Multiple sequence alignment - TraesCS2D01G121000

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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 TraesCS2D01G121000 chr2D 100.000 3119 0 0 1 3119 70382315 70385433 0.000000e+00 5760.0
1 TraesCS2D01G121000 chr2D 93.596 1952 105 9 816 2766 70464020 70465952 0.000000e+00 2894.0
2 TraesCS2D01G121000 chr2D 91.873 1292 86 13 870 2151 70511450 70512732 0.000000e+00 1786.0
3 TraesCS2D01G121000 chr2D 89.565 1265 108 8 1353 2613 70460474 70461718 0.000000e+00 1583.0
4 TraesCS2D01G121000 chr2D 92.944 1063 69 3 1238 2298 69962240 69961182 0.000000e+00 1543.0
5 TraesCS2D01G121000 chr2D 88.809 974 96 8 1837 2803 70512733 70513700 0.000000e+00 1182.0
6 TraesCS2D01G121000 chr2D 89.030 866 76 7 1752 2613 70428025 70428875 0.000000e+00 1055.0
7 TraesCS2D01G121000 chr2D 90.159 691 38 13 546 1235 69963270 69962609 0.000000e+00 872.0
8 TraesCS2D01G121000 chr2D 78.880 1179 204 27 949 2118 70376518 70377660 0.000000e+00 756.0
9 TraesCS2D01G121000 chr2D 90.074 272 19 4 546 815 70463476 70463741 2.300000e-91 346.0
10 TraesCS2D01G121000 chr2D 87.083 240 31 0 2734 2973 70465952 70466191 3.960000e-69 272.0
11 TraesCS2D01G121000 chr2D 78.736 348 63 7 1591 1937 81152378 81152041 4.050000e-54 222.0
12 TraesCS2D01G121000 chr2D 80.000 320 33 13 558 873 70503348 70503640 1.130000e-49 207.0
13 TraesCS2D01G121000 chr2D 91.667 84 3 2 2411 2490 69946396 69946313 2.540000e-21 113.0
14 TraesCS2D01G121000 chr2D 89.855 69 7 0 2796 2864 70514095 70514163 4.280000e-14 89.8
15 TraesCS2D01G121000 chr2B 91.060 2282 153 22 546 2823 106468797 106471031 0.000000e+00 3037.0
16 TraesCS2D01G121000 chr2B 92.353 1700 104 12 546 2235 106154122 106152439 0.000000e+00 2396.0
17 TraesCS2D01G121000 chr2B 89.896 1633 138 17 854 2477 106717722 106719336 0.000000e+00 2076.0
18 TraesCS2D01G121000 chr2B 89.707 1399 108 23 870 2246 106619411 106620795 0.000000e+00 1753.0
19 TraesCS2D01G121000 chr2B 89.738 1374 117 15 870 2242 106149409 106148059 0.000000e+00 1735.0
20 TraesCS2D01G121000 chr2B 86.809 1501 152 30 761 2246 106750527 106751996 0.000000e+00 1633.0
21 TraesCS2D01G121000 chr2B 90.895 637 55 3 2339 2973 106471656 106472291 0.000000e+00 852.0
22 TraesCS2D01G121000 chr2B 91.420 338 22 3 10 343 106155142 106154808 1.020000e-124 457.0
23 TraesCS2D01G121000 chr2B 90.663 332 29 2 2529 2860 106729540 106729869 1.030000e-119 440.0
24 TraesCS2D01G121000 chr2B 89.736 341 27 6 1 337 106467943 106468279 2.220000e-116 429.0
25 TraesCS2D01G121000 chr2B 91.724 145 12 0 344 488 106154497 106154353 5.270000e-48 202.0
26 TraesCS2D01G121000 chr2B 90.345 145 14 0 344 488 106468421 106468565 1.140000e-44 191.0
27 TraesCS2D01G121000 chr2B 94.595 37 2 0 2475 2511 106729503 106729539 1.210000e-04 58.4
28 TraesCS2D01G121000 chr2A 89.091 110 12 0 3005 3114 195108600 195108709 1.510000e-28 137.0
29 TraesCS2D01G121000 chr6D 97.333 75 2 0 3045 3119 75293297 75293371 9.080000e-26 128.0
30 TraesCS2D01G121000 chr5D 97.297 74 2 0 3046 3119 437905480 437905553 3.270000e-25 126.0
31 TraesCS2D01G121000 chr5D 96.053 76 3 0 3044 3119 309059202 309059277 1.170000e-24 124.0
32 TraesCS2D01G121000 chr5D 83.465 127 14 3 2964 3090 501358390 501358271 9.140000e-21 111.0
33 TraesCS2D01G121000 chr3B 97.297 74 2 0 3046 3119 51813943 51813870 3.270000e-25 126.0
34 TraesCS2D01G121000 chr3B 97.297 74 2 0 3046 3119 164641137 164641064 3.270000e-25 126.0
35 TraesCS2D01G121000 chr4B 96.053 76 3 0 3044 3119 25886150 25886075 1.170000e-24 124.0
36 TraesCS2D01G121000 chr3D 96.053 76 3 0 3044 3119 149689572 149689647 1.170000e-24 124.0
37 TraesCS2D01G121000 chr7A 89.011 91 3 3 2962 3052 447286380 447286463 4.250000e-19 106.0
38 TraesCS2D01G121000 chr7B 88.095 84 4 3 2969 3052 4984845 4984922 9.210000e-16 95.3
39 TraesCS2D01G121000 chr7B 88.889 81 3 2 2972 3052 553109870 553109944 9.210000e-16 95.3
40 TraesCS2D01G121000 chr7B 87.952 83 4 2 2970 3052 301615151 301615075 3.310000e-15 93.5
41 TraesCS2D01G121000 chr5A 88.095 84 4 2 2969 3052 280769988 280770065 9.210000e-16 95.3
42 TraesCS2D01G121000 chr5B 87.209 86 5 3 2967 3052 656171898 656171977 3.310000e-15 93.5
43 TraesCS2D01G121000 chr1B 87.952 83 4 2 2970 3052 588295830 588295754 3.310000e-15 93.5


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 TraesCS2D01G121000 chr2D 70382315 70385433 3118 False 5760.000000 5760 100.00000 1 3119 1 chr2D.!!$F2 3118
1 TraesCS2D01G121000 chr2D 70460474 70466191 5717 False 1273.750000 2894 90.07950 546 2973 4 chr2D.!!$F5 2427
2 TraesCS2D01G121000 chr2D 69961182 69963270 2088 True 1207.500000 1543 91.55150 546 2298 2 chr2D.!!$R3 1752
3 TraesCS2D01G121000 chr2D 70428025 70428875 850 False 1055.000000 1055 89.03000 1752 2613 1 chr2D.!!$F3 861
4 TraesCS2D01G121000 chr2D 70511450 70514163 2713 False 1019.266667 1786 90.17900 870 2864 3 chr2D.!!$F6 1994
5 TraesCS2D01G121000 chr2D 70376518 70377660 1142 False 756.000000 756 78.88000 949 2118 1 chr2D.!!$F1 1169
6 TraesCS2D01G121000 chr2B 106717722 106719336 1614 False 2076.000000 2076 89.89600 854 2477 1 chr2B.!!$F2 1623
7 TraesCS2D01G121000 chr2B 106619411 106620795 1384 False 1753.000000 1753 89.70700 870 2246 1 chr2B.!!$F1 1376
8 TraesCS2D01G121000 chr2B 106750527 106751996 1469 False 1633.000000 1633 86.80900 761 2246 1 chr2B.!!$F3 1485
9 TraesCS2D01G121000 chr2B 106148059 106155142 7083 True 1197.500000 2396 91.30875 10 2242 4 chr2B.!!$R1 2232
10 TraesCS2D01G121000 chr2B 106467943 106472291 4348 False 1127.250000 3037 90.50900 1 2973 4 chr2B.!!$F4 2972

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
464 781 0.178068 ACACCGTGACAAGTGCTTCT 59.822 50.0 5.28 0.0 37.51 2.85 F
1519 4648 0.248458 CTTCACCAACACGCACAACC 60.248 55.0 0.00 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 5527 0.73288 AACCGTCGTCGATGAAGCAG 60.733 55.0 16.06 2.23 39.71 4.24 R
2654 7800 0.17691 TCGCGATGACCATGGCTTAA 59.823 50.0 13.04 0.00 39.88 1.85 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
30 31 5.023452 TCTGTGGGACTGACATAACACTAT 58.977 41.667 0.00 0.00 0.00 2.12
36 37 6.150318 GGGACTGACATAACACTATCATACG 58.850 44.000 0.00 0.00 0.00 3.06
68 69 4.030216 AGTCCCTTCAACCAAAACACATT 58.970 39.130 0.00 0.00 0.00 2.71
84 85 4.130118 ACACATTCTCTCAGTGAACAACC 58.870 43.478 0.00 0.00 37.05 3.77
91 92 5.924356 TCTCTCAGTGAACAACCACAAATA 58.076 37.500 0.00 0.00 39.42 1.40
96 97 5.240623 TCAGTGAACAACCACAAATACATCC 59.759 40.000 0.00 0.00 39.42 3.51
178 179 4.171234 TCTCATCCTCTTCCTTCCACTTT 58.829 43.478 0.00 0.00 0.00 2.66
215 216 2.505819 GTCACCACCATATGTTCTCCCT 59.494 50.000 1.24 0.00 0.00 4.20
252 253 1.700186 GTTCACTCCCCCTTTGTCTCT 59.300 52.381 0.00 0.00 0.00 3.10
262 263 2.417933 CCCTTTGTCTCTTCATGCTTCG 59.582 50.000 0.00 0.00 0.00 3.79
268 269 2.665537 GTCTCTTCATGCTTCGTCACTG 59.334 50.000 0.00 0.00 0.00 3.66
319 320 5.763204 CACTGGTTGTGTCTTAATTACCACT 59.237 40.000 9.34 0.00 41.53 4.00
337 342 4.583073 ACCACTTTACACACTTTCCCATTC 59.417 41.667 0.00 0.00 0.00 2.67
340 345 5.765182 CACTTTACACACTTTCCCATTCTCT 59.235 40.000 0.00 0.00 0.00 3.10
380 697 1.449601 CGCGTATCCCTTGTGCCTT 60.450 57.895 0.00 0.00 0.00 4.35
404 721 8.918202 TTTGTCTGGATTTACAAGTTAGTGAT 57.082 30.769 0.00 0.00 36.96 3.06
417 734 2.194951 TAGTGATGCCCCACTCCCCT 62.195 60.000 10.80 0.00 45.37 4.79
464 781 0.178068 ACACCGTGACAAGTGCTTCT 59.822 50.000 5.28 0.00 37.51 2.85
466 783 2.061773 CACCGTGACAAGTGCTTCTAG 58.938 52.381 0.00 0.00 0.00 2.43
473 790 2.935201 GACAAGTGCTTCTAGGCATGAG 59.065 50.000 0.00 0.00 44.34 2.90
482 799 4.443457 GCTTCTAGGCATGAGGACAATGTA 60.443 45.833 0.00 0.00 0.00 2.29
489 806 4.142600 GGCATGAGGACAATGTACAAGTTC 60.143 45.833 0.00 0.33 0.00 3.01
501 823 4.304110 TGTACAAGTTCGACAGTGAATCC 58.696 43.478 0.00 0.00 0.00 3.01
504 826 2.349297 AGTTCGACAGTGAATCCGTC 57.651 50.000 0.00 0.00 0.00 4.79
509 831 1.337821 GACAGTGAATCCGTCGTGTC 58.662 55.000 0.00 0.00 36.31 3.67
532 854 1.207089 ACAAGATCGGAAATGGCTCGA 59.793 47.619 0.00 0.00 37.33 4.04
534 856 1.403814 AGATCGGAAATGGCTCGAGA 58.596 50.000 18.75 0.00 36.34 4.04
535 857 1.757118 AGATCGGAAATGGCTCGAGAA 59.243 47.619 18.75 3.24 36.34 2.87
536 858 2.366916 AGATCGGAAATGGCTCGAGAAT 59.633 45.455 18.75 5.87 36.34 2.40
539 861 2.093711 TCGGAAATGGCTCGAGAATGAA 60.094 45.455 18.75 0.00 0.00 2.57
541 863 3.303593 CGGAAATGGCTCGAGAATGAATG 60.304 47.826 18.75 0.00 0.00 2.67
542 864 3.004106 GGAAATGGCTCGAGAATGAATGG 59.996 47.826 18.75 0.00 0.00 3.16
585 3043 3.256631 CCAGCAAGTGGTAGCTTGATTTT 59.743 43.478 9.65 0.00 46.34 1.82
586 3044 4.262164 CCAGCAAGTGGTAGCTTGATTTTT 60.262 41.667 9.65 0.00 46.34 1.94
620 3078 6.521151 AACCTTCATTTCTAAATGGAGCTG 57.479 37.500 15.53 7.87 46.26 4.24
624 3082 6.350780 CCTTCATTTCTAAATGGAGCTGCTTT 60.351 38.462 15.53 3.26 46.26 3.51
625 3083 5.957798 TCATTTCTAAATGGAGCTGCTTTG 58.042 37.500 6.82 0.00 44.51 2.77
630 3088 6.239217 TCTAAATGGAGCTGCTTTGAGATA 57.761 37.500 14.73 1.11 0.00 1.98
634 3092 6.786967 AATGGAGCTGCTTTGAGATAAATT 57.213 33.333 6.82 0.00 0.00 1.82
644 3102 5.572896 GCTTTGAGATAAATTGAAACCACCG 59.427 40.000 0.00 0.00 0.00 4.94
653 3111 5.982890 AATTGAAACCACCGATTTCTCAT 57.017 34.783 0.00 0.00 37.05 2.90
655 3113 3.000041 TGAAACCACCGATTTCTCATCG 59.000 45.455 0.00 0.00 40.86 3.84
656 3114 1.369625 AACCACCGATTTCTCATCGC 58.630 50.000 0.00 0.00 39.95 4.58
796 3256 4.496341 CCTGCCAGCACAGAAAATTATACG 60.496 45.833 3.24 0.00 40.25 3.06
928 3669 4.082026 GGGCTGTATTAATACGTACGGGAT 60.082 45.833 21.06 9.66 36.06 3.85
1086 3841 2.431601 GCGTTGAGCTCTGCGTCT 60.432 61.111 23.66 0.00 44.04 4.18
1165 3920 2.915659 AGTCGGCGGTGAACCTCA 60.916 61.111 7.21 0.00 0.00 3.86
1223 3978 2.366435 GGCAGGGGGCTACAGGTA 60.366 66.667 0.00 0.00 44.01 3.08
1325 4453 2.040412 AGAAGGTGACCATCCCAAAGAC 59.960 50.000 3.63 0.00 0.00 3.01
1371 4499 4.329545 GGCCACTCCAGCACGGAA 62.330 66.667 0.00 0.00 45.75 4.30
1473 4602 0.732880 CCACCTTCAGTGTCTACGCG 60.733 60.000 3.53 3.53 45.74 6.01
1519 4648 0.248458 CTTCACCAACACGCACAACC 60.248 55.000 0.00 0.00 0.00 3.77
1530 4659 1.226435 GCACAACCGCGTCAACAAA 60.226 52.632 4.92 0.00 0.00 2.83
1730 4859 2.555547 GCTGCACCCTTGTGTCCAC 61.556 63.158 0.00 0.00 44.65 4.02
1824 4956 0.458260 GCGGTTTTGTGTTCAAGGGT 59.542 50.000 0.00 0.00 34.88 4.34
2078 5526 3.430218 GTGAAGAAGTTCGTGGACATGAG 59.570 47.826 0.00 0.00 35.17 2.90
2079 5527 2.086054 AGAAGTTCGTGGACATGAGC 57.914 50.000 0.00 0.73 0.00 4.26
2080 5528 1.620819 AGAAGTTCGTGGACATGAGCT 59.379 47.619 0.00 5.23 39.16 4.09
2127 5578 2.839098 CAGCCATAGCCGGGGATT 59.161 61.111 2.18 0.00 41.25 3.01
2155 5606 2.882777 CGAGTAGCTGGCTGCACG 60.883 66.667 18.84 14.11 45.94 5.34
2323 6361 3.898482 AGGTGAGAAATAAAATCCGGGG 58.102 45.455 0.00 0.00 0.00 5.73
2324 6362 2.956333 GGTGAGAAATAAAATCCGGGGG 59.044 50.000 0.00 0.00 0.00 5.40
2335 6375 2.846665 ATCCGGGGGATTGAACAATT 57.153 45.000 0.00 0.00 39.79 2.32
2388 7530 3.360249 AATTTGCAATGCTATCCGCTC 57.640 42.857 6.82 0.00 40.11 5.03
2405 7547 0.753262 CTCCTCCATTACCCTCACGG 59.247 60.000 0.00 0.00 37.81 4.94
2536 7682 4.872691 AGCAACCAAACTATCAGATTCGAG 59.127 41.667 0.00 0.00 0.00 4.04
2566 7712 0.169672 CTGCACCAAATCTTCGCTGG 59.830 55.000 0.00 0.00 36.24 4.85
2654 7800 2.632377 CATGAGGCTACCACGACAAAT 58.368 47.619 0.00 0.00 0.00 2.32
2656 7802 3.965379 TGAGGCTACCACGACAAATTA 57.035 42.857 0.00 0.00 0.00 1.40
2657 7803 4.274602 TGAGGCTACCACGACAAATTAA 57.725 40.909 0.00 0.00 0.00 1.40
2685 7831 3.432051 ATCGCGAGCTACTGCACCC 62.432 63.158 16.66 0.00 42.74 4.61
2806 8387 0.613260 TCGGTTAGGAGTTGCAGCAT 59.387 50.000 2.55 0.00 0.00 3.79
2809 8390 1.098050 GTTAGGAGTTGCAGCATGGG 58.902 55.000 2.55 0.00 35.86 4.00
2810 8391 0.034186 TTAGGAGTTGCAGCATGGGG 60.034 55.000 2.55 0.00 35.86 4.96
2864 8445 1.667756 CGTTCGATCTGGTTGACGGAA 60.668 52.381 0.00 0.00 38.16 4.30
2871 8452 3.201353 TCTGGTTGACGGAATGTTTCA 57.799 42.857 0.00 0.00 0.00 2.69
2879 8460 4.141287 TGACGGAATGTTTCACCTTTGAT 58.859 39.130 0.00 0.00 0.00 2.57
2883 8464 6.443792 ACGGAATGTTTCACCTTTGATAAAC 58.556 36.000 0.00 0.00 0.00 2.01
2885 8466 7.145323 CGGAATGTTTCACCTTTGATAAACTT 58.855 34.615 0.00 0.00 0.00 2.66
2891 8472 8.690884 TGTTTCACCTTTGATAAACTTTCATCA 58.309 29.630 0.00 0.00 0.00 3.07
2892 8473 9.696917 GTTTCACCTTTGATAAACTTTCATCAT 57.303 29.630 0.00 0.00 31.50 2.45
2894 8475 9.695526 TTCACCTTTGATAAACTTTCATCATTG 57.304 29.630 0.00 0.00 31.50 2.82
2908 8489 4.858850 TCATCATTGCCACCAGATAAACT 58.141 39.130 0.00 0.00 0.00 2.66
2931 8512 4.651778 AGCTACCAACTGCAATAAGTTCA 58.348 39.130 0.00 0.00 38.34 3.18
2987 8569 3.643320 CTCATAAGGCTGGTCATAGTGGA 59.357 47.826 0.00 0.00 0.00 4.02
2994 8576 3.068873 GGCTGGTCATAGTGGAGAGTAAG 59.931 52.174 0.00 0.00 0.00 2.34
2995 8577 3.954904 GCTGGTCATAGTGGAGAGTAAGA 59.045 47.826 0.00 0.00 0.00 2.10
2996 8578 4.037446 GCTGGTCATAGTGGAGAGTAAGAG 59.963 50.000 0.00 0.00 0.00 2.85
2997 8579 5.194473 TGGTCATAGTGGAGAGTAAGAGT 57.806 43.478 0.00 0.00 0.00 3.24
2998 8580 6.323210 TGGTCATAGTGGAGAGTAAGAGTA 57.677 41.667 0.00 0.00 0.00 2.59
2999 8581 6.120905 TGGTCATAGTGGAGAGTAAGAGTAC 58.879 44.000 0.00 0.00 0.00 2.73
3000 8582 6.120905 GGTCATAGTGGAGAGTAAGAGTACA 58.879 44.000 0.00 0.00 32.12 2.90
3059 9320 9.603921 TGTTATTACCTTTACTAGTACAATGCC 57.396 33.333 0.91 0.00 0.00 4.40
3060 9321 9.049523 GTTATTACCTTTACTAGTACAATGCCC 57.950 37.037 0.91 0.00 0.00 5.36
3061 9322 4.133013 ACCTTTACTAGTACAATGCCCG 57.867 45.455 0.91 0.00 0.00 6.13
3062 9323 3.516700 ACCTTTACTAGTACAATGCCCGT 59.483 43.478 0.91 0.00 0.00 5.28
3063 9324 3.869246 CCTTTACTAGTACAATGCCCGTG 59.131 47.826 0.91 0.00 0.00 4.94
3064 9325 2.589798 TACTAGTACAATGCCCGTGC 57.410 50.000 0.00 0.00 38.26 5.34
3065 9326 0.459585 ACTAGTACAATGCCCGTGCG 60.460 55.000 0.00 0.00 41.78 5.34
3066 9327 0.459585 CTAGTACAATGCCCGTGCGT 60.460 55.000 0.00 0.00 41.78 5.24
3087 9348 2.959507 GCCACGGGCTTTTGAAATAT 57.040 45.000 7.58 0.00 46.69 1.28
3088 9349 3.245518 GCCACGGGCTTTTGAAATATT 57.754 42.857 7.58 0.00 46.69 1.28
3089 9350 3.595173 GCCACGGGCTTTTGAAATATTT 58.405 40.909 0.00 0.00 46.69 1.40
3090 9351 4.000325 GCCACGGGCTTTTGAAATATTTT 59.000 39.130 1.43 0.00 46.69 1.82
3094 9750 4.690280 ACGGGCTTTTGAAATATTTTGCTG 59.310 37.500 1.43 3.45 0.00 4.41
3097 9753 5.704978 GGGCTTTTGAAATATTTTGCTGGAA 59.295 36.000 1.43 0.00 0.00 3.53
3098 9754 6.375174 GGGCTTTTGAAATATTTTGCTGGAAT 59.625 34.615 1.43 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.006967 AGTGTTATGTCAGTCCCACAGAC 59.993 47.826 0.00 0.00 46.71 3.51
7 8 3.239449 AGTGTTATGTCAGTCCCACAGA 58.761 45.455 0.00 0.00 0.00 3.41
8 9 3.685139 AGTGTTATGTCAGTCCCACAG 57.315 47.619 0.00 0.00 0.00 3.66
30 31 4.986783 AGGGACTAGATCATGTCGTATGA 58.013 43.478 0.00 7.39 36.02 2.15
36 37 4.162320 TGGTTGAAGGGACTAGATCATGTC 59.838 45.833 0.00 8.92 38.49 3.06
68 69 3.904800 TTGTGGTTGTTCACTGAGAGA 57.095 42.857 0.00 0.00 38.40 3.10
96 97 1.762708 AAATGCATGGTTACCGGGAG 58.237 50.000 6.32 0.00 0.00 4.30
136 137 5.907662 TGAGAAGTGGGAGGAGAATATGAAT 59.092 40.000 0.00 0.00 0.00 2.57
178 179 5.475909 GGTGGTGACGATAACTATGGATCTA 59.524 44.000 0.00 0.00 0.00 1.98
215 216 2.675348 TGAACGCATATTTGTGATCGCA 59.325 40.909 4.45 4.45 37.82 5.10
252 253 1.592064 TTGCAGTGACGAAGCATGAA 58.408 45.000 0.00 0.00 38.19 2.57
262 263 4.083164 TGTCATGACATCAATTGCAGTGAC 60.083 41.667 24.56 9.27 36.21 3.67
268 269 3.119602 ACTGCTGTCATGACATCAATTGC 60.120 43.478 28.00 24.55 41.01 3.56
307 308 8.294577 GGGAAAGTGTGTAAAGTGGTAATTAAG 58.705 37.037 0.00 0.00 0.00 1.85
319 320 8.265055 CCTATAGAGAATGGGAAAGTGTGTAAA 58.735 37.037 0.00 0.00 38.50 2.01
337 342 4.744795 AGCAAACCAGTGTCCTATAGAG 57.255 45.455 0.00 0.00 0.00 2.43
340 345 4.097437 CGACTAGCAAACCAGTGTCCTATA 59.903 45.833 0.00 0.00 0.00 1.31
380 697 7.094805 GCATCACTAACTTGTAAATCCAGACAA 60.095 37.037 0.00 0.00 34.49 3.18
404 721 2.780924 AACAAGGGGAGTGGGGCA 60.781 61.111 0.00 0.00 0.00 5.36
417 734 3.874383 TGTCTTCATCTTGGGGAACAA 57.126 42.857 0.00 0.00 37.55 2.83
464 781 4.225042 ACTTGTACATTGTCCTCATGCCTA 59.775 41.667 0.00 0.00 0.00 3.93
466 783 3.347216 ACTTGTACATTGTCCTCATGCC 58.653 45.455 0.00 0.00 0.00 4.40
473 790 4.056050 ACTGTCGAACTTGTACATTGTCC 58.944 43.478 0.00 0.00 0.00 4.02
482 799 2.223971 ACGGATTCACTGTCGAACTTGT 60.224 45.455 0.00 0.00 31.75 3.16
513 835 1.863454 CTCGAGCCATTTCCGATCTTG 59.137 52.381 0.00 0.00 0.00 3.02
516 838 2.225068 TTCTCGAGCCATTTCCGATC 57.775 50.000 7.81 0.00 0.00 3.69
519 841 1.939974 TCATTCTCGAGCCATTTCCG 58.060 50.000 7.81 0.00 0.00 4.30
520 842 3.004106 CCATTCATTCTCGAGCCATTTCC 59.996 47.826 7.81 0.00 0.00 3.13
521 843 3.879295 TCCATTCATTCTCGAGCCATTTC 59.121 43.478 7.81 0.00 0.00 2.17
522 844 3.889815 TCCATTCATTCTCGAGCCATTT 58.110 40.909 7.81 0.00 0.00 2.32
524 846 3.135348 TCTTCCATTCATTCTCGAGCCAT 59.865 43.478 7.81 0.00 0.00 4.40
526 848 3.185246 TCTTCCATTCATTCTCGAGCC 57.815 47.619 7.81 0.00 0.00 4.70
527 849 4.437239 TCTTCTTCCATTCATTCTCGAGC 58.563 43.478 7.81 0.00 0.00 5.03
529 851 7.744087 TTTTTCTTCTTCCATTCATTCTCGA 57.256 32.000 0.00 0.00 0.00 4.04
588 3046 9.677567 CATTTAGAAATGAAGGTTTCGAAGAAA 57.322 29.630 8.98 0.00 46.72 2.52
620 3078 5.572896 CGGTGGTTTCAATTTATCTCAAAGC 59.427 40.000 0.00 0.00 0.00 3.51
624 3082 7.393234 AGAAATCGGTGGTTTCAATTTATCTCA 59.607 33.333 5.44 0.00 37.89 3.27
625 3083 7.762382 AGAAATCGGTGGTTTCAATTTATCTC 58.238 34.615 5.44 0.00 37.89 2.75
630 3088 5.782893 TGAGAAATCGGTGGTTTCAATTT 57.217 34.783 5.44 0.00 37.89 1.82
634 3092 3.000041 CGATGAGAAATCGGTGGTTTCA 59.000 45.455 5.44 0.00 37.89 2.69
644 3102 3.305964 CATGGCAATGCGATGAGAAATC 58.694 45.455 22.91 0.00 45.27 2.17
866 3604 5.581085 GGCTGGTGATTATATACGCCTTAAG 59.419 44.000 0.00 0.00 37.54 1.85
928 3669 2.125310 CCACCAGGCGCATACGAA 60.125 61.111 10.83 0.00 43.93 3.85
1086 3841 3.986006 GTCCTCGACACCGGCACA 61.986 66.667 0.00 0.00 36.24 4.57
1223 3978 1.602165 CCGAACTGTGTAGCAAGACGT 60.602 52.381 0.00 0.00 0.00 4.34
1362 4490 2.599082 GTCGAAGTAGATTTCCGTGCTG 59.401 50.000 0.00 0.00 0.00 4.41
1371 4499 1.467035 GCGTGGTCGTCGAAGTAGATT 60.467 52.381 0.00 0.00 39.49 2.40
1425 4553 2.891936 GTCAGCATCGCATCGGCA 60.892 61.111 0.00 0.00 41.24 5.69
1495 4624 2.935955 CGTGTTGGTGAAGGCGAC 59.064 61.111 0.00 0.00 0.00 5.19
1519 4648 2.003443 CGTGGCTTTTGTTGACGCG 61.003 57.895 3.53 3.53 0.00 6.01
1530 4659 2.594592 GCTTGGGTGACGTGGCTT 60.595 61.111 0.00 0.00 0.00 4.35
1575 4704 2.436646 CAGCGGTGGAAGGCGATT 60.437 61.111 6.74 0.00 0.00 3.34
2078 5526 2.508891 CCGTCGTCGATGAAGCAGC 61.509 63.158 16.06 0.00 39.71 5.25
2079 5527 0.732880 AACCGTCGTCGATGAAGCAG 60.733 55.000 16.06 2.23 39.71 4.24
2080 5528 1.006825 CAACCGTCGTCGATGAAGCA 61.007 55.000 16.06 0.00 39.71 3.91
2127 5578 1.604278 CAGCTACTCGTGATCCGATCA 59.396 52.381 7.00 7.00 46.23 2.92
2155 5606 6.586344 TCCTGCTATTTCCTATGCTATATGC 58.414 40.000 0.00 0.00 43.25 3.14
2323 6361 7.227049 TCTAAAGTTGGGAATTGTTCAATCC 57.773 36.000 0.00 2.95 0.00 3.01
2324 6362 8.576442 TCTTCTAAAGTTGGGAATTGTTCAATC 58.424 33.333 0.00 0.00 0.00 2.67
2405 7547 6.183360 CCGTGTCTGAAGTTATAAAATGGTCC 60.183 42.308 0.00 0.00 0.00 4.46
2408 7550 6.370442 TGTCCGTGTCTGAAGTTATAAAATGG 59.630 38.462 0.00 0.00 0.00 3.16
2536 7682 2.113860 TTGGTGCAGCTCACTAATCC 57.886 50.000 18.08 0.00 44.98 3.01
2566 7712 1.581934 TCGCAATGGCTACTACATGC 58.418 50.000 0.00 0.00 38.10 4.06
2600 7746 1.490490 GTCCCTTCTGTGGATATGGCA 59.510 52.381 0.00 0.00 33.65 4.92
2643 7789 2.491693 CCATGGCTTAATTTGTCGTGGT 59.508 45.455 0.00 0.00 40.30 4.16
2654 7800 0.176910 TCGCGATGACCATGGCTTAA 59.823 50.000 13.04 0.00 39.88 1.85
2656 7802 1.522355 CTCGCGATGACCATGGCTT 60.522 57.895 13.04 2.83 39.88 4.35
2657 7803 2.107750 CTCGCGATGACCATGGCT 59.892 61.111 13.04 0.00 39.88 4.75
2685 7831 3.387397 GGAAAATATGACGGGAGGTACG 58.613 50.000 0.00 0.00 37.36 3.67
2742 7888 3.321682 TGTGGCAAAAATCAAAGAGAGGG 59.678 43.478 0.00 0.00 0.00 4.30
2806 8387 3.586470 TCTAGCAACAAACTTTCCCCA 57.414 42.857 0.00 0.00 0.00 4.96
2809 8390 6.560711 TCAAAGTTCTAGCAACAAACTTTCC 58.439 36.000 13.49 0.00 45.35 3.13
2810 8391 7.168135 CCATCAAAGTTCTAGCAACAAACTTTC 59.832 37.037 13.49 0.00 45.35 2.62
2864 8445 9.696917 GATGAAAGTTTATCAAAGGTGAAACAT 57.303 29.630 0.00 0.00 39.98 2.71
2871 8452 7.099120 GGCAATGATGAAAGTTTATCAAAGGT 58.901 34.615 2.99 0.00 36.93 3.50
2879 8460 5.076182 TCTGGTGGCAATGATGAAAGTTTA 58.924 37.500 0.00 0.00 0.00 2.01
2883 8464 5.840243 TTATCTGGTGGCAATGATGAAAG 57.160 39.130 0.00 0.00 0.00 2.62
2885 8466 5.263599 AGTTTATCTGGTGGCAATGATGAA 58.736 37.500 0.00 0.00 0.00 2.57
2891 8472 4.510167 AGCTAGTTTATCTGGTGGCAAT 57.490 40.909 0.00 0.00 0.00 3.56
2892 8473 4.383770 GGTAGCTAGTTTATCTGGTGGCAA 60.384 45.833 0.00 0.00 0.00 4.52
2894 8475 3.134081 TGGTAGCTAGTTTATCTGGTGGC 59.866 47.826 0.00 0.00 0.00 5.01
2908 8489 5.800296 TGAACTTATTGCAGTTGGTAGCTA 58.200 37.500 0.00 0.00 37.11 3.32
2931 8512 9.214774 AACTGTATAAGTGAGCTACCAATGGCT 62.215 40.741 0.00 0.00 41.54 4.75
3035 8617 7.927629 CGGGCATTGTACTAGTAAAGGTAATAA 59.072 37.037 3.61 0.00 0.00 1.40
3036 8618 7.069826 ACGGGCATTGTACTAGTAAAGGTAATA 59.930 37.037 3.61 0.00 0.00 0.98
3041 9302 3.869246 CACGGGCATTGTACTAGTAAAGG 59.131 47.826 3.61 4.90 0.00 3.11
3047 9308 0.459585 ACGCACGGGCATTGTACTAG 60.460 55.000 11.77 0.00 41.24 2.57
3052 9313 4.341502 GCAACGCACGGGCATTGT 62.342 61.111 20.63 0.74 44.58 2.71
3069 9330 4.142924 GCAAAATATTTCAAAAGCCCGTGG 60.143 41.667 0.10 0.00 0.00 4.94
3070 9331 4.690280 AGCAAAATATTTCAAAAGCCCGTG 59.310 37.500 0.10 0.00 0.00 4.94
3071 9332 4.690280 CAGCAAAATATTTCAAAAGCCCGT 59.310 37.500 0.10 0.00 0.00 5.28
3072 9333 4.093261 CCAGCAAAATATTTCAAAAGCCCG 59.907 41.667 0.10 0.00 0.00 6.13
3073 9334 5.244755 TCCAGCAAAATATTTCAAAAGCCC 58.755 37.500 0.10 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.