGAAATTCCTC 59.606 52.381 0.00 0.00 0.00 3.71
3801 5313 2.931320 GCGGACGACTTGAAATTCCTCT 60.931 50.000 0.00 0.00 0.00 3.69
3802 5314 2.668457 CGGACGACTTGAAATTCCTCTG 59.332 50.000 0.00 0.00 0.00 3.35
3804 5316 4.508662 GGACGACTTGAAATTCCTCTGAT 58.491 43.478 0.00 0.00 0.00 2.90
3805 5317 5.661458 GGACGACTTGAAATTCCTCTGATA 58.339 41.667 0.00 0.00 0.00 2.15
3806 5318 6.284459 GGACGACTTGAAATTCCTCTGATAT 58.716 40.000 0.00 0.00 0.00 1.63
3807 5319 6.201806 GGACGACTTGAAATTCCTCTGATATG 59.798 42.308 0.00 0.00 0.00 1.78
3808 5320 6.644347 ACGACTTGAAATTCCTCTGATATGT 58.356 36.000 0.00 0.00 0.00 2.29
3809 5321 6.758886 ACGACTTGAAATTCCTCTGATATGTC 59.241 38.462 0.00 0.00 0.00 3.06
3813 5325 7.555554 ACTTGAAATTCCTCTGATATGTCCTTG 59.444 37.037 0.00 0.00 0.00 3.61
3815 5327 7.050377 TGAAATTCCTCTGATATGTCCTTGTC 58.950 38.462 0.00 0.00 0.00 3.18
3816 5328 6.566079 AATTCCTCTGATATGTCCTTGTCA 57.434 37.500 0.00 0.00 0.00 3.58
3817 5329 5.344743 TTCCTCTGATATGTCCTTGTCAC 57.655 43.478 0.00 0.00 0.00 3.67
3828 5440 0.526211 CCTTGTCACGTCGGATCTGA 59.474 55.000 0.00 0.00 0.00 3.27
3833 5445 0.803117 TCACGTCGGATCTGACAGAC 59.197 55.000 29.48 13.38 38.84 3.51
3843 5455 0.105709 TCTGACAGACTGGACCCACA 60.106 55.000 7.51 0.00 0.00 4.17
3859 5475 2.958355 CCCACACCAAATTGACTTCACT 59.042 45.455 0.00 0.00 0.00 3.41
3860 5476 3.243501 CCCACACCAAATTGACTTCACTG 60.244 47.826 0.00 0.00 0.00 3.66
3869 5485 6.744537 CCAAATTGACTTCACTGAAATCGATC 59.255 38.462 0.00 0.00 0.00 3.69
3873 5489 3.512680 ACTTCACTGAAATCGATCGTCC 58.487 45.455 15.94 3.65 0.00 4.79
3879 5495 3.181495 ACTGAAATCGATCGTCCTCTCAC 60.181 47.826 15.94 1.19 0.00 3.51
3880 5496 2.099263 TGAAATCGATCGTCCTCTCACC 59.901 50.000 15.94 0.00 0.00 4.02
3903 5519 1.760613 TGTCCTCCAGTTCTCGTGTTT 59.239 47.619 0.00 0.00 0.00 2.83
3926 5542 1.292223 CGTCACCGTCATCAACCCT 59.708 57.895 0.00 0.00 0.00 4.34
3930 5546 1.303317 ACCGTCATCAACCCTTGCC 60.303 57.895 0.00 0.00 0.00 4.52
3934 5550 3.451894 CATCAACCCTTGCCGCCC 61.452 66.667 0.00 0.00 0.00 6.13
3977 5593 3.261580 CGAGCCATTGTAGATGTTGTCA 58.738 45.455 0.00 0.00 0.00 3.58
3988 5604 1.549170 GATGTTGTCACCGAGTACCCT 59.451 52.381 0.00 0.00 0.00 4.34
4001 5617 3.876255 TACCCTGTCCCCCACCACC 62.876 68.421 0.00 0.00 0.00 4.61
4055 5671 0.962356 CCAGTTGCAAGGCGGAGAAT 60.962 55.000 0.00 0.00 0.00 2.40
4095 5711 1.831652 AAGGAACCAGGGTGAGCGAG 61.832 60.000 0.00 0.00 0.00 5.03
4096 5712 2.283529 GGAACCAGGGTGAGCGAGA 61.284 63.158 0.00 0.00 0.00 4.04
4097 5713 1.671742 GAACCAGGGTGAGCGAGAA 59.328 57.895 0.00 0.00 0.00 2.87
4098 5714 0.390472 GAACCAGGGTGAGCGAGAAG 60.390 60.000 0.00 0.00 0.00 2.85
4114 5730 4.138290 CGAGAAGCTATAGACAAGGAGGA 58.862 47.826 3.21 0.00 0.00 3.71
4123 5739 0.680061 GACAAGGAGGAGGTCAACGT 59.320 55.000 0.00 0.00 0.00 3.99
4124 5740 0.680061 ACAAGGAGGAGGTCAACGTC 59.320 55.000 0.00 0.00 0.00 4.34
4131 5747 0.736325 GGAGGTCAACGTCGACATGG 60.736 60.000 17.16 0.00 37.66 3.66
4140 5756 2.158959 GTCGACATGGACGCTTCCG 61.159 63.158 11.55 0.00 46.37 4.30
4157 5773 4.286320 GCTCCGGTCGCGATGGAT 62.286 66.667 26.78 0.00 0.00 3.41
4160 5776 2.202878 CCGGTCGCGATGGATGTT 60.203 61.111 21.81 0.00 0.00 2.71
4171 5787 2.750237 GGATGTTGTGCCCGTCCC 60.750 66.667 0.00 0.00 32.76 4.46
4196 5812 2.502130 GCCTAGAAGGAAGGTGCTAGTT 59.498 50.000 0.00 0.00 37.67 2.24
4202 5818 0.177373 GGAAGGTGCTAGTTACCCCG 59.823 60.000 12.84 0.00 39.05 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 1.133915 ACAACTGTCAACGTCCCCAAT 60.134 47.619 0.00 0.00 0.00 3.16
104 105 0.874175 CTCGTCGCCACAACTGTCAA 60.874 55.000 0.00 0.00 0.00 3.18
109 110 0.667487 CATCACTCGTCGCCACAACT 60.667 55.000 0.00 0.00 0.00 3.16
130 131 2.046892 ACGCATGAGGACCAGCAC 60.047 61.111 0.00 0.00 0.00 4.40
132 133 2.887568 CGACGCATGAGGACCAGC 60.888 66.667 0.00 0.00 0.00 4.85
147 148 1.765074 CTTTTTCCCCTCCCACCGA 59.235 57.895 0.00 0.00 0.00 4.69
160 161 4.040339 CCCAACAATGCTTAGGACCTTTTT 59.960 41.667 0.00 0.00 0.00 1.94
183 184 4.078516 ACGGCGGTACTTGCTCCC 62.079 66.667 13.24 0.00 0.00 4.30
191 192 2.639883 GATCCCTTCCACGGCGGTAC 62.640 65.000 13.24 0.00 35.57 3.34
221 222 2.803492 GCGGTGACAACAGAGACTTTCT 60.803 50.000 0.00 0.00 36.25 2.52
229 230 0.468226 AAGAAGGCGGTGACAACAGA 59.532 50.000 0.00 0.00 0.00 3.41
231 232 0.468226 AGAAGAAGGCGGTGACAACA 59.532 50.000 0.00 0.00 0.00 3.33
436 439 1.002087 GTCGTCCCTCATGTGGTTCTT 59.998 52.381 12.65 0.00 0.00 2.52
437 440 0.608640 GTCGTCCCTCATGTGGTTCT 59.391 55.000 12.65 0.00 0.00 3.01
478 1757 0.896019 CCGACGCTGATATCCTCCCT 60.896 60.000 0.00 0.00 0.00 4.20
485 1764 4.664677 GCCCGCCGACGCTGATAT 62.665 66.667 0.00 0.00 38.22 1.63
515 1794 1.741706 CCATCGATATGCCATGGAAGC 59.258 52.381 18.40 0.00 39.73 3.86
539 1818 1.393883 GCTTTCTACTACAACCGCTGC 59.606 52.381 0.00 0.00 0.00 5.25
557 1836 3.782443 GGAACCCACCGGATCGCT 61.782 66.667 9.46 0.00 31.68 4.93
693 1972 4.073549 CAACAAAAATGCATGTCCCCAAT 58.926 39.130 0.00 0.00 0.00 3.16
698 1977 3.066380 GGTCCAACAAAAATGCATGTCC 58.934 45.455 0.00 0.00 0.00 4.02
703 1982 3.196469 TCACTTGGTCCAACAAAAATGCA 59.804 39.130 0.00 0.00 0.00 3.96
717 1996 2.358322 AATTGGTTCGGTCACTTGGT 57.642 45.000 0.00 0.00 0.00 3.67
733 2012 7.907841 AACTCCAACACTAACCCTAAAAATT 57.092 32.000 0.00 0.00 0.00 1.82
815 2098 4.005032 GCTGTTTGCGCGGAAAAA 57.995 50.000 27.46 21.39 0.00 1.94
919 2206 1.383386 GGGTTGGGGTTTGGGTTGT 60.383 57.895 0.00 0.00 0.00 3.32
1088 2381 0.999406 CCGACTACAATCACGCCAAG 59.001 55.000 0.00 0.00 0.00 3.61
1215 2509 1.725164 CGGGAAGTCAGCGTAGAAAAC 59.275 52.381 0.00 0.00 0.00 2.43
1235 2529 5.682234 AATCCCCAATGACTTTTCAATCC 57.318 39.130 0.00 0.00 34.61 3.01
1299 2599 0.618458 ACTATCTGCCTTTGCGGGAA 59.382 50.000 0.00 0.00 44.42 3.97
1301 2601 1.154205 CGACTATCTGCCTTTGCGGG 61.154 60.000 0.00 0.00 44.42 6.13
1305 2605 4.106197 GACAGTACGACTATCTGCCTTTG 58.894 47.826 0.00 0.00 33.12 2.77
1388 2688 8.016801 GGATACTACTTAGTGATCTAAACGCTC 58.983 40.741 0.00 0.00 37.10 5.03
1443 2743 5.631172 AGCTACATGTTGCATTAACGCAGT 61.631 41.667 29.37 6.32 44.14 4.40
1534 2834 1.817357 TCAGAGGTTGCAATCAGCTG 58.183 50.000 20.42 20.42 45.94 4.24
1594 2894 0.107165 AGCATACGAAAAGGGGAGCC 60.107 55.000 0.00 0.00 0.00 4.70
1595 2895 2.614829 TAGCATACGAAAAGGGGAGC 57.385 50.000 0.00 0.00 0.00 4.70
1606 2906 7.032377 TGAGCCTCATCTTATATAGCATACG 57.968 40.000 0.00 0.00 0.00 3.06
1611 2911 9.658799 TTGTAAATGAGCCTCATCTTATATAGC 57.341 33.333 7.84 0.00 35.76 2.97
1838 3142 9.975218 AAAGATACCACTGTATTTCCTATTGTT 57.025 29.630 0.00 0.00 37.80 2.83
1841 3145 8.052748 TGCAAAGATACCACTGTATTTCCTATT 58.947 33.333 0.00 0.00 37.80 1.73
1902 3206 4.216411 TCTAAGGGTTCCATTGCACTAC 57.784 45.455 0.00 0.00 0.00 2.73
2017 3322 7.991460 AGAGATCATTGACAAATAGCATTGAGA 59.009 33.333 0.00 0.00 34.38 3.27
2266 3695 3.817647 GGAACTAGGAAATATGCAGCAGG 59.182 47.826 0.00 0.00 0.00 4.85
2304 3733 0.668706 CTGACGAACCAGTGCTCCAG 60.669 60.000 0.00 0.00 0.00 3.86
2318 3747 4.569761 ACTAGGTGCATATACACTGACG 57.430 45.455 6.05 0.00 40.52 4.35
2722 4171 6.092259 GTGACAATCAGACGGCTATTAAGTTT 59.908 38.462 0.00 0.00 0.00 2.66
2790 4261 0.807667 CCACATGACAGCTAGGACGC 60.808 60.000 0.00 0.00 0.00 5.19
2938 4419 7.434307 CACTATGAATCAAATGAAAGCATGGAC 59.566 37.037 0.00 0.00 34.26 4.02
2955 4436 9.897744 CAGTTGTTACACAAAATCACTATGAAT 57.102 29.630 0.00 0.00 40.15 2.57
2995 4476 8.692710 TCGACAAACCATCTCTATGTAAATAGT 58.307 33.333 0.00 0.00 0.00 2.12
3015 4496 6.975197 TGTTTTTCATTGCATAAGTTCGACAA 59.025 30.769 0.00 0.00 0.00 3.18
3065 4548 9.938670 GATGCATTATTAACAAATACCGTGTTA 57.061 29.630 0.00 0.00 39.80 2.41
3082 4565 7.281549 GGCTTGAAATGAAAAAGGATGCATTAT 59.718 33.333 0.00 0.00 31.30 1.28
3096 4579 6.083098 TGAATTTCGAAGGCTTGAAATGAA 57.917 33.333 24.80 17.87 42.37 2.57
3217 4700 3.099002 TCATGGACATGATTGCCCG 57.901 52.632 10.75 0.00 42.42 6.13
3323 4806 1.332375 GCTTTCGCCACAACAGTAACA 59.668 47.619 0.00 0.00 0.00 2.41
3347 4830 2.554142 CTGCATGCTCGGTATCAAGAA 58.446 47.619 20.33 0.00 0.00 2.52
3352 4835 1.331756 CAAACCTGCATGCTCGGTATC 59.668 52.381 25.55 0.00 0.00 2.24
3371 4854 1.405933 CCGACCTGAGTGCATTCATCA 60.406 52.381 12.75 3.25 0.00 3.07
3405 4888 5.063186 GCAAACACAGTATCATCTCTGTCTG 59.937 44.000 0.00 0.00 42.05 3.51
3456 4939 9.070179 CAACATACATAATCCTCCATCATTTCA 57.930 33.333 0.00 0.00 0.00 2.69
3500 4983 1.202405 CCACAGTTGGTTTTGCAGGAC 60.202 52.381 0.00 0.00 38.23 3.85
3621 5105 7.441836 AGGTTCACTGGGAAATTTTATTTCAC 58.558 34.615 12.63 10.09 37.23 3.18
3681 5193 2.951457 TGAAGATCGCATTCCGTACA 57.049 45.000 0.00 0.00 38.35 2.90
3710 5222 3.951680 TCCAAGTTCCAAGTTCCAAGTTC 59.048 43.478 0.00 0.00 0.00 3.01
3711 5223 3.699538 GTCCAAGTTCCAAGTTCCAAGTT 59.300 43.478 0.00 0.00 0.00 2.66
3712 5224 3.288092 GTCCAAGTTCCAAGTTCCAAGT 58.712 45.455 0.00 0.00 0.00 3.16
3713 5225 2.623416 GGTCCAAGTTCCAAGTTCCAAG 59.377 50.000 0.00 0.00 0.00 3.61
3714 5226 2.024846 TGGTCCAAGTTCCAAGTTCCAA 60.025 45.455 0.00 0.00 0.00 3.53
3715 5227 1.566703 TGGTCCAAGTTCCAAGTTCCA 59.433 47.619 0.00 0.00 0.00 3.53
3716 5228 2.358322 TGGTCCAAGTTCCAAGTTCC 57.642 50.000 0.00 0.00 0.00 3.62
3717 5229 3.756117 AGATGGTCCAAGTTCCAAGTTC 58.244 45.455 0.00 0.00 37.27 3.01
3718 5230 3.884037 AGATGGTCCAAGTTCCAAGTT 57.116 42.857 0.00 0.00 37.27 2.66
3719 5231 3.306780 CGTAGATGGTCCAAGTTCCAAGT 60.307 47.826 0.00 0.00 37.27 3.16
3720 5232 3.056107 TCGTAGATGGTCCAAGTTCCAAG 60.056 47.826 0.00 0.00 37.27 3.61
3721 5233 2.901192 TCGTAGATGGTCCAAGTTCCAA 59.099 45.455 0.00 0.00 37.27 3.53
3722 5234 2.232941 GTCGTAGATGGTCCAAGTTCCA 59.767 50.000 0.00 0.00 40.67 3.53
3723 5235 2.496470 AGTCGTAGATGGTCCAAGTTCC 59.504 50.000 0.00 0.00 40.67 3.62
3724 5236 3.512680 CAGTCGTAGATGGTCCAAGTTC 58.487 50.000 0.00 0.00 40.67 3.01
3743 5255 1.065854 AGAGGAATTTGAGGCGTCCAG 60.066 52.381 3.56 0.00 32.19 3.86
3787 5299 7.205515 AGGACATATCAGAGGAATTTCAAGT 57.794 36.000 0.00 0.00 0.00 3.16
3792 5304 6.825721 GTGACAAGGACATATCAGAGGAATTT 59.174 38.462 0.00 0.00 0.00 1.82
3793 5305 6.352516 GTGACAAGGACATATCAGAGGAATT 58.647 40.000 0.00 0.00 0.00 2.17
3794 5306 5.452496 CGTGACAAGGACATATCAGAGGAAT 60.452 44.000 0.00 0.00 0.00 3.01
3795 5307 4.142160 CGTGACAAGGACATATCAGAGGAA 60.142 45.833 0.00 0.00 0.00 3.36
3796 5308 3.381590 CGTGACAAGGACATATCAGAGGA 59.618 47.826 0.00 0.00 0.00 3.71
3797 5309 3.131223 ACGTGACAAGGACATATCAGAGG 59.869 47.826 0.00 0.00 0.00 3.69
3798 5310 4.355437 GACGTGACAAGGACATATCAGAG 58.645 47.826 0.00 0.00 0.00 3.35
3799 5311 3.181500 CGACGTGACAAGGACATATCAGA 60.181 47.826 0.00 0.00 0.00 3.27
3800 5312 3.108881 CGACGTGACAAGGACATATCAG 58.891 50.000 0.00 0.00 0.00 2.90
3801 5313 2.159296 CCGACGTGACAAGGACATATCA 60.159 50.000 0.00 0.00 0.00 2.15
3802 5314 2.098607 TCCGACGTGACAAGGACATATC 59.901 50.000 0.00 0.00 0.00 1.63
3804 5316 1.536940 TCCGACGTGACAAGGACATA 58.463 50.000 0.00 0.00 0.00 2.29
3805 5317 0.895530 ATCCGACGTGACAAGGACAT 59.104 50.000 0.00 0.00 35.36 3.06
3806 5318 0.242825 GATCCGACGTGACAAGGACA 59.757 55.000 0.00 0.00 35.36 4.02
3807 5319 0.526662 AGATCCGACGTGACAAGGAC 59.473 55.000 0.00 0.00 35.36 3.85
3808 5320 0.526211 CAGATCCGACGTGACAAGGA 59.474 55.000 0.00 0.00 37.17 3.36
3809 5321 0.526211 TCAGATCCGACGTGACAAGG 59.474 55.000 0.00 0.00 0.00 3.61
3813 5325 0.803117 TCTGTCAGATCCGACGTGAC 59.197 55.000 8.84 8.84 40.89 3.67
3815 5327 0.805614 AGTCTGTCAGATCCGACGTG 59.194 55.000 5.68 0.87 38.84 4.49
3816 5328 0.805614 CAGTCTGTCAGATCCGACGT 59.194 55.000 5.68 0.00 38.84 4.34
3817 5329 0.099613 CCAGTCTGTCAGATCCGACG 59.900 60.000 5.68 0.51 38.84 5.12
3828 5440 0.986019 TTGGTGTGGGTCCAGTCTGT 60.986 55.000 0.00 0.00 36.28 3.41
3833 5445 1.613437 GTCAATTTGGTGTGGGTCCAG 59.387 52.381 0.00 0.00 36.28 3.86
3843 5455 5.530915 TCGATTTCAGTGAAGTCAATTTGGT 59.469 36.000 23.35 0.00 29.48 3.67
3859 5475 2.099263 GGTGAGAGGACGATCGATTTCA 59.901 50.000 24.34 14.31 0.00 2.69
3860 5476 2.359531 AGGTGAGAGGACGATCGATTTC 59.640 50.000 24.34 14.78 0.00 2.17
3869 5485 0.322997 AGGACAGAGGTGAGAGGACG 60.323 60.000 0.00 0.00 0.00 4.79
3873 5489 3.679935 TGGAGGACAGAGGTGAGAG 57.320 57.895 0.00 0.00 0.00 3.20
3947 5563 3.797353 AATGGCTCGGATGCGGGT 61.797 61.111 8.73 0.00 0.00 5.28
3949 5565 1.224069 CTACAATGGCTCGGATGCGG 61.224 60.000 6.82 0.00 0.00 5.69
3950 5566 0.249447 TCTACAATGGCTCGGATGCG 60.249 55.000 0.00 0.00 0.00 4.73
3977 5593 2.038490 GGGGACAGGGTACTCGGT 59.962 66.667 0.00 0.00 0.00 4.69
4032 5648 2.670934 CGCCTTGCAACTGGCTCT 60.671 61.111 22.97 0.00 46.42 4.09
4049 5665 1.032114 CCCTTCGGGCAACATTCTCC 61.032 60.000 0.00 0.00 35.35 3.71
4050 5666 0.035439 TCCCTTCGGGCAACATTCTC 60.035 55.000 0.00 0.00 43.94 2.87
4055 5671 4.697756 CGCTCCCTTCGGGCAACA 62.698 66.667 0.00 0.00 43.94 3.33
4095 5711 4.219919 ACCTCCTCCTTGTCTATAGCTTC 58.780 47.826 0.00 0.00 0.00 3.86
4096 5712 4.219919 GACCTCCTCCTTGTCTATAGCTT 58.780 47.826 0.00 0.00 0.00 3.74
4097 5713 3.205507 TGACCTCCTCCTTGTCTATAGCT 59.794 47.826 0.00 0.00 0.00 3.32
4098 5714 3.567397 TGACCTCCTCCTTGTCTATAGC 58.433 50.000 0.00 0.00 0.00 2.97
4099 5715 4.036971 CGTTGACCTCCTCCTTGTCTATAG 59.963 50.000 0.00 0.00 0.00 1.31
4100 5716 3.952323 CGTTGACCTCCTCCTTGTCTATA 59.048 47.826 0.00 0.00 0.00 1.31
4101 5717 2.761208 CGTTGACCTCCTCCTTGTCTAT 59.239 50.000 0.00 0.00 0.00 1.98
4102 5718 2.168496 CGTTGACCTCCTCCTTGTCTA 58.832 52.381 0.00 0.00 0.00 2.59
4103 5719 0.969894 CGTTGACCTCCTCCTTGTCT 59.030 55.000 0.00 0.00 0.00 3.41
4104 5720 0.680061 ACGTTGACCTCCTCCTTGTC 59.320 55.000 0.00 0.00 0.00 3.18
4105 5721 0.680061 GACGTTGACCTCCTCCTTGT 59.320 55.000 0.00 0.00 0.00 3.16
4110 5726 0.526662 ATGTCGACGTTGACCTCCTC 59.473 55.000 28.83 7.58 38.11 3.71
4114 5730 0.038526 GTCCATGTCGACGTTGACCT 60.039 55.000 28.83 18.98 38.11 3.85
4123 5739 2.180769 CGGAAGCGTCCATGTCGA 59.819 61.111 19.13 0.00 45.26 4.20
4140 5756 4.286320 ATCCATCGCGACCGGAGC 62.286 66.667 27.34 13.00 34.56 4.70
4151 5767 1.376609 GGACGGGCACAACATCCATC 61.377 60.000 0.00 0.00 0.00 3.51
4154 5770 2.750237 GGGACGGGCACAACATCC 60.750 66.667 0.00 0.00 0.00 3.51
4171 5787 2.107141 CCTTCCTTCTAGGCGGCG 59.893 66.667 0.51 0.51 34.61 6.46


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

AutoCloner maintained by Alex Coulton.