Multiple sequence alignment - TraesCS4B01G049000

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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 TraesCS4B01G049000 chr4B 100.000 2547 0 0 1 2547 37298430 37295884 0.000000e+00 4704
1 TraesCS4B01G049000 chr4B 90.628 1035 87 6 983 2016 37174481 37173456 0.000000e+00 1365
2 TraesCS4B01G049000 chr4B 78.631 833 145 18 1137 1963 36013811 36013006 3.450000e-144 521
3 TraesCS4B01G049000 chr4B 77.700 861 153 21 1137 1989 35912248 35911419 9.720000e-135 490
4 TraesCS4B01G049000 chr4B 86.067 445 51 4 2114 2547 37267799 37267355 4.550000e-128 468
5 TraesCS4B01G049000 chr4B 100.000 109 0 0 2909 3017 37295522 37295414 5.100000e-48 202
6 TraesCS4B01G049000 chr4D 92.641 2283 123 16 1 2273 25364981 25362734 0.000000e+00 3243
7 TraesCS4B01G049000 chr4D 89.470 1396 121 12 925 2317 25321329 25319957 0.000000e+00 1740
8 TraesCS4B01G049000 chr4D 90.048 1035 93 8 983 2016 25194510 25193485 0.000000e+00 1332
9 TraesCS4B01G049000 chr4D 89.053 338 28 5 592 926 25338848 25338517 7.780000e-111 411
10 TraesCS4B01G049000 chr4D 88.475 295 23 2 2264 2547 25360951 25360657 2.230000e-91 346
11 TraesCS4B01G049000 chr4D 87.273 110 8 2 2909 3017 25221137 25221033 1.470000e-23 121
12 TraesCS4B01G049000 chr4A 91.893 2208 127 26 1 2193 578177180 578175010 0.000000e+00 3038
13 TraesCS4B01G049000 chr4A 91.032 2141 143 19 1 2132 578006037 578008137 0.000000e+00 2844
14 TraesCS4B01G049000 chr4A 90.145 1035 92 8 983 2016 578233566 578234591 0.000000e+00 1338
15 TraesCS4B01G049000 chr4A 84.703 353 33 11 112 460 578104756 578104421 1.730000e-87 333
16 TraesCS4B01G049000 chr3B 89.661 1683 128 24 563 2216 39544727 39546392 0.000000e+00 2102
17 TraesCS4B01G049000 chr3B 90.751 346 25 3 2203 2542 39547023 39547367 3.550000e-124 455


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 TraesCS4B01G049000 chr4B 37295414 37298430 3016 True 2453.0 4704 100.000 1 3017 2 chr4B.!!$R5 3016
1 TraesCS4B01G049000 chr4B 37173456 37174481 1025 True 1365.0 1365 90.628 983 2016 1 chr4B.!!$R3 1033
2 TraesCS4B01G049000 chr4B 36013006 36013811 805 True 521.0 521 78.631 1137 1963 1 chr4B.!!$R2 826
3 TraesCS4B01G049000 chr4B 35911419 35912248 829 True 490.0 490 77.700 1137 1989 1 chr4B.!!$R1 852
4 TraesCS4B01G049000 chr4D 25360657 25364981 4324 True 1794.5 3243 90.558 1 2547 2 chr4D.!!$R5 2546
5 TraesCS4B01G049000 chr4D 25319957 25321329 1372 True 1740.0 1740 89.470 925 2317 1 chr4D.!!$R3 1392
6 TraesCS4B01G049000 chr4D 25193485 25194510 1025 True 1332.0 1332 90.048 983 2016 1 chr4D.!!$R1 1033
7 TraesCS4B01G049000 chr4A 578175010 578177180 2170 True 3038.0 3038 91.893 1 2193 1 chr4A.!!$R2 2192
8 TraesCS4B01G049000 chr4A 578006037 578008137 2100 False 2844.0 2844 91.032 1 2132 1 chr4A.!!$F1 2131
9 TraesCS4B01G049000 chr4A 578233566 578234591 1025 False 1338.0 1338 90.145 983 2016 1 chr4A.!!$F2 1033
10 TraesCS4B01G049000 chr3B 39544727 39547367 2640 False 1278.5 2102 90.206 563 2542 2 chr3B.!!$F1 1979

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
632 663 0.727398 CGAAGCATCCGGAAGAAACC 59.273 55.0 9.01 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 4860 1.319614 GCCTAGATTTTGCCGGCCAA 61.32 55.0 26.77 18.03 34.75 4.52 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
21 22 1.796459 CTACCGTGCTACAAACACACC 59.204 52.381 0.00 0.00 37.93 4.16
33 34 3.932089 ACAAACACACCAGCAAATTTGAC 59.068 39.130 22.31 12.64 32.63 3.18
34 35 4.183101 CAAACACACCAGCAAATTTGACT 58.817 39.130 22.31 14.62 30.35 3.41
37 38 4.932146 ACACACCAGCAAATTTGACTTAC 58.068 39.130 22.31 3.56 0.00 2.34
38 39 4.400884 ACACACCAGCAAATTTGACTTACA 59.599 37.500 22.31 0.00 0.00 2.41
48 49 8.199449 AGCAAATTTGACTTACATGATATTGGG 58.801 33.333 22.31 0.00 0.00 4.12
65 66 5.715439 ATTGGGAAGGACATCATGTTCTA 57.285 39.130 0.00 0.00 34.45 2.10
165 167 9.357161 TGGTTAGTGGACTTAAATTATGTTTGT 57.643 29.630 0.00 0.00 0.00 2.83
274 300 8.704234 GCTAGTCTAACAATGTATTGATAGCAC 58.296 37.037 11.29 11.56 40.70 4.40
275 301 7.700322 AGTCTAACAATGTATTGATAGCACG 57.300 36.000 11.29 0.00 40.70 5.34
276 302 6.701841 AGTCTAACAATGTATTGATAGCACGG 59.298 38.462 11.29 0.00 40.70 4.94
277 303 6.479001 GTCTAACAATGTATTGATAGCACGGT 59.521 38.462 11.29 0.00 40.70 4.83
278 304 5.734855 AACAATGTATTGATAGCACGGTC 57.265 39.130 11.29 0.00 40.14 4.79
279 305 4.765273 ACAATGTATTGATAGCACGGTCA 58.235 39.130 11.29 0.00 40.14 4.02
280 306 4.570772 ACAATGTATTGATAGCACGGTCAC 59.429 41.667 11.29 0.00 40.14 3.67
281 307 4.318050 CAATGTATTGATAGCACGGTCACG 60.318 45.833 0.00 0.00 42.29 4.35
282 308 2.424246 TGTATTGATAGCACGGTCACGA 59.576 45.455 0.00 0.00 44.60 4.35
283 309 2.665649 ATTGATAGCACGGTCACGAA 57.334 45.000 0.00 0.00 44.60 3.85
284 310 2.442212 TTGATAGCACGGTCACGAAA 57.558 45.000 0.00 0.00 44.60 3.46
285 311 2.442212 TGATAGCACGGTCACGAAAA 57.558 45.000 0.00 0.00 44.60 2.29
286 312 2.967362 TGATAGCACGGTCACGAAAAT 58.033 42.857 0.00 0.00 44.60 1.82
287 313 4.112716 TGATAGCACGGTCACGAAAATA 57.887 40.909 0.00 0.00 44.60 1.40
288 314 4.496360 TGATAGCACGGTCACGAAAATAA 58.504 39.130 0.00 0.00 44.60 1.40
289 315 4.930405 TGATAGCACGGTCACGAAAATAAA 59.070 37.500 0.00 0.00 44.60 1.40
290 316 5.408909 TGATAGCACGGTCACGAAAATAAAA 59.591 36.000 0.00 0.00 44.60 1.52
353 381 1.212490 GCAGTAGCGGCAATTGCAA 59.788 52.632 30.32 0.00 44.36 4.08
460 488 1.025041 GCTGCCTAGGCCAAATACAC 58.975 55.000 30.81 7.42 41.09 2.90
472 500 4.158384 GCCAAATACACACATCAAACTCG 58.842 43.478 0.00 0.00 0.00 4.18
535 565 8.644318 ATTAAGCTTACAAGTGTATCTTACCG 57.356 34.615 5.45 0.00 34.66 4.02
632 663 0.727398 CGAAGCATCCGGAAGAAACC 59.273 55.000 9.01 0.00 0.00 3.27
704 738 3.074412 ACGTTTGGCATAACTCTCCTTG 58.926 45.455 9.66 0.00 0.00 3.61
788 858 6.202516 TGACATCGTTTTCAAAAGAAAGGT 57.797 33.333 0.00 0.00 30.58 3.50
852 922 3.130516 GTCAGCCAAATTTAAGGTAGGGC 59.869 47.826 5.53 5.53 40.18 5.19
880 955 1.577468 CCGCCACATCGCAGTATAAA 58.423 50.000 0.00 0.00 0.00 1.40
881 956 1.526887 CCGCCACATCGCAGTATAAAG 59.473 52.381 0.00 0.00 0.00 1.85
882 957 1.070577 CGCCACATCGCAGTATAAAGC 60.071 52.381 0.00 0.00 0.00 3.51
883 958 1.939934 GCCACATCGCAGTATAAAGCA 59.060 47.619 0.00 0.00 0.00 3.91
890 965 5.235186 ACATCGCAGTATAAAGCAAGCTAAG 59.765 40.000 0.00 0.00 0.00 2.18
901 976 1.731720 CAAGCTAAGCTCACCTCCAC 58.268 55.000 0.00 0.00 38.25 4.02
948 1030 9.940166 CGATCATCAATTTCATCATACTTTTGA 57.060 29.630 0.00 0.00 0.00 2.69
2017 2119 1.202973 CGAGCAGCGGTGTCGATAAG 61.203 60.000 24.94 6.04 39.00 1.73
2018 2120 1.483424 GAGCAGCGGTGTCGATAAGC 61.483 60.000 17.07 0.00 39.00 3.09
2019 2121 1.809619 GCAGCGGTGTCGATAAGCA 60.810 57.895 17.07 0.00 39.00 3.91
2020 2122 1.358725 GCAGCGGTGTCGATAAGCAA 61.359 55.000 17.07 0.00 39.00 3.91
2021 2123 1.290203 CAGCGGTGTCGATAAGCAAT 58.710 50.000 6.41 0.00 39.00 3.56
2022 2124 1.665679 CAGCGGTGTCGATAAGCAATT 59.334 47.619 6.41 0.00 39.00 2.32
2023 2125 2.863740 CAGCGGTGTCGATAAGCAATTA 59.136 45.455 6.41 0.00 39.00 1.40
2024 2126 3.308595 CAGCGGTGTCGATAAGCAATTAA 59.691 43.478 6.41 0.00 39.00 1.40
2048 2160 1.323791 GCGCGTGTAAATGTTGAACC 58.676 50.000 8.43 0.00 0.00 3.62
2095 2207 4.580167 CCTAAGCTAGGCATTTGCACATAA 59.420 41.667 4.74 0.00 44.36 1.90
2096 2208 5.242393 CCTAAGCTAGGCATTTGCACATAAT 59.758 40.000 4.74 0.00 44.36 1.28
2097 2209 6.430925 CCTAAGCTAGGCATTTGCACATAATA 59.569 38.462 4.74 0.00 44.36 0.98
2125 2237 5.048846 AGTGGACCATACTTTGAACTTGT 57.951 39.130 0.00 0.00 0.00 3.16
2132 2244 7.081857 ACCATACTTTGAACTTGTAAGGGTA 57.918 36.000 0.00 0.00 31.61 3.69
2138 2250 7.970102 ACTTTGAACTTGTAAGGGTATCACTA 58.030 34.615 0.00 0.00 0.00 2.74
2140 2252 8.786826 TTTGAACTTGTAAGGGTATCACTATG 57.213 34.615 0.00 0.00 0.00 2.23
2242 2999 0.250038 CATCCGGACATCAGCGGAAT 60.250 55.000 6.12 0.00 34.35 3.01
2248 3005 2.600731 GGACATCAGCGGAATAGATCG 58.399 52.381 0.00 0.00 0.00 3.69
2280 4830 7.396418 TGTTTACTGTAAAACCGAATATCCCT 58.604 34.615 14.10 0.00 38.35 4.20
2310 4860 2.234300 TCTTCTTCCTTTCACGCGTT 57.766 45.000 10.22 0.00 0.00 4.84
2325 4875 1.288752 CGTTTGGCCGGCAAAATCT 59.711 52.632 30.97 0.00 0.00 2.40
2335 4885 0.457443 GGCAAAATCTAGGCAGGCAC 59.543 55.000 0.00 0.00 0.00 5.01
2369 4929 2.183300 GAGTGCGGTGCGGATACA 59.817 61.111 0.00 0.00 0.00 2.29
2464 5024 3.468326 GATGGAAGAGGGAGCCCGC 62.468 68.421 0.47 0.47 41.95 6.13
2495 5055 2.355115 GAGGCAACGGGGTTGGAT 59.645 61.111 10.19 0.00 42.99 3.41
2497 5057 2.282887 GGCAACGGGGTTGGATGT 60.283 61.111 10.19 0.00 42.99 3.06
2933 5493 7.680442 TTTTCCACGAATTCTGAACATATGA 57.320 32.000 10.38 0.00 0.00 2.15
2934 5494 6.908870 TTCCACGAATTCTGAACATATGAG 57.091 37.500 10.38 0.00 0.00 2.90
2935 5495 6.220726 TCCACGAATTCTGAACATATGAGA 57.779 37.500 10.38 0.00 0.00 3.27
2936 5496 6.820335 TCCACGAATTCTGAACATATGAGAT 58.180 36.000 10.38 0.00 0.00 2.75
2937 5497 7.951591 TCCACGAATTCTGAACATATGAGATA 58.048 34.615 10.38 0.00 0.00 1.98
2938 5498 8.588472 TCCACGAATTCTGAACATATGAGATAT 58.412 33.333 10.38 0.00 0.00 1.63
2939 5499 9.212641 CCACGAATTCTGAACATATGAGATATT 57.787 33.333 10.38 5.22 0.00 1.28
2941 5501 9.212641 ACGAATTCTGAACATATGAGATATTGG 57.787 33.333 10.38 8.31 0.00 3.16
2942 5502 9.428097 CGAATTCTGAACATATGAGATATTGGA 57.572 33.333 10.38 0.00 0.00 3.53
2945 5505 8.557592 TTCTGAACATATGAGATATTGGATGC 57.442 34.615 10.38 0.00 0.00 3.91
2946 5506 7.914859 TCTGAACATATGAGATATTGGATGCT 58.085 34.615 10.38 0.00 0.00 3.79
2947 5507 8.039538 TCTGAACATATGAGATATTGGATGCTC 58.960 37.037 10.38 0.00 0.00 4.26
2948 5508 6.815142 TGAACATATGAGATATTGGATGCTCG 59.185 38.462 10.38 0.00 0.00 5.03
2949 5509 6.291648 ACATATGAGATATTGGATGCTCGT 57.708 37.500 10.38 0.00 0.00 4.18
2950 5510 6.705302 ACATATGAGATATTGGATGCTCGTT 58.295 36.000 10.38 0.00 0.00 3.85
2951 5511 7.164122 ACATATGAGATATTGGATGCTCGTTT 58.836 34.615 10.38 0.00 0.00 3.60
2952 5512 7.663081 ACATATGAGATATTGGATGCTCGTTTT 59.337 33.333 10.38 0.00 0.00 2.43
2953 5513 9.154847 CATATGAGATATTGGATGCTCGTTTTA 57.845 33.333 0.00 0.00 0.00 1.52
2954 5514 9.725019 ATATGAGATATTGGATGCTCGTTTTAA 57.275 29.630 0.00 0.00 0.00 1.52
2955 5515 7.482654 TGAGATATTGGATGCTCGTTTTAAG 57.517 36.000 0.00 0.00 0.00 1.85
2956 5516 6.483307 TGAGATATTGGATGCTCGTTTTAAGG 59.517 38.462 0.00 0.00 0.00 2.69
2957 5517 6.357367 AGATATTGGATGCTCGTTTTAAGGT 58.643 36.000 0.00 0.00 0.00 3.50
2958 5518 6.828785 AGATATTGGATGCTCGTTTTAAGGTT 59.171 34.615 0.00 0.00 0.00 3.50
2959 5519 5.722021 ATTGGATGCTCGTTTTAAGGTTT 57.278 34.783 0.00 0.00 0.00 3.27
2960 5520 5.523438 TTGGATGCTCGTTTTAAGGTTTT 57.477 34.783 0.00 0.00 0.00 2.43
2961 5521 5.116069 TGGATGCTCGTTTTAAGGTTTTC 57.884 39.130 0.00 0.00 0.00 2.29
2962 5522 4.022676 TGGATGCTCGTTTTAAGGTTTTCC 60.023 41.667 0.00 0.00 41.05 3.13
2988 5548 5.900865 AAAAAGGAAAAATATACGGGCGA 57.099 34.783 0.00 0.00 0.00 5.54
2989 5549 5.494632 AAAAGGAAAAATATACGGGCGAG 57.505 39.130 0.00 0.00 0.00 5.03
2990 5550 2.490991 AGGAAAAATATACGGGCGAGC 58.509 47.619 0.00 0.00 0.00 5.03
2991 5551 1.534163 GGAAAAATATACGGGCGAGCC 59.466 52.381 5.37 5.37 0.00 4.70
2992 5552 2.215196 GAAAAATATACGGGCGAGCCA 58.785 47.619 16.65 0.00 37.98 4.75
2993 5553 2.335316 AAAATATACGGGCGAGCCAA 57.665 45.000 16.65 0.94 37.98 4.52
2994 5554 2.561478 AAATATACGGGCGAGCCAAT 57.439 45.000 16.65 8.51 37.98 3.16
2995 5555 2.561478 AATATACGGGCGAGCCAATT 57.439 45.000 16.65 4.59 37.98 2.32
2996 5556 2.561478 ATATACGGGCGAGCCAATTT 57.439 45.000 16.65 1.19 37.98 1.82
2997 5557 2.335316 TATACGGGCGAGCCAATTTT 57.665 45.000 16.65 0.00 37.98 1.82
2998 5558 0.738389 ATACGGGCGAGCCAATTTTG 59.262 50.000 16.65 0.88 37.98 2.44
2999 5559 0.321741 TACGGGCGAGCCAATTTTGA 60.322 50.000 16.65 0.00 37.98 2.69
3000 5560 1.137404 CGGGCGAGCCAATTTTGAG 59.863 57.895 16.65 0.00 37.98 3.02
3001 5561 1.512694 GGGCGAGCCAATTTTGAGG 59.487 57.895 16.65 0.00 37.98 3.86
3002 5562 1.512694 GGCGAGCCAATTTTGAGGG 59.487 57.895 9.58 0.00 35.81 4.30
3003 5563 0.965363 GGCGAGCCAATTTTGAGGGA 60.965 55.000 9.58 0.00 35.81 4.20
3004 5564 1.106285 GCGAGCCAATTTTGAGGGAT 58.894 50.000 0.00 0.00 0.00 3.85
3005 5565 1.202336 GCGAGCCAATTTTGAGGGATG 60.202 52.381 0.00 0.00 0.00 3.51
3006 5566 2.094675 CGAGCCAATTTTGAGGGATGT 58.905 47.619 0.00 0.00 0.00 3.06
3007 5567 3.278574 CGAGCCAATTTTGAGGGATGTA 58.721 45.455 0.00 0.00 0.00 2.29
3008 5568 3.885297 CGAGCCAATTTTGAGGGATGTAT 59.115 43.478 0.00 0.00 0.00 2.29
3009 5569 4.023707 CGAGCCAATTTTGAGGGATGTATC 60.024 45.833 0.00 0.00 0.00 2.24
3010 5570 3.885297 AGCCAATTTTGAGGGATGTATCG 59.115 43.478 0.00 0.00 0.00 2.92
3011 5571 3.004734 GCCAATTTTGAGGGATGTATCGG 59.995 47.826 0.00 0.00 0.00 4.18
3012 5572 3.569701 CCAATTTTGAGGGATGTATCGGG 59.430 47.826 0.00 0.00 0.00 5.14
3013 5573 4.207165 CAATTTTGAGGGATGTATCGGGT 58.793 43.478 0.00 0.00 0.00 5.28
3014 5574 3.553828 TTTTGAGGGATGTATCGGGTC 57.446 47.619 0.00 0.00 0.00 4.46
3015 5575 2.168458 TTGAGGGATGTATCGGGTCA 57.832 50.000 0.00 0.00 0.00 4.02
3016 5576 1.704641 TGAGGGATGTATCGGGTCAG 58.295 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.021202 TGCTGGTGTGTTTGTAGCAC 58.979 50.000 0.00 0.00 39.26 4.40
21 22 9.027129 CCAATATCATGTAAGTCAAATTTGCTG 57.973 33.333 13.54 3.59 0.00 4.41
33 34 7.226441 TGATGTCCTTCCCAATATCATGTAAG 58.774 38.462 0.00 0.00 0.00 2.34
34 35 7.147958 TGATGTCCTTCCCAATATCATGTAA 57.852 36.000 0.00 0.00 0.00 2.41
37 38 6.510879 CATGATGTCCTTCCCAATATCATG 57.489 41.667 0.00 0.00 42.79 3.07
38 39 6.210172 ACATGATGTCCTTCCCAATATCAT 57.790 37.500 0.00 0.00 36.12 2.45
48 49 8.983724 GCTACTATTTAGAACATGATGTCCTTC 58.016 37.037 0.00 0.00 0.00 3.46
139 141 9.357161 ACAAACATAATTTAAGTCCACTAACCA 57.643 29.630 0.00 0.00 0.00 3.67
165 167 7.336176 ACATCTATCTACAGTGTCACGAAGTTA 59.664 37.037 0.00 0.00 41.61 2.24
171 173 6.359480 TGTACATCTATCTACAGTGTCACG 57.641 41.667 0.00 0.00 0.00 4.35
236 245 9.464714 CATTGTTAGACTAGCGAAGTGTTATAT 57.535 33.333 0.00 0.00 39.07 0.86
274 300 5.390567 CCTTCTCCTTTTATTTTCGTGACCG 60.391 44.000 0.00 0.00 0.00 4.79
275 301 5.472478 ACCTTCTCCTTTTATTTTCGTGACC 59.528 40.000 0.00 0.00 0.00 4.02
276 302 6.371389 CACCTTCTCCTTTTATTTTCGTGAC 58.629 40.000 0.00 0.00 0.00 3.67
277 303 5.472137 CCACCTTCTCCTTTTATTTTCGTGA 59.528 40.000 0.00 0.00 0.00 4.35
278 304 5.472137 TCCACCTTCTCCTTTTATTTTCGTG 59.528 40.000 0.00 0.00 0.00 4.35
279 305 5.627135 TCCACCTTCTCCTTTTATTTTCGT 58.373 37.500 0.00 0.00 0.00 3.85
280 306 5.123979 CCTCCACCTTCTCCTTTTATTTTCG 59.876 44.000 0.00 0.00 0.00 3.46
281 307 5.105716 GCCTCCACCTTCTCCTTTTATTTTC 60.106 44.000 0.00 0.00 0.00 2.29
282 308 4.772624 GCCTCCACCTTCTCCTTTTATTTT 59.227 41.667 0.00 0.00 0.00 1.82
283 309 4.344978 GCCTCCACCTTCTCCTTTTATTT 58.655 43.478 0.00 0.00 0.00 1.40
284 310 3.622455 CGCCTCCACCTTCTCCTTTTATT 60.622 47.826 0.00 0.00 0.00 1.40
285 311 2.092914 CGCCTCCACCTTCTCCTTTTAT 60.093 50.000 0.00 0.00 0.00 1.40
286 312 1.278127 CGCCTCCACCTTCTCCTTTTA 59.722 52.381 0.00 0.00 0.00 1.52
287 313 0.036875 CGCCTCCACCTTCTCCTTTT 59.963 55.000 0.00 0.00 0.00 2.27
288 314 1.679898 CGCCTCCACCTTCTCCTTT 59.320 57.895 0.00 0.00 0.00 3.11
289 315 2.294078 CCGCCTCCACCTTCTCCTT 61.294 63.158 0.00 0.00 0.00 3.36
290 316 2.685380 CCGCCTCCACCTTCTCCT 60.685 66.667 0.00 0.00 0.00 3.69
318 346 2.278857 CCGCCTCGTCATTCTCCG 60.279 66.667 0.00 0.00 0.00 4.63
353 381 4.648307 ACTTTGCTACGCTATACCCTAACT 59.352 41.667 0.00 0.00 0.00 2.24
372 400 7.664731 ACATGTCTTGAGATCAATCTTCACTTT 59.335 33.333 0.00 0.00 37.25 2.66
460 488 6.961554 GCTTTAGGAATTACGAGTTTGATGTG 59.038 38.462 0.00 0.00 0.00 3.21
614 645 1.095600 GGGTTTCTTCCGGATGCTTC 58.904 55.000 4.15 1.14 0.00 3.86
880 955 0.251634 GGAGGTGAGCTTAGCTTGCT 59.748 55.000 11.87 12.77 39.88 3.91
881 956 0.036010 TGGAGGTGAGCTTAGCTTGC 60.036 55.000 11.87 4.29 39.88 4.01
882 957 1.002430 TGTGGAGGTGAGCTTAGCTTG 59.998 52.381 11.87 0.00 39.88 4.01
883 958 1.352083 TGTGGAGGTGAGCTTAGCTT 58.648 50.000 11.87 0.00 39.88 3.74
948 1030 6.127758 TGTGTGTTTTGCAAGAACTGTATTCT 60.128 34.615 18.68 0.00 0.00 2.40
1308 1406 1.143183 GTGGCACCGGACGATGTAT 59.857 57.895 9.46 0.00 0.00 2.29
1994 2096 2.951745 GACACCGCTGCTCGATCG 60.952 66.667 9.36 9.36 41.67 3.69
2017 2119 2.202298 ACGCGCGTGCTTAATTGC 60.202 55.556 37.37 0.00 39.65 3.56
2018 2120 3.649466 CACGCGCGTGCTTAATTG 58.351 55.556 44.73 23.09 39.39 2.32
2048 2160 5.621635 ATTTACGATTCGAGAATGTGACG 57.378 39.130 13.95 3.48 0.00 4.35
2095 2207 7.914427 TCAAAGTATGGTCCACTATCTGTAT 57.086 36.000 0.00 0.00 0.00 2.29
2096 2208 7.399191 AGTTCAAAGTATGGTCCACTATCTGTA 59.601 37.037 0.00 0.00 0.00 2.74
2097 2209 6.213600 AGTTCAAAGTATGGTCCACTATCTGT 59.786 38.462 0.00 0.00 0.00 3.41
2125 2237 5.454966 TGCTCTCACATAGTGATACCCTTA 58.545 41.667 0.00 0.00 41.94 2.69
2132 2244 6.183360 TGCTAAAGATGCTCTCACATAGTGAT 60.183 38.462 0.00 0.00 41.94 3.06
2138 2250 4.750021 TCTGCTAAAGATGCTCTCACAT 57.250 40.909 0.00 0.00 0.00 3.21
2140 2252 5.816777 AGAAATCTGCTAAAGATGCTCTCAC 59.183 40.000 0.00 0.00 45.37 3.51
2152 2264 8.086522 GGTACCGTGATATAAGAAATCTGCTAA 58.913 37.037 0.00 0.00 0.00 3.09
2201 2958 5.923204 TGGTACCGTAAAACAGGTTTAAGA 58.077 37.500 7.57 0.00 41.63 2.10
2242 2999 8.686397 TTTACAGTAAACATTTACGCGATCTA 57.314 30.769 15.93 0.00 45.77 1.98
2248 3005 6.361899 TCGGTTTTACAGTAAACATTTACGC 58.638 36.000 5.16 0.00 45.77 4.42
2280 4830 4.982241 AAGGAAGAAGAAGATGACCACA 57.018 40.909 0.00 0.00 0.00 4.17
2310 4860 1.319614 GCCTAGATTTTGCCGGCCAA 61.320 55.000 26.77 18.03 34.75 4.52
2443 5003 2.735772 GGCTCCCTCTTCCATCGCA 61.736 63.158 0.00 0.00 0.00 5.10
2464 5024 3.083997 CCTCCTCCTTCCCCGTGG 61.084 72.222 0.00 0.00 0.00 4.94
2908 5468 8.279970 TCATATGTTCAGAATTCGTGGAAAAT 57.720 30.769 13.89 13.89 0.00 1.82
2909 5469 7.606073 TCTCATATGTTCAGAATTCGTGGAAAA 59.394 33.333 1.90 7.16 0.00 2.29
2910 5470 7.102993 TCTCATATGTTCAGAATTCGTGGAAA 58.897 34.615 1.90 0.00 0.00 3.13
2911 5471 6.639563 TCTCATATGTTCAGAATTCGTGGAA 58.360 36.000 1.90 3.22 0.00 3.53
2912 5472 6.220726 TCTCATATGTTCAGAATTCGTGGA 57.779 37.500 1.90 0.00 0.00 4.02
2913 5473 8.768957 ATATCTCATATGTTCAGAATTCGTGG 57.231 34.615 1.90 0.00 0.00 4.94
2915 5475 9.212641 CCAATATCTCATATGTTCAGAATTCGT 57.787 33.333 1.90 0.00 0.00 3.85
2916 5476 9.428097 TCCAATATCTCATATGTTCAGAATTCG 57.572 33.333 1.90 0.00 0.00 3.34
2919 5479 9.175312 GCATCCAATATCTCATATGTTCAGAAT 57.825 33.333 1.90 0.00 0.00 2.40
2920 5480 8.380867 AGCATCCAATATCTCATATGTTCAGAA 58.619 33.333 1.90 0.00 0.00 3.02
2921 5481 7.914859 AGCATCCAATATCTCATATGTTCAGA 58.085 34.615 1.90 0.00 0.00 3.27
2922 5482 7.010275 CGAGCATCCAATATCTCATATGTTCAG 59.990 40.741 1.90 0.00 0.00 3.02
2923 5483 6.815142 CGAGCATCCAATATCTCATATGTTCA 59.185 38.462 1.90 0.00 0.00 3.18
2924 5484 6.815641 ACGAGCATCCAATATCTCATATGTTC 59.184 38.462 1.90 0.00 0.00 3.18
2925 5485 6.705302 ACGAGCATCCAATATCTCATATGTT 58.295 36.000 1.90 0.00 0.00 2.71
2926 5486 6.291648 ACGAGCATCCAATATCTCATATGT 57.708 37.500 1.90 0.00 0.00 2.29
2927 5487 7.606858 AAACGAGCATCCAATATCTCATATG 57.393 36.000 0.00 0.00 0.00 1.78
2928 5488 9.725019 TTAAAACGAGCATCCAATATCTCATAT 57.275 29.630 0.00 0.00 0.00 1.78
2929 5489 9.208022 CTTAAAACGAGCATCCAATATCTCATA 57.792 33.333 0.00 0.00 0.00 2.15
2930 5490 7.173907 CCTTAAAACGAGCATCCAATATCTCAT 59.826 37.037 0.00 0.00 0.00 2.90
2931 5491 6.483307 CCTTAAAACGAGCATCCAATATCTCA 59.517 38.462 0.00 0.00 0.00 3.27
2932 5492 6.483640 ACCTTAAAACGAGCATCCAATATCTC 59.516 38.462 0.00 0.00 0.00 2.75
2933 5493 6.357367 ACCTTAAAACGAGCATCCAATATCT 58.643 36.000 0.00 0.00 0.00 1.98
2934 5494 6.619801 ACCTTAAAACGAGCATCCAATATC 57.380 37.500 0.00 0.00 0.00 1.63
2935 5495 7.404671 AAACCTTAAAACGAGCATCCAATAT 57.595 32.000 0.00 0.00 0.00 1.28
2936 5496 6.827586 AAACCTTAAAACGAGCATCCAATA 57.172 33.333 0.00 0.00 0.00 1.90
2937 5497 5.722021 AAACCTTAAAACGAGCATCCAAT 57.278 34.783 0.00 0.00 0.00 3.16
2938 5498 5.508320 GGAAAACCTTAAAACGAGCATCCAA 60.508 40.000 0.00 0.00 0.00 3.53
2939 5499 4.022676 GGAAAACCTTAAAACGAGCATCCA 60.023 41.667 0.00 0.00 0.00 3.41
2940 5500 4.217767 AGGAAAACCTTAAAACGAGCATCC 59.782 41.667 0.00 0.00 0.00 3.51
2941 5501 5.048991 TGAGGAAAACCTTAAAACGAGCATC 60.049 40.000 0.00 0.00 0.00 3.91
2942 5502 4.825085 TGAGGAAAACCTTAAAACGAGCAT 59.175 37.500 0.00 0.00 0.00 3.79
2943 5503 4.200874 TGAGGAAAACCTTAAAACGAGCA 58.799 39.130 0.00 0.00 0.00 4.26
2944 5504 4.823790 TGAGGAAAACCTTAAAACGAGC 57.176 40.909 0.00 0.00 0.00 5.03
2966 5526 5.677852 GCTCGCCCGTATATTTTTCCTTTTT 60.678 40.000 0.00 0.00 0.00 1.94
2967 5527 4.201980 GCTCGCCCGTATATTTTTCCTTTT 60.202 41.667 0.00 0.00 0.00 2.27
2968 5528 3.314357 GCTCGCCCGTATATTTTTCCTTT 59.686 43.478 0.00 0.00 0.00 3.11
2969 5529 2.876550 GCTCGCCCGTATATTTTTCCTT 59.123 45.455 0.00 0.00 0.00 3.36
2970 5530 2.490991 GCTCGCCCGTATATTTTTCCT 58.509 47.619 0.00 0.00 0.00 3.36
2971 5531 1.534163 GGCTCGCCCGTATATTTTTCC 59.466 52.381 0.00 0.00 0.00 3.13
2972 5532 2.215196 TGGCTCGCCCGTATATTTTTC 58.785 47.619 5.33 0.00 35.87 2.29
2973 5533 2.335316 TGGCTCGCCCGTATATTTTT 57.665 45.000 5.33 0.00 35.87 1.94
2974 5534 2.335316 TTGGCTCGCCCGTATATTTT 57.665 45.000 5.33 0.00 35.87 1.82
2975 5535 2.561478 ATTGGCTCGCCCGTATATTT 57.439 45.000 5.33 0.00 35.87 1.40
2976 5536 2.561478 AATTGGCTCGCCCGTATATT 57.439 45.000 5.33 0.00 35.87 1.28
2977 5537 2.552315 CAAAATTGGCTCGCCCGTATAT 59.448 45.455 5.33 0.00 35.87 0.86
2978 5538 1.944024 CAAAATTGGCTCGCCCGTATA 59.056 47.619 5.33 0.00 35.87 1.47
2979 5539 0.738389 CAAAATTGGCTCGCCCGTAT 59.262 50.000 5.33 0.00 35.87 3.06
2980 5540 0.321741 TCAAAATTGGCTCGCCCGTA 60.322 50.000 5.33 0.00 35.87 4.02
2981 5541 1.586154 CTCAAAATTGGCTCGCCCGT 61.586 55.000 5.33 0.00 35.87 5.28
2982 5542 1.137404 CTCAAAATTGGCTCGCCCG 59.863 57.895 5.33 0.00 35.87 6.13
2983 5543 1.512694 CCTCAAAATTGGCTCGCCC 59.487 57.895 5.33 0.00 34.56 6.13
2984 5544 0.965363 TCCCTCAAAATTGGCTCGCC 60.965 55.000 0.00 0.00 0.00 5.54
2985 5545 1.106285 ATCCCTCAAAATTGGCTCGC 58.894 50.000 0.00 0.00 0.00 5.03
2986 5546 2.094675 ACATCCCTCAAAATTGGCTCG 58.905 47.619 0.00 0.00 0.00 5.03
2987 5547 4.023707 CGATACATCCCTCAAAATTGGCTC 60.024 45.833 0.00 0.00 0.00 4.70
2988 5548 3.885297 CGATACATCCCTCAAAATTGGCT 59.115 43.478 0.00 0.00 0.00 4.75
2989 5549 3.004734 CCGATACATCCCTCAAAATTGGC 59.995 47.826 0.00 0.00 0.00 4.52
2990 5550 3.569701 CCCGATACATCCCTCAAAATTGG 59.430 47.826 0.00 0.00 0.00 3.16
2991 5551 4.207165 ACCCGATACATCCCTCAAAATTG 58.793 43.478 0.00 0.00 0.00 2.32
2992 5552 4.080015 TGACCCGATACATCCCTCAAAATT 60.080 41.667 0.00 0.00 0.00 1.82
2993 5553 3.458118 TGACCCGATACATCCCTCAAAAT 59.542 43.478 0.00 0.00 0.00 1.82
2994 5554 2.841266 TGACCCGATACATCCCTCAAAA 59.159 45.455 0.00 0.00 0.00 2.44
2995 5555 2.434336 CTGACCCGATACATCCCTCAAA 59.566 50.000 0.00 0.00 0.00 2.69
2996 5556 2.039418 CTGACCCGATACATCCCTCAA 58.961 52.381 0.00 0.00 0.00 3.02
2997 5557 1.704641 CTGACCCGATACATCCCTCA 58.295 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.