Multiple sequence alignment - TraesCS2D01G402500

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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 TraesCS2D01G402500 chr2D 100.000 3047 0 0 1 3047 517265706 517262660 0.000000e+00 5627.0
1 TraesCS2D01G402500 chr2A 92.109 2674 126 36 343 2992 661586475 661583863 0.000000e+00 3690.0
2 TraesCS2D01G402500 chr2A 97.101 69 1 1 32 100 661589061 661588994 6.900000e-22 115.0
3 TraesCS2D01G402500 chr2B 92.123 2628 123 35 361 2973 609202922 609200364 0.000000e+00 3629.0
4 TraesCS2D01G402500 chr2B 92.903 155 8 3 32 186 609203810 609203659 3.950000e-54 222.0
5 TraesCS2D01G402500 chr6A 77.073 1025 180 48 1058 2047 469110030 469111034 9.610000e-150 540.0
6 TraesCS2D01G402500 chr6D 76.390 1025 187 45 1058 2047 329884864 329885868 4.540000e-138 501.0
7 TraesCS2D01G402500 chr6B 75.964 1011 194 40 1069 2047 490565815 490564822 2.750000e-130 475.0
8 TraesCS2D01G402500 chr4D 76.238 303 38 23 1219 1495 485163793 485164087 2.470000e-26 130.0
9 TraesCS2D01G402500 chr4B 74.747 297 49 17 1221 1495 618347484 618347776 3.210000e-20 110.0
10 TraesCS2D01G402500 chr5A 74.333 300 47 20 1220 1495 666204341 666204634 1.930000e-17 100.0
11 TraesCS2D01G402500 chr7A 74.747 198 34 11 1309 1498 722128360 722128549 1.170000e-09 75.0
12 TraesCS2D01G402500 chr7A 90.385 52 5 0 1313 1364 722019763 722019814 5.450000e-08 69.4
13 TraesCS2D01G402500 chr7D 88.679 53 6 0 1312 1364 626597677 626597625 7.050000e-07 65.8
14 TraesCS2D01G402500 chr7B 87.500 56 7 0 1309 1364 726697391 726697446 7.050000e-07 65.8
15 TraesCS2D01G402500 chr7B 72.959 196 45 5 1309 1500 726754896 726755087 9.120000e-06 62.1
16 TraesCS2D01G402500 chr7B 74.699 166 24 14 1317 1473 726267674 726267518 1.180000e-04 58.4


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 TraesCS2D01G402500 chr2D 517262660 517265706 3046 True 5627.0 5627 100.000 1 3047 1 chr2D.!!$R1 3046
1 TraesCS2D01G402500 chr2A 661583863 661589061 5198 True 1902.5 3690 94.605 32 2992 2 chr2A.!!$R1 2960
2 TraesCS2D01G402500 chr2B 609200364 609203810 3446 True 1925.5 3629 92.513 32 2973 2 chr2B.!!$R1 2941
3 TraesCS2D01G402500 chr6A 469110030 469111034 1004 False 540.0 540 77.073 1058 2047 1 chr6A.!!$F1 989
4 TraesCS2D01G402500 chr6D 329884864 329885868 1004 False 501.0 501 76.390 1058 2047 1 chr6D.!!$F1 989
5 TraesCS2D01G402500 chr6B 490564822 490565815 993 True 475.0 475 75.964 1069 2047 1 chr6B.!!$R1 978

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
993 4004 0.0293 GCAAAAAGCACGAGCAGTCA 59.971 50.0 7.77 0.0 45.49 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2835 5898 0.249615 CCGCACCGACTCATCATCAT 60.25 55.0 0.0 0.0 0.0 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
111 112 3.243501 TGCTTTCTGCTTTGCTCGAAAAT 60.244 39.130 0.00 0.00 43.37 1.82
117 118 3.641648 TGCTTTGCTCGAAAATTCCAAG 58.358 40.909 0.00 0.00 0.00 3.61
127 128 3.669023 CGAAAATTCCAAGAGTCAGCAGC 60.669 47.826 0.00 0.00 0.00 5.25
139 140 4.020396 AGAGTCAGCAGCCATATTATGAGG 60.020 45.833 5.21 0.00 0.00 3.86
146 147 5.537674 AGCAGCCATATTATGAGGGAAAAAG 59.462 40.000 5.21 0.00 0.00 2.27
148 149 6.040842 GCAGCCATATTATGAGGGAAAAAGAA 59.959 38.462 5.21 0.00 0.00 2.52
149 150 7.256083 GCAGCCATATTATGAGGGAAAAAGAAT 60.256 37.037 5.21 0.00 0.00 2.40
152 153 9.077885 GCCATATTATGAGGGAAAAAGAATGTA 57.922 33.333 5.21 0.00 0.00 2.29
214 215 8.928270 AAGTAGTGTATGTACTAACTTGCATC 57.072 34.615 0.00 0.00 35.12 3.91
229 849 0.249238 GCATCGGGCACACACAAAAA 60.249 50.000 0.00 0.00 43.97 1.94
230 850 1.486439 CATCGGGCACACACAAAAAC 58.514 50.000 0.00 0.00 0.00 2.43
289 3280 8.255111 AGATATCACTTCTACCACATGATCAA 57.745 34.615 5.32 0.00 32.42 2.57
307 3305 4.116747 TCAAAACAAAGCATTCCACGTT 57.883 36.364 0.00 0.00 0.00 3.99
309 3307 5.651530 TCAAAACAAAGCATTCCACGTTAA 58.348 33.333 0.00 0.00 0.00 2.01
310 3308 6.100004 TCAAAACAAAGCATTCCACGTTAAA 58.900 32.000 0.00 0.00 0.00 1.52
311 3309 6.590292 TCAAAACAAAGCATTCCACGTTAAAA 59.410 30.769 0.00 0.00 0.00 1.52
312 3310 6.969828 AAACAAAGCATTCCACGTTAAAAA 57.030 29.167 0.00 0.00 0.00 1.94
313 3311 5.959652 ACAAAGCATTCCACGTTAAAAAC 57.040 34.783 0.00 0.00 0.00 2.43
314 3312 4.806775 ACAAAGCATTCCACGTTAAAAACC 59.193 37.500 0.00 0.00 0.00 3.27
315 3313 3.276882 AGCATTCCACGTTAAAAACCG 57.723 42.857 0.00 0.00 0.00 4.44
316 3314 1.717113 GCATTCCACGTTAAAAACCGC 59.283 47.619 0.00 0.00 0.00 5.68
317 3315 2.606065 GCATTCCACGTTAAAAACCGCT 60.606 45.455 0.00 0.00 0.00 5.52
318 3316 3.634283 CATTCCACGTTAAAAACCGCTT 58.366 40.909 0.00 0.00 0.00 4.68
319 3317 2.759538 TCCACGTTAAAAACCGCTTG 57.240 45.000 0.00 0.00 0.00 4.01
320 3318 2.286872 TCCACGTTAAAAACCGCTTGA 58.713 42.857 0.00 0.00 0.00 3.02
321 3319 2.681848 TCCACGTTAAAAACCGCTTGAA 59.318 40.909 0.00 0.00 0.00 2.69
322 3320 3.040099 CCACGTTAAAAACCGCTTGAAG 58.960 45.455 0.00 0.00 0.00 3.02
323 3321 3.487879 CCACGTTAAAAACCGCTTGAAGT 60.488 43.478 0.00 0.00 0.00 3.01
324 3322 4.260702 CCACGTTAAAAACCGCTTGAAGTA 60.261 41.667 0.00 0.00 0.00 2.24
325 3323 5.264712 CACGTTAAAAACCGCTTGAAGTAA 58.735 37.500 0.00 0.00 0.00 2.24
326 3324 5.738225 CACGTTAAAAACCGCTTGAAGTAAA 59.262 36.000 0.00 0.00 0.00 2.01
327 3325 5.738693 ACGTTAAAAACCGCTTGAAGTAAAC 59.261 36.000 0.00 0.00 0.00 2.01
328 3326 5.109039 CGTTAAAAACCGCTTGAAGTAAACG 60.109 40.000 0.00 0.00 0.00 3.60
331 3329 2.922779 CCGCTTGAAGTAAACGGGT 58.077 52.632 1.69 0.00 40.18 5.28
332 3330 0.515564 CCGCTTGAAGTAAACGGGTG 59.484 55.000 1.69 0.00 40.18 4.61
333 3331 0.515564 CGCTTGAAGTAAACGGGTGG 59.484 55.000 0.00 0.00 0.00 4.61
334 3332 0.240145 GCTTGAAGTAAACGGGTGGC 59.760 55.000 0.00 0.00 0.00 5.01
335 3333 1.892209 CTTGAAGTAAACGGGTGGCT 58.108 50.000 0.00 0.00 0.00 4.75
336 3334 2.872842 GCTTGAAGTAAACGGGTGGCTA 60.873 50.000 0.00 0.00 0.00 3.93
337 3335 3.606687 CTTGAAGTAAACGGGTGGCTAT 58.393 45.455 0.00 0.00 0.00 2.97
338 3336 3.255969 TGAAGTAAACGGGTGGCTATC 57.744 47.619 0.00 0.00 0.00 2.08
339 3337 2.835764 TGAAGTAAACGGGTGGCTATCT 59.164 45.455 0.00 0.00 0.00 1.98
340 3338 3.118884 TGAAGTAAACGGGTGGCTATCTC 60.119 47.826 0.00 0.00 0.00 2.75
341 3339 2.463752 AGTAAACGGGTGGCTATCTCA 58.536 47.619 0.00 0.00 0.00 3.27
370 3368 7.449934 AACATCAACAACTCAAAAATTCGAC 57.550 32.000 0.00 0.00 0.00 4.20
372 3370 5.224562 TCAACAACTCAAAAATTCGACGT 57.775 34.783 0.00 0.00 0.00 4.34
473 3471 0.458669 ACATACATGGACGACGGACC 59.541 55.000 0.00 2.95 0.00 4.46
538 3536 2.604174 CCACAAACGGACGAGCCAC 61.604 63.158 0.00 0.00 35.94 5.01
668 3669 1.971695 CCCAGCCCCAAGACGTTTC 60.972 63.158 0.00 0.00 0.00 2.78
670 3671 1.515521 CCAGCCCCAAGACGTTTCAC 61.516 60.000 0.00 0.00 0.00 3.18
852 3859 4.021368 ACCTGTATAAAAGACACGAGCACT 60.021 41.667 0.00 0.00 0.00 4.40
947 3958 1.080366 CCGGCCTTTAAAAACCCGC 60.080 57.895 0.00 0.67 37.73 6.13
992 4003 2.788535 GCAAAAAGCACGAGCAGTC 58.211 52.632 7.77 0.00 45.49 3.51
993 4004 0.029300 GCAAAAAGCACGAGCAGTCA 59.971 50.000 7.77 0.00 45.49 3.41
994 4005 1.533756 GCAAAAAGCACGAGCAGTCAA 60.534 47.619 7.77 0.00 45.49 3.18
1026 4037 3.845259 TACCGGCGCACCATCTCC 61.845 66.667 10.83 0.00 34.57 3.71
1724 4735 1.517832 CCTCAAGATTCTCCGCCGT 59.482 57.895 0.00 0.00 0.00 5.68
1868 4906 4.736896 GTCCACCTCGTCCACGGC 62.737 72.222 0.00 0.00 40.29 5.68
2043 5090 0.779997 ACATCCTCAGCCCAACCTTT 59.220 50.000 0.00 0.00 0.00 3.11
2054 5101 0.527565 CCAACCTTTTGATCCCGCAG 59.472 55.000 0.00 0.00 34.24 5.18
2056 5103 0.539438 AACCTTTTGATCCCGCAGCA 60.539 50.000 0.00 0.00 0.00 4.41
2058 5105 1.138247 CTTTTGATCCCGCAGCAGC 59.862 57.895 0.00 0.00 37.42 5.25
2059 5106 1.303561 TTTTGATCCCGCAGCAGCT 60.304 52.632 0.00 0.00 39.10 4.24
2060 5107 1.308069 TTTTGATCCCGCAGCAGCTC 61.308 55.000 0.00 0.00 39.10 4.09
2061 5108 3.687321 TTGATCCCGCAGCAGCTCC 62.687 63.158 0.00 0.00 39.10 4.70
2062 5109 4.166888 GATCCCGCAGCAGCTCCA 62.167 66.667 0.00 0.00 39.10 3.86
2063 5110 3.687321 GATCCCGCAGCAGCTCCAA 62.687 63.158 0.00 0.00 39.10 3.53
2064 5111 2.955022 GATCCCGCAGCAGCTCCAAT 62.955 60.000 0.00 0.00 39.10 3.16
2065 5112 2.955022 ATCCCGCAGCAGCTCCAATC 62.955 60.000 0.00 0.00 39.10 2.67
2066 5113 3.207669 CCGCAGCAGCTCCAATCC 61.208 66.667 0.00 0.00 39.10 3.01
2126 5173 7.328737 GCTTGGACAGGATTTGTATATAGTACG 59.671 40.741 0.00 0.00 41.05 3.67
2128 5175 7.654568 TGGACAGGATTTGTATATAGTACGTG 58.345 38.462 0.00 0.00 41.05 4.49
2134 5182 9.730705 AGGATTTGTATATAGTACGTGCTACTA 57.269 33.333 15.91 7.33 41.36 1.82
2147 5195 6.461110 ACGTGCTACTAGTGGTATATTGTT 57.539 37.500 5.39 0.00 0.00 2.83
2154 5202 2.484602 AGTGGTATATTGTTCCCCGGT 58.515 47.619 0.00 0.00 0.00 5.28
2292 5343 1.695893 ATGAATTCAGACGCCGCGTG 61.696 55.000 25.60 10.32 41.37 5.34
2358 5409 3.004944 GGACTTTCTAGATCGAGCGGAAT 59.995 47.826 11.50 0.66 0.00 3.01
2380 5431 1.761244 TTGGCTTATGTGATCGCGCG 61.761 55.000 26.76 26.76 0.00 6.86
2410 5461 0.250727 TCGGGTTGCCAAGAAAGAGG 60.251 55.000 0.00 0.00 0.00 3.69
2470 5525 1.090052 CCGAACCGCAAGAAGGGATC 61.090 60.000 0.00 0.00 43.02 3.36
2471 5526 1.090052 CGAACCGCAAGAAGGGATCC 61.090 60.000 1.92 1.92 43.02 3.36
2794 5857 3.490759 GATCCACGGTGCGCACTG 61.491 66.667 40.42 40.42 43.20 3.66
2800 5863 3.777925 CGGTGCGCACTGTACTGC 61.778 66.667 35.80 19.08 32.62 4.40
2835 5898 0.296349 CATAATGCGTTCGCGTTCGA 59.704 50.000 24.21 11.49 43.89 3.71
2842 5905 0.846401 CGTTCGCGTTCGATGATGAT 59.154 50.000 17.18 0.00 45.04 2.45
2845 5908 1.758783 TCGCGTTCGATGATGATGAG 58.241 50.000 5.77 0.00 40.21 2.90
2846 5909 1.065551 TCGCGTTCGATGATGATGAGT 59.934 47.619 5.77 0.00 40.21 3.41
2847 5910 1.449789 CGCGTTCGATGATGATGAGTC 59.550 52.381 0.00 0.00 38.10 3.36
2849 5912 2.047040 CGTTCGATGATGATGAGTCGG 58.953 52.381 0.00 0.00 35.01 4.79
2850 5913 2.541794 CGTTCGATGATGATGAGTCGGT 60.542 50.000 0.00 0.00 35.01 4.69
2851 5914 2.781945 TCGATGATGATGAGTCGGTG 57.218 50.000 0.00 0.00 35.01 4.94
2884 5947 2.821810 GCCCTCTTCGCTGCCTTC 60.822 66.667 0.00 0.00 0.00 3.46
2894 5957 1.303155 GCTGCCTTCTCCACTTGCT 60.303 57.895 0.00 0.00 0.00 3.91
2896 5959 1.004560 TGCCTTCTCCACTTGCTCG 60.005 57.895 0.00 0.00 0.00 5.03
2949 6013 4.950744 CCGTCAGCTTGGCAAAAG 57.049 55.556 0.00 0.00 0.00 2.27
2962 6026 2.161410 TGGCAAAAGTATCATGTGCGTC 59.839 45.455 0.00 0.00 36.04 5.19
2965 6029 3.407252 CAAAAGTATCATGTGCGTCGTG 58.593 45.455 0.00 0.00 34.61 4.35
3000 6064 4.516195 GAGCTCCTCGAACCGGGC 62.516 72.222 6.32 0.00 0.00 6.13
3002 6066 4.516195 GCTCCTCGAACCGGGCTC 62.516 72.222 6.32 0.12 0.00 4.70
3003 6067 3.839432 CTCCTCGAACCGGGCTCC 61.839 72.222 6.32 0.00 0.00 4.70
3004 6068 4.377760 TCCTCGAACCGGGCTCCT 62.378 66.667 6.32 0.00 0.00 3.69
3005 6069 3.391382 CCTCGAACCGGGCTCCTT 61.391 66.667 6.32 0.00 0.00 3.36
3006 6070 2.056223 CCTCGAACCGGGCTCCTTA 61.056 63.158 6.32 0.00 0.00 2.69
3007 6071 1.610554 CCTCGAACCGGGCTCCTTAA 61.611 60.000 6.32 0.00 0.00 1.85
3008 6072 0.248289 CTCGAACCGGGCTCCTTAAA 59.752 55.000 6.32 0.00 0.00 1.52
3009 6073 0.037046 TCGAACCGGGCTCCTTAAAC 60.037 55.000 6.32 0.00 0.00 2.01
3010 6074 0.036671 CGAACCGGGCTCCTTAAACT 60.037 55.000 6.32 0.00 0.00 2.66
3011 6075 1.450025 GAACCGGGCTCCTTAAACTG 58.550 55.000 6.32 0.00 0.00 3.16
3012 6076 0.769247 AACCGGGCTCCTTAAACTGT 59.231 50.000 6.32 0.00 0.00 3.55
3013 6077 0.323957 ACCGGGCTCCTTAAACTGTC 59.676 55.000 6.32 0.00 0.00 3.51
3014 6078 0.392595 CCGGGCTCCTTAAACTGTCC 60.393 60.000 0.00 0.00 0.00 4.02
3015 6079 0.323629 CGGGCTCCTTAAACTGTCCA 59.676 55.000 0.00 0.00 0.00 4.02
3016 6080 1.822506 GGGCTCCTTAAACTGTCCAC 58.177 55.000 0.00 0.00 0.00 4.02
3017 6081 1.351350 GGGCTCCTTAAACTGTCCACT 59.649 52.381 0.00 0.00 0.00 4.00
3018 6082 2.570302 GGGCTCCTTAAACTGTCCACTA 59.430 50.000 0.00 0.00 0.00 2.74
3019 6083 3.200165 GGGCTCCTTAAACTGTCCACTAT 59.800 47.826 0.00 0.00 0.00 2.12
3020 6084 4.192317 GGCTCCTTAAACTGTCCACTATG 58.808 47.826 0.00 0.00 0.00 2.23
3021 6085 4.192317 GCTCCTTAAACTGTCCACTATGG 58.808 47.826 0.00 0.00 39.43 2.74
3022 6086 4.770795 CTCCTTAAACTGTCCACTATGGG 58.229 47.826 0.00 0.00 38.32 4.00
3023 6087 4.431378 TCCTTAAACTGTCCACTATGGGA 58.569 43.478 0.00 0.00 38.32 4.37
3024 6088 4.469945 TCCTTAAACTGTCCACTATGGGAG 59.530 45.833 0.00 0.00 38.32 4.30
3025 6089 4.225267 CCTTAAACTGTCCACTATGGGAGT 59.775 45.833 0.00 0.00 38.32 3.85
3036 6100 3.751518 ACTATGGGAGTGTTTGGTTCAC 58.248 45.455 0.00 0.00 36.87 3.18
3037 6101 2.746279 ATGGGAGTGTTTGGTTCACA 57.254 45.000 0.00 0.00 38.16 3.58
3038 6102 2.746279 TGGGAGTGTTTGGTTCACAT 57.254 45.000 0.00 0.00 38.16 3.21
3039 6103 2.582052 TGGGAGTGTTTGGTTCACATC 58.418 47.619 0.00 0.00 38.16 3.06
3040 6104 2.174639 TGGGAGTGTTTGGTTCACATCT 59.825 45.455 0.00 0.00 38.16 2.90
3041 6105 2.814336 GGGAGTGTTTGGTTCACATCTC 59.186 50.000 0.00 0.00 38.16 2.75
3042 6106 3.496870 GGGAGTGTTTGGTTCACATCTCT 60.497 47.826 0.00 0.00 38.16 3.10
3043 6107 4.137543 GGAGTGTTTGGTTCACATCTCTT 58.862 43.478 0.00 0.00 38.16 2.85
3044 6108 4.580580 GGAGTGTTTGGTTCACATCTCTTT 59.419 41.667 0.00 0.00 38.16 2.52
3045 6109 5.067805 GGAGTGTTTGGTTCACATCTCTTTT 59.932 40.000 0.00 0.00 38.16 2.27
3046 6110 6.405842 GGAGTGTTTGGTTCACATCTCTTTTT 60.406 38.462 0.00 0.00 38.16 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.488762 CCCCCTAAGTCATATATAGTGATACAA 57.511 37.037 0.00 0.00 0.00 2.41
19 20 8.630091 ACCCCCTAAGTCATATATAGTGATACA 58.370 37.037 0.00 0.00 0.00 2.29
20 21 9.134055 GACCCCCTAAGTCATATATAGTGATAC 57.866 40.741 0.00 0.00 34.27 2.24
21 22 9.081508 AGACCCCCTAAGTCATATATAGTGATA 57.918 37.037 0.00 0.00 36.68 2.15
22 23 7.956357 AGACCCCCTAAGTCATATATAGTGAT 58.044 38.462 0.00 0.00 36.68 3.06
23 24 7.358255 AGACCCCCTAAGTCATATATAGTGA 57.642 40.000 0.00 0.00 36.68 3.41
24 25 9.543231 TTTAGACCCCCTAAGTCATATATAGTG 57.457 37.037 0.00 0.00 38.48 2.74
28 29 8.826765 CACATTTAGACCCCCTAAGTCATATAT 58.173 37.037 0.00 0.00 38.48 0.86
29 30 7.236847 CCACATTTAGACCCCCTAAGTCATATA 59.763 40.741 0.00 0.00 38.48 0.86
30 31 6.044404 CCACATTTAGACCCCCTAAGTCATAT 59.956 42.308 0.00 0.00 38.48 1.78
40 41 6.614694 AAATAAAACCACATTTAGACCCCC 57.385 37.500 0.00 0.00 0.00 5.40
111 112 0.694771 ATGGCTGCTGACTCTTGGAA 59.305 50.000 0.00 0.00 0.00 3.53
117 118 4.252073 CCTCATAATATGGCTGCTGACTC 58.748 47.826 0.00 0.00 0.00 3.36
139 140 6.033831 CGATGCACAACATACATTCTTTTTCC 59.966 38.462 0.00 0.00 39.84 3.13
146 147 3.403613 TGCGATGCACAACATACATTC 57.596 42.857 0.00 0.00 39.84 2.67
148 149 3.009026 TCTTGCGATGCACAACATACAT 58.991 40.909 0.00 0.00 39.84 2.29
149 150 2.421619 TCTTGCGATGCACAACATACA 58.578 42.857 0.00 0.00 39.84 2.29
152 153 2.553602 TCTTTCTTGCGATGCACAACAT 59.446 40.909 0.00 0.00 43.54 2.71
191 192 6.417044 CCGATGCAAGTTAGTACATACACTAC 59.583 42.308 0.00 0.00 30.76 2.73
214 215 1.587613 CCGTTTTTGTGTGTGCCCG 60.588 57.895 0.00 0.00 0.00 6.13
280 3271 5.697633 GTGGAATGCTTTGTTTTGATCATGT 59.302 36.000 0.00 0.00 0.00 3.21
289 3280 6.183360 GGTTTTTAACGTGGAATGCTTTGTTT 60.183 34.615 0.00 0.00 0.00 2.83
314 3312 0.515564 CCACCCGTTTACTTCAAGCG 59.484 55.000 0.00 0.00 40.20 4.68
315 3313 0.240145 GCCACCCGTTTACTTCAAGC 59.760 55.000 0.00 0.00 0.00 4.01
316 3314 1.892209 AGCCACCCGTTTACTTCAAG 58.108 50.000 0.00 0.00 0.00 3.02
317 3315 3.262405 AGATAGCCACCCGTTTACTTCAA 59.738 43.478 0.00 0.00 0.00 2.69
318 3316 2.835764 AGATAGCCACCCGTTTACTTCA 59.164 45.455 0.00 0.00 0.00 3.02
319 3317 3.118884 TGAGATAGCCACCCGTTTACTTC 60.119 47.826 0.00 0.00 0.00 3.01
320 3318 2.835764 TGAGATAGCCACCCGTTTACTT 59.164 45.455 0.00 0.00 0.00 2.24
321 3319 2.463752 TGAGATAGCCACCCGTTTACT 58.536 47.619 0.00 0.00 0.00 2.24
322 3320 2.973694 TGAGATAGCCACCCGTTTAC 57.026 50.000 0.00 0.00 0.00 2.01
323 3321 3.985019 TTTGAGATAGCCACCCGTTTA 57.015 42.857 0.00 0.00 0.00 2.01
324 3322 2.871096 TTTGAGATAGCCACCCGTTT 57.129 45.000 0.00 0.00 0.00 3.60
325 3323 2.871096 TTTTGAGATAGCCACCCGTT 57.129 45.000 0.00 0.00 0.00 4.44
326 3324 2.871096 TTTTTGAGATAGCCACCCGT 57.129 45.000 0.00 0.00 0.00 5.28
354 3352 7.876596 TGTTTTAACGTCGAATTTTTGAGTTG 58.123 30.769 0.00 0.00 0.00 3.16
358 3356 9.728774 CTTTTTGTTTTAACGTCGAATTTTTGA 57.271 25.926 0.00 0.00 0.00 2.69
359 3357 8.980623 CCTTTTTGTTTTAACGTCGAATTTTTG 58.019 29.630 0.00 0.00 0.00 2.44
370 3368 5.108027 CGCCAGAATCCTTTTTGTTTTAACG 60.108 40.000 0.00 0.00 0.00 3.18
372 3370 4.747605 GCGCCAGAATCCTTTTTGTTTTAA 59.252 37.500 0.00 0.00 0.00 1.52
538 3536 3.403057 CGGAAGGTGTGTGTCGCG 61.403 66.667 0.00 0.00 0.00 5.87
541 3539 2.251642 GCCACGGAAGGTGTGTGTC 61.252 63.158 0.00 0.00 45.52 3.67
560 3560 2.639327 GCGGAGTGGCAGGCATTTT 61.639 57.895 0.00 0.00 0.00 1.82
603 3603 1.029947 GTGGATTGGATTTCCGGCGT 61.030 55.000 6.01 0.00 39.43 5.68
604 3604 1.724582 GGTGGATTGGATTTCCGGCG 61.725 60.000 0.00 0.00 39.43 6.46
782 3788 1.307343 CAGGTGGACTCTGGGGGAT 60.307 63.158 0.00 0.00 0.00 3.85
988 3999 2.693762 CGGCCATGGTGCTTGACTG 61.694 63.158 14.67 0.00 0.00 3.51
989 4000 2.360350 CGGCCATGGTGCTTGACT 60.360 61.111 14.67 0.00 0.00 3.41
990 4001 3.443045 CCGGCCATGGTGCTTGAC 61.443 66.667 14.67 0.00 0.00 3.18
991 4002 4.738998 CCCGGCCATGGTGCTTGA 62.739 66.667 14.67 0.00 0.00 3.02
992 4003 3.636929 TACCCGGCCATGGTGCTTG 62.637 63.158 21.42 1.25 36.57 4.01
993 4004 3.334891 TACCCGGCCATGGTGCTT 61.335 61.111 21.42 0.00 36.57 3.91
994 4005 4.109675 GTACCCGGCCATGGTGCT 62.110 66.667 21.42 0.25 36.57 4.40
1026 4037 4.468689 GCCTTCGGGGTCGGGAAG 62.469 72.222 0.00 0.00 39.44 3.46
2043 5090 2.124983 GAGCTGCTGCGGGATCAA 60.125 61.111 7.01 0.00 45.42 2.57
2054 5101 3.701040 TCCTAAATTTGGATTGGAGCTGC 59.299 43.478 2.65 0.00 0.00 5.25
2056 5103 5.105756 CGTTTCCTAAATTTGGATTGGAGCT 60.106 40.000 2.65 0.00 33.09 4.09
2058 5105 6.267496 ACGTTTCCTAAATTTGGATTGGAG 57.733 37.500 2.65 0.00 33.09 3.86
2059 5106 6.658188 AACGTTTCCTAAATTTGGATTGGA 57.342 33.333 2.65 0.00 33.09 3.53
2060 5107 7.571892 CAAAACGTTTCCTAAATTTGGATTGG 58.428 34.615 15.01 2.68 33.09 3.16
2061 5108 7.042119 AGCAAAACGTTTCCTAAATTTGGATTG 60.042 33.333 15.01 4.69 33.09 2.67
2062 5109 6.989759 AGCAAAACGTTTCCTAAATTTGGATT 59.010 30.769 15.01 0.00 33.09 3.01
2063 5110 6.521162 AGCAAAACGTTTCCTAAATTTGGAT 58.479 32.000 15.01 0.00 33.09 3.41
2064 5111 5.908341 AGCAAAACGTTTCCTAAATTTGGA 58.092 33.333 15.01 4.36 0.00 3.53
2065 5112 6.256757 TGAAGCAAAACGTTTCCTAAATTTGG 59.743 34.615 15.01 0.00 34.12 3.28
2066 5113 7.227992 TGAAGCAAAACGTTTCCTAAATTTG 57.772 32.000 15.01 7.33 34.12 2.32
2126 5173 6.221659 GGGAACAATATACCACTAGTAGCAC 58.778 44.000 0.00 0.00 33.42 4.40
2128 5175 5.566230 CGGGGAACAATATACCACTAGTAGC 60.566 48.000 0.00 0.00 33.42 3.58
2134 5182 2.484602 ACCGGGGAACAATATACCACT 58.515 47.619 6.32 0.00 0.00 4.00
2154 5202 3.809775 GCATGCAAAGGCCGCGTA 61.810 61.111 14.21 0.00 40.13 4.42
2270 5321 0.811616 GCGGCGTCTGAATTCATCCT 60.812 55.000 8.96 0.00 0.00 3.24
2272 5323 1.273887 CGCGGCGTCTGAATTCATC 59.726 57.895 15.36 4.78 0.00 2.92
2292 5343 5.006649 GTGGATTTTTGCCAGAAACAAGAAC 59.993 40.000 0.00 0.00 35.77 3.01
2335 5386 1.950909 CCGCTCGATCTAGAAAGTCCT 59.049 52.381 0.00 0.00 0.00 3.85
2337 5388 3.694535 TTCCGCTCGATCTAGAAAGTC 57.305 47.619 0.00 0.00 0.00 3.01
2358 5409 2.730715 GCGCGATCACATAAGCCAAAAA 60.731 45.455 12.10 0.00 0.00 1.94
2392 5443 0.537371 ACCTCTTTCTTGGCAACCCG 60.537 55.000 0.00 0.00 0.00 5.28
2574 5630 2.940410 ACTTGTGTGTGGTTCGGTTAAG 59.060 45.455 0.00 0.00 0.00 1.85
2799 5862 4.969604 GCGTGTGCAGTGCAGTGC 62.970 66.667 34.65 34.65 40.08 4.40
2835 5898 0.249615 CCGCACCGACTCATCATCAT 60.250 55.000 0.00 0.00 0.00 2.45
2884 5947 2.032528 TTGGCCGAGCAAGTGGAG 59.967 61.111 0.00 0.00 0.00 3.86
2912 5975 2.608268 GCGTCCTAGGTCTTTCTGAAC 58.392 52.381 9.08 0.00 0.00 3.18
2962 6026 1.007336 GGTGTAGTTGCTCCGTCACG 61.007 60.000 0.00 0.00 0.00 4.35
2965 6029 1.445582 CGGGTGTAGTTGCTCCGTC 60.446 63.158 0.00 0.00 36.38 4.79
2992 6056 1.271217 ACAGTTTAAGGAGCCCGGTTC 60.271 52.381 0.00 0.00 0.00 3.62
2993 6057 0.769247 ACAGTTTAAGGAGCCCGGTT 59.231 50.000 0.00 0.00 0.00 4.44
2994 6058 0.323957 GACAGTTTAAGGAGCCCGGT 59.676 55.000 0.00 0.00 0.00 5.28
2995 6059 0.392595 GGACAGTTTAAGGAGCCCGG 60.393 60.000 0.00 0.00 0.00 5.73
2996 6060 0.323629 TGGACAGTTTAAGGAGCCCG 59.676 55.000 0.00 0.00 0.00 6.13
2997 6061 1.351350 AGTGGACAGTTTAAGGAGCCC 59.649 52.381 0.00 0.00 0.00 5.19
2998 6062 2.861147 AGTGGACAGTTTAAGGAGCC 57.139 50.000 0.00 0.00 0.00 4.70
2999 6063 4.192317 CCATAGTGGACAGTTTAAGGAGC 58.808 47.826 0.00 0.00 40.96 4.70
3000 6064 4.469945 TCCCATAGTGGACAGTTTAAGGAG 59.530 45.833 0.00 0.00 40.96 3.69
3001 6065 4.431378 TCCCATAGTGGACAGTTTAAGGA 58.569 43.478 0.00 0.00 40.96 3.36
3002 6066 4.225267 ACTCCCATAGTGGACAGTTTAAGG 59.775 45.833 0.00 0.00 40.96 2.69
3003 6067 5.422214 ACTCCCATAGTGGACAGTTTAAG 57.578 43.478 0.00 0.00 40.96 1.85
3015 6079 3.137544 TGTGAACCAAACACTCCCATAGT 59.862 43.478 0.00 0.00 39.81 2.12
3016 6080 3.750371 TGTGAACCAAACACTCCCATAG 58.250 45.455 0.00 0.00 38.81 2.23
3017 6081 3.866703 TGTGAACCAAACACTCCCATA 57.133 42.857 0.00 0.00 38.81 2.74
3018 6082 2.746279 TGTGAACCAAACACTCCCAT 57.254 45.000 0.00 0.00 38.81 4.00
3019 6083 2.174639 AGATGTGAACCAAACACTCCCA 59.825 45.455 0.00 0.00 38.81 4.37
3020 6084 2.814336 GAGATGTGAACCAAACACTCCC 59.186 50.000 0.00 0.00 38.81 4.30
3021 6085 3.744660 AGAGATGTGAACCAAACACTCC 58.255 45.455 0.00 0.00 38.81 3.85
3022 6086 5.757850 AAAGAGATGTGAACCAAACACTC 57.242 39.130 0.00 0.00 38.81 3.51
3023 6087 6.530019 AAAAAGAGATGTGAACCAAACACT 57.470 33.333 0.00 0.00 38.81 3.55


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

AutoCloner maintained by Alex Coulton.