Multiple sequence alignment - TraesCS1D01G081400

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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 TraesCS1D01G081400 chr1D 100.000 4045 0 0 1 4045 63632744 63636788 0.000000e+00 7470.0
1 TraesCS1D01G081400 chr1B 95.079 2479 81 12 880 3320 104464478 104466953 0.000000e+00 3864.0
2 TraesCS1D01G081400 chr1B 91.694 903 49 12 1 887 104463515 104464407 0.000000e+00 1229.0
3 TraesCS1D01G081400 chr1B 91.841 429 18 6 3621 4045 104467258 104467673 2.100000e-162 582.0
4 TraesCS1D01G081400 chr1B 86.555 119 13 2 2585 2701 589055520 589055403 1.180000e-25 128.0
5 TraesCS1D01G081400 chr1A 95.214 1776 54 11 867 2630 62611447 62613203 0.000000e+00 2780.0
6 TraesCS1D01G081400 chr1A 88.362 1392 84 40 2668 4045 62613273 62614600 0.000000e+00 1602.0
7 TraesCS1D01G081400 chr1A 92.325 899 43 6 13 887 62610495 62611391 0.000000e+00 1254.0
8 TraesCS1D01G081400 chr4D 89.565 115 8 4 2586 2697 18693543 18693430 4.210000e-30 143.0
9 TraesCS1D01G081400 chr7D 88.034 117 11 2 2582 2696 267124051 267124166 7.050000e-28 135.0
10 TraesCS1D01G081400 chr7D 100.000 30 0 0 3543 3572 60676585 60676556 5.650000e-04 56.5
11 TraesCS1D01G081400 chr7D 94.444 36 2 0 3546 3581 101029457 101029422 5.650000e-04 56.5
12 TraesCS1D01G081400 chr7B 89.815 108 8 2 2589 2694 633676836 633676730 7.050000e-28 135.0
13 TraesCS1D01G081400 chr7B 97.059 34 0 1 3543 3575 228772944 228772977 5.650000e-04 56.5
14 TraesCS1D01G081400 chr7A 89.815 108 8 2 2589 2694 663949560 663949666 7.050000e-28 135.0
15 TraesCS1D01G081400 chr4B 87.931 116 9 3 2589 2702 583994596 583994484 9.120000e-27 132.0
16 TraesCS1D01G081400 chr4B 86.087 115 13 3 2586 2698 795799 795912 1.970000e-23 121.0
17 TraesCS1D01G081400 chr4B 79.646 113 11 6 3472 3574 598456930 598457040 2.020000e-08 71.3
18 TraesCS1D01G081400 chr2B 86.555 119 13 2 2589 2705 514395767 514395884 1.180000e-25 128.0
19 TraesCS1D01G081400 chr2B 100.000 30 0 0 3543 3572 136171355 136171326 5.650000e-04 56.5
20 TraesCS1D01G081400 chr2B 100.000 29 0 0 1880 1908 265219152 265219180 2.000000e-03 54.7
21 TraesCS1D01G081400 chr3A 81.308 107 20 0 2896 3002 262522801 262522695 2.000000e-13 87.9
22 TraesCS1D01G081400 chr3A 83.146 89 15 0 2896 2984 163923979 163924067 9.320000e-12 82.4
23 TraesCS1D01G081400 chr3D 83.908 87 14 0 2898 2984 144291483 144291569 2.590000e-12 84.2
24 TraesCS1D01G081400 chr3D 83.908 87 14 0 2896 2982 192058869 192058955 2.590000e-12 84.2
25 TraesCS1D01G081400 chr4A 84.000 75 10 2 3501 3574 681609196 681609123 2.020000e-08 71.3
26 TraesCS1D01G081400 chr5D 100.000 31 0 0 3546 3576 495311512 495311482 1.570000e-04 58.4
27 TraesCS1D01G081400 chr3B 96.970 33 0 1 3543 3574 753752415 753752447 2.000000e-03 54.7
28 TraesCS1D01G081400 chr2A 100.000 29 0 0 1880 1908 262576672 262576700 2.000000e-03 54.7


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 TraesCS1D01G081400 chr1D 63632744 63636788 4044 False 7470.000000 7470 100.000000 1 4045 1 chr1D.!!$F1 4044
1 TraesCS1D01G081400 chr1B 104463515 104467673 4158 False 1891.666667 3864 92.871333 1 4045 3 chr1B.!!$F1 4044
2 TraesCS1D01G081400 chr1A 62610495 62614600 4105 False 1878.666667 2780 91.967000 13 4045 3 chr1A.!!$F1 4032

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
447 469 0.594602 GTGGTTGTTAGTTTCCGCCC 59.405 55.000 0.00 0.00 0.00 6.13 F
907 1019 0.971386 TGTTCCCAACCGAGTACTCC 59.029 55.000 17.23 0.43 0.00 3.85 F
2610 2739 1.066918 CCCTCCGTCCGGAATTACG 59.933 63.158 5.23 5.98 44.66 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1526 0.107945 GGTCTGGCTGCTTACTGGAG 60.108 60.0 0.0 0.0 37.17 3.86 R
2679 2865 0.106819 GCTAGTACTCCCTCCGTCCA 60.107 60.0 0.0 0.0 0.00 4.02 R
3816 4135 1.833860 CAACTAGCTCGCTCTGTAGC 58.166 55.0 0.0 0.0 45.86 3.58 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
42 43 1.601759 TTGAGCTGTGGGCAAGAGC 60.602 57.895 2.06 2.06 44.79 4.09
58 59 1.067915 AGAGCGAGTGAAGAACTGAGC 60.068 52.381 0.00 0.00 40.07 4.26
223 242 0.666374 GGCGGTTGCACTTGTTTACT 59.334 50.000 0.00 0.00 45.35 2.24
224 243 1.874872 GGCGGTTGCACTTGTTTACTA 59.125 47.619 0.00 0.00 45.35 1.82
225 244 2.095919 GGCGGTTGCACTTGTTTACTAG 60.096 50.000 0.00 0.00 45.35 2.57
443 465 3.501062 GCTGGTAGTGGTTGTTAGTTTCC 59.499 47.826 0.00 0.00 0.00 3.13
447 469 0.594602 GTGGTTGTTAGTTTCCGCCC 59.405 55.000 0.00 0.00 0.00 6.13
453 475 1.353022 TGTTAGTTTCCGCCCTCCATT 59.647 47.619 0.00 0.00 0.00 3.16
455 477 3.009253 TGTTAGTTTCCGCCCTCCATTTA 59.991 43.478 0.00 0.00 0.00 1.40
632 660 3.098377 TCCCTTACTGCATGTACCGTAA 58.902 45.455 0.00 0.00 0.00 3.18
720 752 6.540914 AGATACAGAGGAGAGAAAGTAAGACG 59.459 42.308 0.00 0.00 0.00 4.18
751 783 7.158099 AGCAAAGTAGTGGGATAAAATGAAC 57.842 36.000 0.00 0.00 0.00 3.18
779 811 7.496747 AGAGGAGAAATTTAGCTGTACATCTC 58.503 38.462 1.74 6.42 33.12 2.75
788 820 4.212143 AGCTGTACATCTCAAGCATTCA 57.788 40.909 0.00 0.00 0.00 2.57
817 851 9.023967 CACTTGTTTCCTAAAATTCAACTTCTG 57.976 33.333 0.00 0.00 0.00 3.02
903 1015 3.587923 CGTTTATGTTCCCAACCGAGTA 58.412 45.455 0.00 0.00 0.00 2.59
907 1019 0.971386 TGTTCCCAACCGAGTACTCC 59.029 55.000 17.23 0.43 0.00 3.85
919 1031 3.497262 CCGAGTACTCCCTTGTTTGTTTC 59.503 47.826 17.23 0.00 0.00 2.78
935 1047 8.703604 TGTTTGTTTCTGTATGAGCTATCTAC 57.296 34.615 0.00 0.00 0.00 2.59
949 1061 4.822350 AGCTATCTACGTTCATACTGCTGA 59.178 41.667 0.00 0.00 0.00 4.26
992 1104 1.214175 TCCAGCCAGGACTTGTTTTCA 59.786 47.619 0.00 0.00 43.07 2.69
1098 1210 6.555315 CCATCCAGCAAGTAATAACTTTGAC 58.445 40.000 0.00 0.00 43.60 3.18
1134 1253 9.778741 GTTACCATTCTATCATACCATTTCTCA 57.221 33.333 0.00 0.00 0.00 3.27
1226 1345 1.966901 TACCGCACTGCCGATCCAAT 61.967 55.000 0.00 0.00 0.00 3.16
1305 1424 6.590656 ATGGATGAAATTAGGGAGGTTACA 57.409 37.500 0.00 0.00 0.00 2.41
1323 1442 5.508994 GGTTACAAAGGGTTTTGGTGATGAG 60.509 44.000 5.17 0.00 46.33 2.90
1653 1772 4.517952 TGCTTCATGGTATGGTTTTGTG 57.482 40.909 0.00 0.00 0.00 3.33
1675 1794 6.817641 TGTGCAATTTGAAGTCTTGAACATTT 59.182 30.769 0.00 0.00 34.30 2.32
1830 1951 1.740025 GTGAAGATAGCTGTTGGTGCC 59.260 52.381 0.00 0.00 0.00 5.01
2053 2174 8.739972 AGTATGTTCTTGTTTTCTTTCAGTTGT 58.260 29.630 0.00 0.00 0.00 3.32
2121 2242 7.593273 TGTTTAAACTTTTTGATCAGGTATGCG 59.407 33.333 18.72 0.00 0.00 4.73
2259 2380 5.695816 CCTTGTCACATGGGTAATTTTTGTG 59.304 40.000 1.49 0.00 39.16 3.33
2553 2682 9.668497 AAAATACTGATCTTACTGGAACTTACC 57.332 33.333 0.00 0.00 0.00 2.85
2610 2739 1.066918 CCCTCCGTCCGGAATTACG 59.933 63.158 5.23 5.98 44.66 3.18
2630 2804 2.215587 CGTACGCTCAAACGGATGTATG 59.784 50.000 0.52 0.00 37.37 2.39
2636 2810 6.138603 ACGCTCAAACGGATGTATGTAACAT 61.139 40.000 0.00 0.00 43.31 2.71
2667 2841 4.151335 GTGCTAGATACATCCATTTGAGCG 59.849 45.833 0.00 0.00 0.00 5.03
2678 2864 5.957842 TCCATTTGAGCGTCAAGTAATTT 57.042 34.783 0.00 0.00 37.70 1.82
2679 2865 6.325919 TCCATTTGAGCGTCAAGTAATTTT 57.674 33.333 0.00 0.00 37.70 1.82
2741 2927 8.559536 AGAAACTGTGTTTGTTGTCACATATAG 58.440 33.333 0.10 0.00 42.42 1.31
2742 2928 7.801716 AACTGTGTTTGTTGTCACATATAGT 57.198 32.000 0.00 0.00 42.42 2.12
2743 2929 8.896320 AACTGTGTTTGTTGTCACATATAGTA 57.104 30.769 0.00 0.00 42.42 1.82
2763 2950 5.703876 AGTAAAAAGTATTTCTGCAGCTGC 58.296 37.500 31.89 31.89 37.28 5.25
2788 2975 7.538678 GCTTTTATGCTCATAAAATATGTCCCG 59.461 37.037 21.21 12.14 46.20 5.14
2795 2982 6.413783 TCATAAAATATGTCCCGCTACTGA 57.586 37.500 0.00 0.00 0.00 3.41
2796 2983 6.822442 TCATAAAATATGTCCCGCTACTGAA 58.178 36.000 0.00 0.00 0.00 3.02
2887 3074 3.181476 GCCACTTGTGACACCATTTCTTT 60.181 43.478 2.45 0.00 0.00 2.52
2894 3081 4.402155 TGTGACACCATTTCTTTTTCTGCT 59.598 37.500 2.45 0.00 0.00 4.24
2903 3090 7.148423 ACCATTTCTTTTTCTGCTTGTTGTTTC 60.148 33.333 0.00 0.00 0.00 2.78
3351 3570 9.912634 TTTCTCATTTTGTGTTGGATTTATCTC 57.087 29.630 0.00 0.00 0.00 2.75
3427 3646 4.867086 ACAGAAACAGAAGGGGAAAAGAA 58.133 39.130 0.00 0.00 0.00 2.52
3442 3661 5.278022 GGGAAAAGAATCGCATAATGGACTC 60.278 44.000 0.00 0.00 32.88 3.36
3458 3677 7.765695 AATGGACTCAAGAAGCAAGAATTAA 57.234 32.000 0.00 0.00 0.00 1.40
3460 3679 6.061441 TGGACTCAAGAAGCAAGAATTAACA 58.939 36.000 0.00 0.00 0.00 2.41
3470 3689 9.683069 AGAAGCAAGAATTAACAATGTACTTTG 57.317 29.630 17.42 17.42 0.00 2.77
3471 3690 8.816640 AAGCAAGAATTAACAATGTACTTTGG 57.183 30.769 21.54 7.59 0.00 3.28
3478 3697 9.774742 GAATTAACAATGTACTTTGGTGATCTC 57.225 33.333 19.38 13.09 0.00 2.75
3485 3704 6.801539 TGTACTTTGGTGATCTCAAACATC 57.198 37.500 9.61 0.00 31.71 3.06
3489 3708 9.167311 GTACTTTGGTGATCTCAAACATCTTAT 57.833 33.333 9.61 0.00 31.71 1.73
3516 3735 8.836268 TGTACTTTGGTGATCTAAAACGTATT 57.164 30.769 0.00 0.00 0.00 1.89
3517 3736 9.926158 TGTACTTTGGTGATCTAAAACGTATTA 57.074 29.630 0.00 0.00 0.00 0.98
3587 3809 6.548251 AGAGGAAGTAGATGCTAAAGAGTACC 59.452 42.308 0.00 0.00 0.00 3.34
3592 3814 8.723942 AAGTAGATGCTAAAGAGTACCAAATG 57.276 34.615 0.00 0.00 0.00 2.32
3598 3820 9.331282 GATGCTAAAGAGTACCAAATGTCTTAT 57.669 33.333 0.00 0.00 0.00 1.73
3816 4135 2.416431 GCACATGGCTGGCTTCTTAAAG 60.416 50.000 2.00 0.00 40.25 1.85
3849 4168 4.195225 GCTAGTTGCTCACCTAAAGTCT 57.805 45.455 0.00 0.00 38.95 3.24
3850 4169 5.326200 GCTAGTTGCTCACCTAAAGTCTA 57.674 43.478 0.00 0.00 38.95 2.59
3851 4170 5.344884 GCTAGTTGCTCACCTAAAGTCTAG 58.655 45.833 0.00 0.00 38.95 2.43
3852 4171 5.125739 GCTAGTTGCTCACCTAAAGTCTAGA 59.874 44.000 0.00 0.00 38.95 2.43
3853 4172 5.652994 AGTTGCTCACCTAAAGTCTAGAG 57.347 43.478 0.00 0.00 0.00 2.43
3854 4173 5.081032 AGTTGCTCACCTAAAGTCTAGAGT 58.919 41.667 0.00 0.00 0.00 3.24
3855 4174 5.184287 AGTTGCTCACCTAAAGTCTAGAGTC 59.816 44.000 0.00 0.00 0.00 3.36
3856 4175 4.924625 TGCTCACCTAAAGTCTAGAGTCT 58.075 43.478 0.00 0.00 0.00 3.24
3857 4176 4.944930 TGCTCACCTAAAGTCTAGAGTCTC 59.055 45.833 0.00 0.00 0.00 3.36
3858 4177 4.337274 GCTCACCTAAAGTCTAGAGTCTCC 59.663 50.000 0.00 0.00 0.00 3.71
3877 4196 6.071616 AGTCTCCAACTTCTCTACACAAGATC 60.072 42.308 0.00 0.00 33.03 2.75
3890 4209 2.802247 CACAAGATCACGCTGTTCTCAA 59.198 45.455 0.00 0.00 0.00 3.02
4028 4347 1.417145 GCCATCTGATCCTTGAGCTCT 59.583 52.381 16.19 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.609151 CAACCAGCCATGCAATTCCA 59.391 50.000 0.00 0.00 0.00 3.53
42 43 1.707632 CCAGCTCAGTTCTTCACTCG 58.292 55.000 0.00 0.00 30.92 4.18
142 161 0.550914 ACCTGGTCCACAGCTTTGAA 59.449 50.000 0.17 0.00 46.14 2.69
161 180 2.116238 GAGGGTGGGAGTACATTGCTA 58.884 52.381 0.00 0.00 0.00 3.49
164 183 2.187958 TGAGAGGGTGGGAGTACATTG 58.812 52.381 0.00 0.00 0.00 2.82
223 242 6.262601 GCAAATTATGCGCTTCCTTTTACTA 58.737 36.000 9.73 0.00 46.87 1.82
224 243 5.102313 GCAAATTATGCGCTTCCTTTTACT 58.898 37.500 9.73 0.00 46.87 2.24
225 244 5.375544 GCAAATTATGCGCTTCCTTTTAC 57.624 39.130 9.73 0.00 46.87 2.01
248 270 0.320771 ACCGCACCAGATGAACACTC 60.321 55.000 0.00 0.00 0.00 3.51
281 303 7.148641 ACGTGTTAGATTATTCATCCAGCTAG 58.851 38.462 0.00 0.00 31.20 3.42
368 390 5.819379 TCTGCATCAACATCCTTGATACTTC 59.181 40.000 0.00 0.00 37.06 3.01
424 446 2.481568 GCGGAAACTAACAACCACTACC 59.518 50.000 0.00 0.00 0.00 3.18
443 465 2.638480 TGGAATCTAAATGGAGGGCG 57.362 50.000 0.00 0.00 0.00 6.13
447 469 6.939163 CAGGTAGGATTGGAATCTAAATGGAG 59.061 42.308 0.00 0.00 35.73 3.86
453 475 4.903149 TCCCAGGTAGGATTGGAATCTAA 58.097 43.478 0.00 0.00 41.22 2.10
455 477 3.438131 TCCCAGGTAGGATTGGAATCT 57.562 47.619 0.00 0.00 41.22 2.40
720 752 2.039879 TCCCACTACTTTGCTTCCCTTC 59.960 50.000 0.00 0.00 0.00 3.46
751 783 6.100004 TGTACAGCTAAATTTCTCCTCTTCG 58.900 40.000 0.00 0.00 0.00 3.79
779 811 5.535333 AGGAAACAAGTGAATGAATGCTTG 58.465 37.500 0.00 0.00 42.65 4.01
903 1015 5.690865 TCATACAGAAACAAACAAGGGAGT 58.309 37.500 0.00 0.00 0.00 3.85
907 1019 5.695851 AGCTCATACAGAAACAAACAAGG 57.304 39.130 0.00 0.00 0.00 3.61
919 1031 7.960195 CAGTATGAACGTAGATAGCTCATACAG 59.040 40.741 24.99 18.03 45.85 2.74
935 1047 7.468922 TTTATCAGAATCAGCAGTATGAACG 57.531 36.000 0.00 0.00 39.69 3.95
949 1061 9.312904 TGGAACCAAGAATCTTTTTATCAGAAT 57.687 29.630 0.00 0.00 0.00 2.40
965 1077 4.330056 TCCTGGCTGGAACCAAGA 57.670 55.556 11.07 0.00 42.94 3.02
989 1101 6.942005 TCCAAAGCAAGACATATTCTTCTGAA 59.058 34.615 0.00 0.00 43.23 3.02
992 1104 6.183360 GCATCCAAAGCAAGACATATTCTTCT 60.183 38.462 0.00 0.00 43.23 2.85
1134 1253 5.711976 AGGCAACAGAAGTAAAATGCAGTAT 59.288 36.000 0.00 0.00 41.41 2.12
1209 1328 2.051804 GAATTGGATCGGCAGTGCGG 62.052 60.000 16.07 16.07 0.00 5.69
1305 1424 1.970640 GCCTCATCACCAAAACCCTTT 59.029 47.619 0.00 0.00 0.00 3.11
1323 1442 1.546029 GAACCCTCACCAATCAAAGCC 59.454 52.381 0.00 0.00 0.00 4.35
1407 1526 0.107945 GGTCTGGCTGCTTACTGGAG 60.108 60.000 0.00 0.00 37.17 3.86
1653 1772 6.198966 ACGAAATGTTCAAGACTTCAAATTGC 59.801 34.615 0.00 0.00 0.00 3.56
1687 1806 6.639632 ACTGCGCCAATAGATGAATAAAAT 57.360 33.333 4.18 0.00 0.00 1.82
1830 1951 1.609555 AGATACTCTAGGCCTTTCGCG 59.390 52.381 12.58 0.00 38.94 5.87
1938 2059 4.497340 GCTTGGTTTGACAAATCGAAGTCA 60.497 41.667 17.25 12.79 42.55 3.41
2053 2174 4.561938 CCAAAGCTTCATGGAGCAAATGAA 60.562 41.667 27.76 8.03 45.12 2.57
2078 2199 9.516314 AGTTTAAACAAGCTTAAGTTGAATGAC 57.484 29.630 20.06 0.00 0.00 3.06
2121 2242 4.464069 AGAGCTAAGTTGACCAGTCATC 57.536 45.455 0.48 0.99 39.64 2.92
2259 2380 1.533625 TCACTTGTGCAGTATTGGGC 58.466 50.000 0.00 0.00 32.76 5.36
2538 2667 4.083271 GCAAGCTTGGTAAGTTCCAGTAAG 60.083 45.833 27.10 0.00 38.80 2.34
2553 2682 5.232610 TCAAAACAAAAATGGCAAGCTTG 57.767 34.783 22.44 22.44 0.00 4.01
2610 2739 3.184541 ACATACATCCGTTTGAGCGTAC 58.815 45.455 0.00 0.00 0.00 3.67
2649 2823 4.406648 TGACGCTCAAATGGATGTATCT 57.593 40.909 0.00 0.00 0.00 1.98
2659 2833 6.149633 GTCCAAAATTACTTGACGCTCAAAT 58.850 36.000 2.82 0.00 35.73 2.32
2667 2841 3.439129 CCCTCCGTCCAAAATTACTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
2678 2864 1.684248 GCTAGTACTCCCTCCGTCCAA 60.684 57.143 0.00 0.00 0.00 3.53
2679 2865 0.106819 GCTAGTACTCCCTCCGTCCA 60.107 60.000 0.00 0.00 0.00 4.02
2741 2927 5.703876 AGCAGCTGCAGAAATACTTTTTAC 58.296 37.500 38.24 4.68 45.16 2.01
2742 2928 5.964958 AGCAGCTGCAGAAATACTTTTTA 57.035 34.783 38.24 0.00 45.16 1.52
2743 2929 4.861102 AGCAGCTGCAGAAATACTTTTT 57.139 36.364 38.24 11.97 45.16 1.94
2756 2943 2.865343 ATGAGCATAAAAGCAGCTGC 57.135 45.000 31.53 31.53 39.02 5.25
2761 2948 8.359642 GGGACATATTTTATGAGCATAAAAGCA 58.640 33.333 24.24 17.83 38.23 3.91
2762 2949 7.538678 CGGGACATATTTTATGAGCATAAAAGC 59.461 37.037 24.24 14.76 38.23 3.51
2763 2950 7.538678 GCGGGACATATTTTATGAGCATAAAAG 59.461 37.037 24.24 16.90 38.23 2.27
2788 2975 8.677300 TCCAAGAATGATGTTAATTTCAGTAGC 58.323 33.333 0.00 0.00 0.00 3.58
2795 2982 6.759827 GCATGCTCCAAGAATGATGTTAATTT 59.240 34.615 11.37 0.00 32.78 1.82
2796 2983 6.097839 AGCATGCTCCAAGAATGATGTTAATT 59.902 34.615 16.30 0.00 32.78 1.40
2874 3061 5.351458 ACAAGCAGAAAAAGAAATGGTGTC 58.649 37.500 0.00 0.00 0.00 3.67
2894 3081 4.084118 GCTGCAAACTGTTTGAAACAACAA 60.084 37.500 31.35 8.95 43.26 2.83
2903 3090 0.929824 CGACGGCTGCAAACTGTTTG 60.930 55.000 24.98 24.98 43.44 2.93
3292 3489 3.507162 TCTGGACTTGGAAGCAAATGA 57.493 42.857 0.00 0.00 0.00 2.57
3347 3566 5.957771 TCCAAACAAGGCTATACAGAGAT 57.042 39.130 0.00 0.00 0.00 2.75
3351 3570 4.396166 CCTGTTCCAAACAAGGCTATACAG 59.604 45.833 0.00 0.00 41.61 2.74
3427 3646 3.812053 GCTTCTTGAGTCCATTATGCGAT 59.188 43.478 0.00 0.00 0.00 4.58
3442 3661 9.683069 AAGTACATTGTTAATTCTTGCTTCTTG 57.317 29.630 0.00 0.00 0.00 3.02
3458 3677 6.545666 TGTTTGAGATCACCAAAGTACATTGT 59.454 34.615 9.76 0.00 34.59 2.71
3460 3679 7.667219 AGATGTTTGAGATCACCAAAGTACATT 59.333 33.333 11.88 0.00 34.59 2.71
3470 3689 9.988815 AGTACATATAAGATGTTTGAGATCACC 57.011 33.333 0.00 0.00 33.76 4.02
3519 3738 9.877178 CATTCTACTGTTCCTCTGTAAACTAAT 57.123 33.333 0.00 0.00 31.83 1.73
3520 3739 8.867097 ACATTCTACTGTTCCTCTGTAAACTAA 58.133 33.333 0.00 0.00 31.83 2.24
3521 3740 8.418597 ACATTCTACTGTTCCTCTGTAAACTA 57.581 34.615 0.00 0.00 31.83 2.24
3522 3741 7.233757 AGACATTCTACTGTTCCTCTGTAAACT 59.766 37.037 0.00 0.00 31.83 2.66
3523 3742 7.379750 AGACATTCTACTGTTCCTCTGTAAAC 58.620 38.462 0.00 0.00 31.83 2.01
3524 3743 7.540474 AGACATTCTACTGTTCCTCTGTAAA 57.460 36.000 0.00 0.00 31.83 2.01
3525 3744 7.540474 AAGACATTCTACTGTTCCTCTGTAA 57.460 36.000 0.00 0.00 31.83 2.41
3526 3745 8.824756 ATAAGACATTCTACTGTTCCTCTGTA 57.175 34.615 0.00 0.00 0.00 2.74
3527 3746 7.726033 ATAAGACATTCTACTGTTCCTCTGT 57.274 36.000 0.00 0.00 0.00 3.41
3760 4079 5.265989 TGTAAAATTAGGTTTAGGCCTGGG 58.734 41.667 17.99 0.00 39.60 4.45
3796 4115 3.498927 CTTTAAGAAGCCAGCCATGTG 57.501 47.619 0.00 0.00 0.00 3.21
3816 4135 1.833860 CAACTAGCTCGCTCTGTAGC 58.166 55.000 0.00 0.00 45.86 3.58
3845 4164 5.514500 AGAGAAGTTGGAGACTCTAGACT 57.486 43.478 1.74 1.72 37.72 3.24
3846 4165 6.093082 GTGTAGAGAAGTTGGAGACTCTAGAC 59.907 46.154 0.00 0.00 43.44 2.59
3848 4167 5.941058 TGTGTAGAGAAGTTGGAGACTCTAG 59.059 44.000 1.74 0.00 40.87 2.43
3849 4168 5.877491 TGTGTAGAGAAGTTGGAGACTCTA 58.123 41.667 1.74 0.00 37.72 2.43
3850 4169 4.730966 TGTGTAGAGAAGTTGGAGACTCT 58.269 43.478 1.74 0.00 37.72 3.24
3851 4170 5.241949 TCTTGTGTAGAGAAGTTGGAGACTC 59.758 44.000 0.00 0.00 37.72 3.36
3852 4171 5.141182 TCTTGTGTAGAGAAGTTGGAGACT 58.859 41.667 0.00 0.00 41.47 3.24
3853 4172 5.455056 TCTTGTGTAGAGAAGTTGGAGAC 57.545 43.478 0.00 0.00 0.00 3.36
3854 4173 5.775195 TGATCTTGTGTAGAGAAGTTGGAGA 59.225 40.000 0.00 0.00 36.02 3.71
3855 4174 5.866633 GTGATCTTGTGTAGAGAAGTTGGAG 59.133 44.000 0.00 0.00 36.02 3.86
3856 4175 5.564848 CGTGATCTTGTGTAGAGAAGTTGGA 60.565 44.000 0.00 0.00 36.02 3.53
3857 4176 4.623167 CGTGATCTTGTGTAGAGAAGTTGG 59.377 45.833 0.00 0.00 36.02 3.77
3858 4177 4.090642 GCGTGATCTTGTGTAGAGAAGTTG 59.909 45.833 0.00 0.00 36.02 3.16


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

AutoCloner maintained by Alex Coulton.