Multiple sequence alignment - TraesCS2B01G289300

Loading Multiple Alignment...

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 TraesCS2B01G289300 chr2B 100.000 2381 0 0 1 2381 399936254 399933874 0.000000e+00 4397.0
1 TraesCS2B01G289300 chr2D 94.612 1819 52 18 576 2379 331739077 331737290 0.000000e+00 2774.0
2 TraesCS2B01G289300 chr2D 82.500 720 66 30 989 1685 73286457 73285775 5.710000e-161 577.0
3 TraesCS2B01G289300 chr2D 80.702 513 61 17 79 586 331739802 331739323 4.840000e-97 364.0
4 TraesCS2B01G289300 chr2A 93.500 1123 60 12 581 1696 439201419 439200303 0.000000e+00 1657.0
5 TraesCS2B01G289300 chr2A 94.953 535 24 3 1747 2279 439200062 439199529 0.000000e+00 835.0
6 TraesCS2B01G289300 chr2A 86.170 94 13 0 39 132 439209336 439209243 4.190000e-18 102.0
7 TraesCS2B01G289300 chr7A 83.401 735 90 21 1013 1729 139200793 139200073 0.000000e+00 652.0
8 TraesCS2B01G289300 chr7A 84.692 503 51 16 1241 1729 607561670 607562160 1.660000e-131 479.0
9 TraesCS2B01G289300 chr4B 81.806 720 85 18 1026 1729 134954225 134954914 1.600000e-156 562.0
10 TraesCS2B01G289300 chr3D 83.359 637 74 21 1048 1671 556842215 556842832 5.750000e-156 560.0
11 TraesCS2B01G289300 chr7D 83.871 93 15 0 1 93 106632551 106632459 3.260000e-14 89.8
12 TraesCS2B01G289300 chr7D 81.081 74 13 1 17 90 580335425 580335497 9.190000e-05 58.4
13 TraesCS2B01G289300 chr4A 92.157 51 4 0 22 72 575803669 575803719 3.280000e-09 73.1


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 TraesCS2B01G289300 chr2B 399933874 399936254 2380 True 4397 4397 100.0000 1 2381 1 chr2B.!!$R1 2380
1 TraesCS2B01G289300 chr2D 331737290 331739802 2512 True 1569 2774 87.6570 79 2379 2 chr2D.!!$R2 2300
2 TraesCS2B01G289300 chr2D 73285775 73286457 682 True 577 577 82.5000 989 1685 1 chr2D.!!$R1 696
3 TraesCS2B01G289300 chr2A 439199529 439201419 1890 True 1246 1657 94.2265 581 2279 2 chr2A.!!$R2 1698
4 TraesCS2B01G289300 chr7A 139200073 139200793 720 True 652 652 83.4010 1013 1729 1 chr7A.!!$R1 716
5 TraesCS2B01G289300 chr4B 134954225 134954914 689 False 562 562 81.8060 1026 1729 1 chr4B.!!$F1 703
6 TraesCS2B01G289300 chr3D 556842215 556842832 617 False 560 560 83.3590 1048 1671 1 chr3D.!!$F1 623

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
336 338 0.034477 CTTTGTTAGGCCCGACCCAT 60.034 55.0 0.0 0.0 40.58 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 2001 1.47528 GTACATACCGGAGCAGTGTGA 59.525 52.381 9.46 0.0 31.48 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
29 30 2.123554 GGATACCCGACCCGGTCT 60.124 66.667 15.70 0.00 46.80 3.85
30 31 1.759692 GGATACCCGACCCGGTCTT 60.760 63.158 15.70 2.57 46.80 3.01
31 32 1.440476 GATACCCGACCCGGTCTTG 59.560 63.158 15.70 8.59 46.80 3.02
32 33 2.639883 GATACCCGACCCGGTCTTGC 62.640 65.000 15.70 0.00 46.80 4.01
62 63 3.356814 GCCTGGGCCTAAGTTTTGA 57.643 52.632 4.53 0.00 34.56 2.69
63 64 1.177401 GCCTGGGCCTAAGTTTTGAG 58.823 55.000 4.53 0.00 34.56 3.02
64 65 1.547901 GCCTGGGCCTAAGTTTTGAGT 60.548 52.381 4.53 0.00 34.56 3.41
65 66 2.437413 CCTGGGCCTAAGTTTTGAGTC 58.563 52.381 4.53 0.00 0.00 3.36
66 67 2.040412 CCTGGGCCTAAGTTTTGAGTCT 59.960 50.000 4.53 0.00 0.00 3.24
67 68 3.077359 CTGGGCCTAAGTTTTGAGTCTG 58.923 50.000 4.53 0.00 0.00 3.51
68 69 2.708861 TGGGCCTAAGTTTTGAGTCTGA 59.291 45.455 4.53 0.00 0.00 3.27
69 70 3.137544 TGGGCCTAAGTTTTGAGTCTGAA 59.862 43.478 4.53 0.00 0.00 3.02
70 71 3.753797 GGGCCTAAGTTTTGAGTCTGAAG 59.246 47.826 0.84 0.00 0.00 3.02
71 72 3.753797 GGCCTAAGTTTTGAGTCTGAAGG 59.246 47.826 0.00 0.00 0.00 3.46
72 73 4.505039 GGCCTAAGTTTTGAGTCTGAAGGA 60.505 45.833 0.00 0.00 0.00 3.36
73 74 4.452795 GCCTAAGTTTTGAGTCTGAAGGAC 59.547 45.833 0.00 0.00 44.80 3.85
74 75 5.611374 CCTAAGTTTTGAGTCTGAAGGACA 58.389 41.667 0.00 0.00 46.72 4.02
75 76 5.467063 CCTAAGTTTTGAGTCTGAAGGACAC 59.533 44.000 0.00 0.00 46.72 3.67
76 77 3.458189 AGTTTTGAGTCTGAAGGACACG 58.542 45.455 0.00 0.00 46.72 4.49
77 78 3.118738 AGTTTTGAGTCTGAAGGACACGT 60.119 43.478 0.00 0.00 46.72 4.49
118 119 0.843309 TTTTGAGCCCAGAGGACACA 59.157 50.000 0.00 0.00 33.47 3.72
119 120 0.108585 TTTGAGCCCAGAGGACACAC 59.891 55.000 0.00 0.00 33.47 3.82
120 121 1.053835 TTGAGCCCAGAGGACACACA 61.054 55.000 0.00 0.00 33.47 3.72
121 122 0.837691 TGAGCCCAGAGGACACACAT 60.838 55.000 0.00 0.00 33.47 3.21
150 151 1.685820 GGGCCTAAGTGTTGAGCCT 59.314 57.895 0.84 0.00 43.36 4.58
160 161 0.836606 TGTTGAGCCTGAAGGACACA 59.163 50.000 0.00 0.00 37.39 3.72
189 190 1.895238 CCTGGGCTTGCCATTCTTG 59.105 57.895 14.04 0.00 0.00 3.02
190 191 1.217244 CTGGGCTTGCCATTCTTGC 59.783 57.895 14.04 0.00 0.00 4.01
191 192 1.533513 TGGGCTTGCCATTCTTGCA 60.534 52.632 14.04 0.00 36.84 4.08
192 193 0.905809 TGGGCTTGCCATTCTTGCAT 60.906 50.000 14.04 0.00 38.76 3.96
193 194 0.179092 GGGCTTGCCATTCTTGCATC 60.179 55.000 14.04 0.00 38.76 3.91
196 197 2.428171 GGCTTGCCATTCTTGCATCTTA 59.572 45.455 6.79 0.00 38.76 2.10
197 198 3.490419 GGCTTGCCATTCTTGCATCTTAG 60.490 47.826 6.79 0.00 38.76 2.18
210 212 2.311463 CATCTTAGGGAAGAGGCTCGA 58.689 52.381 9.22 0.00 44.90 4.04
211 213 2.757894 TCTTAGGGAAGAGGCTCGAT 57.242 50.000 9.22 1.75 36.75 3.59
212 214 2.588620 TCTTAGGGAAGAGGCTCGATC 58.411 52.381 9.22 11.49 36.75 3.69
214 216 0.556258 TAGGGAAGAGGCTCGATCCA 59.444 55.000 30.58 16.84 31.56 3.41
223 225 1.152881 GCTCGATCCAAGGCCCAAT 60.153 57.895 0.00 0.00 0.00 3.16
224 226 0.753111 GCTCGATCCAAGGCCCAATT 60.753 55.000 0.00 0.00 0.00 2.32
226 228 0.623194 TCGATCCAAGGCCCAATTGA 59.377 50.000 7.12 0.00 0.00 2.57
238 240 2.365293 GCCCAATTGACCTTTTCACTGT 59.635 45.455 7.12 0.00 32.26 3.55
239 241 3.552890 GCCCAATTGACCTTTTCACTGTC 60.553 47.826 7.12 0.00 32.26 3.51
241 243 3.563808 CCAATTGACCTTTTCACTGTCGA 59.436 43.478 7.12 0.00 32.26 4.20
244 246 1.149148 GACCTTTTCACTGTCGAGCC 58.851 55.000 0.00 0.00 0.00 4.70
245 247 0.600255 ACCTTTTCACTGTCGAGCCG 60.600 55.000 0.00 0.00 0.00 5.52
254 256 4.011517 GTCGAGCCGGGGTTTGGA 62.012 66.667 2.18 0.00 0.00 3.53
258 260 3.182996 AGCCGGGGTTTGGACCTT 61.183 61.111 2.18 0.00 45.75 3.50
263 265 2.531771 CCGGGGTTTGGACCTTAAAAT 58.468 47.619 0.00 0.00 45.75 1.82
271 273 4.685513 TTGGACCTTAAAATTAGGCCCT 57.314 40.909 0.00 0.00 36.36 5.19
273 275 6.349897 TTGGACCTTAAAATTAGGCCCTAT 57.650 37.500 0.00 0.00 36.36 2.57
285 287 2.773918 CCCTATGGCTGCCCTGGA 60.774 66.667 17.53 0.00 0.00 3.86
287 289 2.512896 CTATGGCTGCCCTGGACC 59.487 66.667 17.53 0.00 0.00 4.46
297 299 3.483869 CCTGGACCAGGCCCTAGC 61.484 72.222 27.72 0.00 45.13 3.42
309 311 2.333688 GCCCTAGCCTAGGTTTTCTG 57.666 55.000 16.54 1.34 44.73 3.02
310 312 1.838077 GCCCTAGCCTAGGTTTTCTGA 59.162 52.381 16.54 0.00 44.73 3.27
313 315 4.628959 GCCCTAGCCTAGGTTTTCTGATTT 60.629 45.833 16.54 0.00 44.73 2.17
335 337 1.377229 CTTTGTTAGGCCCGACCCA 59.623 57.895 0.00 0.00 40.58 4.51
336 338 0.034477 CTTTGTTAGGCCCGACCCAT 60.034 55.000 0.00 0.00 40.58 4.00
337 339 1.210967 CTTTGTTAGGCCCGACCCATA 59.789 52.381 0.00 0.00 40.58 2.74
338 340 0.834612 TTGTTAGGCCCGACCCATAG 59.165 55.000 0.00 0.00 40.58 2.23
339 341 1.070957 GTTAGGCCCGACCCATAGC 59.929 63.158 0.00 0.00 40.58 2.97
340 342 2.144738 TTAGGCCCGACCCATAGCC 61.145 63.158 0.00 0.00 46.13 3.93
343 345 3.804329 GCCCGACCCATAGCCCAA 61.804 66.667 0.00 0.00 0.00 4.12
344 346 2.192175 CCCGACCCATAGCCCAAC 59.808 66.667 0.00 0.00 0.00 3.77
345 347 2.192175 CCGACCCATAGCCCAACC 59.808 66.667 0.00 0.00 0.00 3.77
346 348 2.675242 CCGACCCATAGCCCAACCA 61.675 63.158 0.00 0.00 0.00 3.67
347 349 1.153168 CGACCCATAGCCCAACCAG 60.153 63.158 0.00 0.00 0.00 4.00
348 350 1.227383 GACCCATAGCCCAACCAGG 59.773 63.158 0.00 0.00 37.03 4.45
396 398 5.527951 TCGATGTAGAAGCGAGTAAGATTCT 59.472 40.000 3.07 3.07 46.85 2.40
397 399 5.849081 CGATGTAGAAGCGAGTAAGATTCTC 59.151 44.000 0.59 0.00 42.43 2.87
417 419 3.671716 TCGGATAATCGAGGAATCGAGA 58.328 45.455 6.50 0.00 45.70 4.04
423 425 3.881780 ATCGAGGAATCGAGACTAACG 57.118 47.619 6.50 0.00 45.70 3.18
471 473 0.673985 TGAACTCTCCCAGTCACGTG 59.326 55.000 9.94 9.94 32.30 4.49
492 494 8.048436 CACGTGAATAAAGTACATAAGCTTACG 58.952 37.037 10.90 2.47 31.81 3.18
493 495 7.221452 ACGTGAATAAAGTACATAAGCTTACGG 59.779 37.037 8.70 6.87 30.58 4.02
505 508 3.538634 AGCTTACGGGTCTATGGTTTC 57.461 47.619 0.00 0.00 0.00 2.78
510 513 5.452917 GCTTACGGGTCTATGGTTTCACTAT 60.453 44.000 0.00 0.00 0.00 2.12
515 518 3.802685 GGTCTATGGTTTCACTATGACGC 59.197 47.826 0.00 0.00 0.00 5.19
531 534 3.435566 TGACGCTTTAGATCGCAACTAG 58.564 45.455 0.00 0.00 0.00 2.57
568 571 5.004448 TGCCGAGAACACCAATAATGTTAA 58.996 37.500 0.00 0.00 40.36 2.01
569 572 5.473846 TGCCGAGAACACCAATAATGTTAAA 59.526 36.000 0.00 0.00 40.36 1.52
617 876 6.404954 GCCTCAAAATTTACGGGTAGCATTTA 60.405 38.462 0.00 0.00 0.00 1.40
628 887 5.221263 ACGGGTAGCATTTAGATGTGACTAG 60.221 44.000 0.00 0.00 35.63 2.57
695 955 1.228124 CTTTTGGGTCGGGAGCACA 60.228 57.895 0.00 0.00 0.00 4.57
753 1015 9.710979 TTATTATTTTGTTAATACTCGTGCAGC 57.289 29.630 0.00 0.00 0.00 5.25
891 1155 2.823154 TCCATCGTTCCAATTTCCCAAC 59.177 45.455 0.00 0.00 0.00 3.77
928 1192 5.402867 GCCGTGAACGAAAAATAAAAATCCA 59.597 36.000 4.03 0.00 43.02 3.41
934 1198 6.795098 ACGAAAAATAAAAATCCAAAGGGC 57.205 33.333 0.00 0.00 0.00 5.19
983 1247 2.097791 CGAGAGAGTAAGGAAACGAGGG 59.902 54.545 0.00 0.00 0.00 4.30
1427 1729 1.234821 GGGTCGTTGATGCTTGTTGA 58.765 50.000 0.00 0.00 0.00 3.18
1696 2192 1.476891 ACACTGCTCCGGTATGTACTG 59.523 52.381 0.00 0.00 0.00 2.74
1995 2513 2.223971 ACTGTCGTGATTCGGTGAGTTT 60.224 45.455 0.00 0.00 40.32 2.66
2189 2716 3.888930 TGACCTTTCTGTTGAATGTTCCC 59.111 43.478 0.00 0.00 31.56 3.97
2205 2732 4.085733 TGTTCCCGTCATCCAAAATCAAT 58.914 39.130 0.00 0.00 0.00 2.57
2231 2758 5.902613 TGGGATTCAAGTAATGCTTTGAG 57.097 39.130 0.00 0.00 36.25 3.02
2303 2830 2.904915 GCGACTTGCTTACACAGAAAC 58.095 47.619 0.00 0.00 41.73 2.78
2304 2831 2.286833 GCGACTTGCTTACACAGAAACA 59.713 45.455 0.00 0.00 41.73 2.83
2368 2895 5.402398 GTTAAAAGGATGTGCCAGATTGTC 58.598 41.667 0.00 0.00 40.02 3.18
2379 2906 1.808945 CCAGATTGTCGCTTGAGCTTT 59.191 47.619 1.07 0.00 39.32 3.51
2380 2907 2.227388 CCAGATTGTCGCTTGAGCTTTT 59.773 45.455 1.07 0.00 39.32 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.770557 GGGTATCCCATGGCCAGGTA 60.771 60.000 17.55 4.21 44.65 3.08
1 2 2.084930 GGGTATCCCATGGCCAGGT 61.085 63.158 17.55 0.00 44.65 4.00
2 3 2.846532 GGGTATCCCATGGCCAGG 59.153 66.667 13.05 12.17 44.65 4.45
3 4 2.146724 TCGGGTATCCCATGGCCAG 61.147 63.158 13.05 2.86 45.83 4.85
4 5 2.040359 TCGGGTATCCCATGGCCA 60.040 61.111 8.56 8.56 45.83 5.36
5 6 2.430367 GTCGGGTATCCCATGGCC 59.570 66.667 6.09 1.21 45.83 5.36
6 7 2.430367 GGTCGGGTATCCCATGGC 59.570 66.667 6.09 0.00 45.83 4.40
7 8 2.879233 CGGGTCGGGTATCCCATGG 61.879 68.421 4.14 4.14 45.83 3.66
8 9 2.741092 CGGGTCGGGTATCCCATG 59.259 66.667 5.64 0.00 45.83 3.66
9 10 2.525877 CCGGGTCGGGTATCCCAT 60.526 66.667 5.64 0.00 45.83 4.00
44 45 1.177401 CTCAAAACTTAGGCCCAGGC 58.823 55.000 0.00 0.00 41.06 4.85
45 46 2.040412 AGACTCAAAACTTAGGCCCAGG 59.960 50.000 0.00 0.00 0.00 4.45
46 47 3.077359 CAGACTCAAAACTTAGGCCCAG 58.923 50.000 0.00 0.00 0.00 4.45
47 48 2.708861 TCAGACTCAAAACTTAGGCCCA 59.291 45.455 0.00 0.00 0.00 5.36
48 49 3.418684 TCAGACTCAAAACTTAGGCCC 57.581 47.619 0.00 0.00 0.00 5.80
49 50 3.753797 CCTTCAGACTCAAAACTTAGGCC 59.246 47.826 0.00 0.00 0.00 5.19
50 51 4.452795 GTCCTTCAGACTCAAAACTTAGGC 59.547 45.833 0.00 0.00 42.69 3.93
51 52 5.467063 GTGTCCTTCAGACTCAAAACTTAGG 59.533 44.000 0.00 0.00 46.46 2.69
52 53 5.175856 CGTGTCCTTCAGACTCAAAACTTAG 59.824 44.000 0.00 0.00 46.46 2.18
53 54 5.047847 CGTGTCCTTCAGACTCAAAACTTA 58.952 41.667 0.00 0.00 46.46 2.24
54 55 3.871594 CGTGTCCTTCAGACTCAAAACTT 59.128 43.478 0.00 0.00 46.46 2.66
55 56 3.118738 ACGTGTCCTTCAGACTCAAAACT 60.119 43.478 0.00 0.00 46.46 2.66
56 57 3.195661 ACGTGTCCTTCAGACTCAAAAC 58.804 45.455 0.00 0.00 46.46 2.43
57 58 3.454375 GACGTGTCCTTCAGACTCAAAA 58.546 45.455 0.00 0.00 46.46 2.44
58 59 2.543031 CGACGTGTCCTTCAGACTCAAA 60.543 50.000 0.00 0.00 46.46 2.69
59 60 1.001706 CGACGTGTCCTTCAGACTCAA 60.002 52.381 0.00 0.00 46.46 3.02
60 61 0.591659 CGACGTGTCCTTCAGACTCA 59.408 55.000 0.00 0.00 46.46 3.41
61 62 0.109689 CCGACGTGTCCTTCAGACTC 60.110 60.000 0.00 0.00 46.46 3.36
62 63 1.524863 CCCGACGTGTCCTTCAGACT 61.525 60.000 0.00 0.00 46.46 3.24
63 64 1.080705 CCCGACGTGTCCTTCAGAC 60.081 63.158 0.00 0.00 46.51 3.51
64 65 2.927580 GCCCGACGTGTCCTTCAGA 61.928 63.158 0.00 0.00 0.00 3.27
65 66 2.432628 GCCCGACGTGTCCTTCAG 60.433 66.667 0.00 0.00 0.00 3.02
66 67 3.998672 GGCCCGACGTGTCCTTCA 61.999 66.667 0.00 0.00 0.00 3.02
93 94 2.087646 CCTCTGGGCTCAAAACTTAGC 58.912 52.381 0.00 0.00 38.03 3.09
95 96 2.708861 TGTCCTCTGGGCTCAAAACTTA 59.291 45.455 0.00 0.00 0.00 2.24
110 111 1.377725 CCCAGCCATGTGTGTCCTC 60.378 63.158 0.00 0.00 0.00 3.71
142 143 1.230324 GTGTGTCCTTCAGGCTCAAC 58.770 55.000 0.00 0.00 34.44 3.18
150 151 3.948719 GGCCCGGTGTGTCCTTCA 61.949 66.667 0.00 0.00 0.00 3.02
173 174 1.533513 TGCAAGAATGGCAAGCCCA 60.534 52.632 8.89 0.00 46.27 5.36
174 175 3.379880 TGCAAGAATGGCAAGCCC 58.620 55.556 8.89 0.00 46.27 5.19
185 186 2.171448 GCCTCTTCCCTAAGATGCAAGA 59.829 50.000 9.58 0.00 46.63 3.02
186 187 2.570135 GCCTCTTCCCTAAGATGCAAG 58.430 52.381 9.58 0.00 46.63 4.01
190 191 2.311463 TCGAGCCTCTTCCCTAAGATG 58.689 52.381 0.00 0.00 40.92 2.90
191 192 2.757894 TCGAGCCTCTTCCCTAAGAT 57.242 50.000 0.00 0.00 40.92 2.40
192 193 2.588620 GATCGAGCCTCTTCCCTAAGA 58.411 52.381 0.00 0.00 39.47 2.10
193 194 1.616374 GGATCGAGCCTCTTCCCTAAG 59.384 57.143 13.71 0.00 0.00 2.18
196 197 0.325671 TTGGATCGAGCCTCTTCCCT 60.326 55.000 22.18 0.00 0.00 4.20
197 198 0.105778 CTTGGATCGAGCCTCTTCCC 59.894 60.000 22.18 0.00 0.00 3.97
207 209 0.623194 TCAATTGGGCCTTGGATCGA 59.377 50.000 4.53 0.00 0.00 3.59
208 210 0.740737 GTCAATTGGGCCTTGGATCG 59.259 55.000 4.53 0.00 0.00 3.69
210 212 0.712380 AGGTCAATTGGGCCTTGGAT 59.288 50.000 14.17 0.00 0.00 3.41
211 213 0.486879 AAGGTCAATTGGGCCTTGGA 59.513 50.000 24.50 0.00 40.71 3.53
212 214 1.351076 AAAGGTCAATTGGGCCTTGG 58.649 50.000 25.28 0.00 41.31 3.61
214 216 2.368548 GTGAAAAGGTCAATTGGGCCTT 59.631 45.455 21.56 21.56 43.75 4.35
223 225 2.210116 GCTCGACAGTGAAAAGGTCAA 58.790 47.619 0.00 0.00 38.23 3.18
224 226 1.540363 GGCTCGACAGTGAAAAGGTCA 60.540 52.381 0.00 0.00 0.00 4.02
226 228 0.600255 CGGCTCGACAGTGAAAAGGT 60.600 55.000 0.00 0.00 0.00 3.50
238 240 4.011517 GTCCAAACCCCGGCTCGA 62.012 66.667 0.00 0.00 0.00 4.04
271 273 2.286045 TGGTCCAGGGCAGCCATA 60.286 61.111 15.19 0.00 0.00 2.74
294 296 4.855340 CCCAAATCAGAAAACCTAGGCTA 58.145 43.478 9.30 0.00 0.00 3.93
295 297 3.701664 CCCAAATCAGAAAACCTAGGCT 58.298 45.455 9.30 0.00 0.00 4.58
297 299 3.701664 AGCCCAAATCAGAAAACCTAGG 58.298 45.455 7.41 7.41 0.00 3.02
309 311 2.672961 GGCCTAACAAAGCCCAAATC 57.327 50.000 0.00 0.00 43.76 2.17
329 331 1.153168 CTGGTTGGGCTATGGGTCG 60.153 63.158 0.00 0.00 0.00 4.79
341 343 4.431131 ATCTGCCGGGCCTGGTTG 62.431 66.667 31.62 22.98 0.00 3.77
342 344 4.431131 CATCTGCCGGGCCTGGTT 62.431 66.667 31.62 11.79 0.00 3.67
353 355 1.599542 GAAGTATTCGTGGCCATCTGC 59.400 52.381 9.72 0.00 34.17 4.26
366 368 5.502153 ACTCGCTTCTACATCGAAGTATT 57.498 39.130 0.29 0.00 41.84 1.89
471 473 7.924947 AGACCCGTAAGCTTATGTACTTTATTC 59.075 37.037 21.40 7.93 0.00 1.75
492 494 4.369182 CGTCATAGTGAAACCATAGACCC 58.631 47.826 0.00 0.00 37.80 4.46
493 495 3.802685 GCGTCATAGTGAAACCATAGACC 59.197 47.826 0.00 0.00 37.80 3.85
505 508 3.372060 TGCGATCTAAAGCGTCATAGTG 58.628 45.455 0.00 0.00 36.46 2.74
510 513 2.363788 AGTTGCGATCTAAAGCGTCA 57.636 45.000 0.00 0.00 36.46 4.35
515 518 7.087639 CCTTATCTCCTAGTTGCGATCTAAAG 58.912 42.308 0.00 0.00 0.00 1.85
531 534 4.909678 GGCAAGGCCCTTATCTCC 57.090 61.111 0.00 0.00 44.06 3.71
581 584 8.410141 CCGTAAATTTTGAGGCAAAAGGATATA 58.590 33.333 10.56 0.00 44.72 0.86
586 589 3.993736 CCCGTAAATTTTGAGGCAAAAGG 59.006 43.478 10.56 6.29 44.72 3.11
587 590 4.627058 ACCCGTAAATTTTGAGGCAAAAG 58.373 39.130 10.56 0.00 44.72 2.27
695 955 1.747355 CAATTTGGCTTCCGAGAGCAT 59.253 47.619 11.26 0.00 44.49 3.79
753 1015 9.237846 GTTTCTGTCAGAAAATCCAACTTAAAG 57.762 33.333 25.87 0.00 44.84 1.85
863 1127 0.970640 TTGGAACGATGGAAGTCCGA 59.029 50.000 0.00 0.00 39.43 4.55
904 1168 5.402867 TGGATTTTTATTTTTCGTTCACGGC 59.597 36.000 0.00 0.00 40.29 5.68
907 1171 8.279800 CCCTTTGGATTTTTATTTTTCGTTCAC 58.720 33.333 0.00 0.00 0.00 3.18
928 1192 1.533033 CCCCCTTTCGTTGCCCTTT 60.533 57.895 0.00 0.00 0.00 3.11
1427 1729 5.123186 TCAAAATCTACCGCAACAAATCGAT 59.877 36.000 0.00 0.00 0.00 3.59
1674 2001 1.475280 GTACATACCGGAGCAGTGTGA 59.525 52.381 9.46 0.00 31.48 3.58
1696 2192 6.438259 TGGAAGCTACGCATACTCTATATC 57.562 41.667 0.00 0.00 0.00 1.63
1757 2274 1.645034 CTGCGGATAACACCAGACAG 58.355 55.000 0.00 0.00 0.00 3.51
1995 2513 7.831691 TCCAAGAACATCCTGACAATTTTTA 57.168 32.000 0.00 0.00 0.00 1.52
2189 2716 5.299028 TCCCATACATTGATTTTGGATGACG 59.701 40.000 0.00 0.00 37.58 4.35
2205 2732 6.889177 TCAAAGCATTACTTGAATCCCATACA 59.111 34.615 0.00 0.00 39.09 2.29
2231 2758 5.348451 ACAAAATTGACAAGCAACTTCACAC 59.652 36.000 0.00 0.00 39.78 3.82
2283 2810 2.286833 TGTTTCTGTGTAAGCAAGTCGC 59.713 45.455 0.00 0.00 42.91 5.19
2284 2811 3.802139 TCTGTTTCTGTGTAAGCAAGTCG 59.198 43.478 0.00 0.00 0.00 4.18
2302 2829 5.180492 CGTGTTTACCACAAATACCATCTGT 59.820 40.000 0.00 0.00 44.78 3.41
2303 2830 5.391523 CCGTGTTTACCACAAATACCATCTG 60.392 44.000 0.00 0.00 44.78 2.90
2304 2831 4.698304 CCGTGTTTACCACAAATACCATCT 59.302 41.667 0.00 0.00 44.78 2.90


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

AutoCloner maintained by Alex Coulton.