Multiple sequence alignment - TraesCS1B01G232800

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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 TraesCS1B01G232800 chr1B 100.000 4914 0 0 1 4914 418668270 418673183 0.000000e+00 9075.0
1 TraesCS1B01G232800 chr1B 81.379 290 50 3 137 425 162810125 162810411 2.960000e-57 233.0
2 TraesCS1B01G232800 chr1D 94.192 4907 192 39 70 4914 308581371 308586246 0.000000e+00 7396.0
3 TraesCS1B01G232800 chr1A 93.546 3099 152 23 139 3216 388155914 388158985 0.000000e+00 4571.0
4 TraesCS1B01G232800 chr1A 95.667 1708 60 9 3212 4914 388159016 388160714 0.000000e+00 2732.0
5 TraesCS1B01G232800 chr1A 92.063 63 5 0 70 132 388154098 388154160 6.770000e-14 89.8
6 TraesCS1B01G232800 chr7A 76.078 464 85 15 139 593 24960440 24959994 8.280000e-53 219.0
7 TraesCS1B01G232800 chr7D 78.039 255 39 13 216 456 454069273 454069524 1.430000e-30 145.0
8 TraesCS1B01G232800 chr5B 77.617 277 36 15 216 474 559563713 559563981 1.430000e-30 145.0
9 TraesCS1B01G232800 chr4D 75.610 287 56 8 216 489 473986960 473986675 3.990000e-26 130.0
10 TraesCS1B01G232800 chr4D 84.496 129 15 4 1863 1989 295574428 295574553 6.680000e-24 122.0
11 TraesCS1B01G232800 chr2D 89.691 97 10 0 230 326 452327270 452327174 1.860000e-24 124.0
12 TraesCS1B01G232800 chr2A 86.726 113 11 4 216 326 775084815 775084925 6.680000e-24 122.0
13 TraesCS1B01G232800 chr2A 85.455 110 16 0 217 326 13817027 13816918 1.120000e-21 115.0
14 TraesCS1B01G232800 chr4B 83.333 132 16 5 1866 1995 364042836 364042709 3.110000e-22 117.0
15 TraesCS1B01G232800 chr4A 83.333 132 16 5 1866 1995 195968559 195968432 3.110000e-22 117.0
16 TraesCS1B01G232800 chr4A 92.727 55 4 0 1862 1916 448513036 448512982 4.080000e-11 80.5
17 TraesCS1B01G232800 chr3D 95.082 61 3 0 1144 1204 64642481 64642541 4.050000e-16 97.1
18 TraesCS1B01G232800 chr3B 95.082 61 3 0 1144 1204 107663521 107663581 4.050000e-16 97.1
19 TraesCS1B01G232800 chr3B 86.765 68 9 0 1853 1920 2517070 2517137 5.270000e-10 76.8
20 TraesCS1B01G232800 chr3A 93.443 61 4 0 1144 1204 75406290 75406350 1.880000e-14 91.6
21 TraesCS1B01G232800 chr2B 73.285 277 55 11 338 597 611186119 611186393 3.150000e-12 84.2
22 TraesCS1B01G232800 chr2B 93.878 49 2 1 1935 1983 191749487 191749440 6.820000e-09 73.1
23 TraesCS1B01G232800 chr2B 93.750 48 2 1 1936 1983 581997589 581997543 2.450000e-08 71.3
24 TraesCS1B01G232800 chr6D 91.837 49 3 1 1935 1983 437590076 437590029 3.170000e-07 67.6


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 TraesCS1B01G232800 chr1B 418668270 418673183 4913 False 9075.000000 9075 100.000000 1 4914 1 chr1B.!!$F2 4913
1 TraesCS1B01G232800 chr1D 308581371 308586246 4875 False 7396.000000 7396 94.192000 70 4914 1 chr1D.!!$F1 4844
2 TraesCS1B01G232800 chr1A 388154098 388160714 6616 False 2464.266667 4571 93.758667 70 4914 3 chr1A.!!$F1 4844

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
509 2261 0.036388 GTTTCTGATGAGTCGGGGCA 60.036 55.000 0.00 0.0 0.00 5.36 F
524 2276 0.250234 GGGCATGTCAGAGTGCTACA 59.750 55.000 0.00 0.0 41.04 2.74 F
696 2450 0.315886 TTCGCGTTGGAGAAGCAGTA 59.684 50.000 5.77 0.0 0.00 2.74 F
1005 2763 0.914417 TCCACAGTCAATCCCCTCCC 60.914 60.000 0.00 0.0 0.00 4.30 F
2603 4368 0.387202 TTGACATTTGTTGCACCCCG 59.613 50.000 0.00 0.0 0.00 5.73 F
3011 4788 1.000896 AAAGGGTGATTGGCGAGGG 60.001 57.895 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 3316 1.032014 AGGACAGCACACGCAAAAAT 58.968 45.000 0.00 0.00 42.27 1.82 R
1922 3685 1.604755 CTCGCGCTTATCTCACCTAGT 59.395 52.381 5.56 0.00 0.00 2.57 R
2224 3989 2.293122 TCAAGCTTTGGCATGTGTACAC 59.707 45.455 19.36 19.36 41.70 2.90 R
2877 4654 1.313772 AAACGTTGCACACAGCCATA 58.686 45.000 0.00 0.00 44.83 2.74 R
3434 5246 2.241176 TGGAGGTAATGGTGGGTGATTC 59.759 50.000 0.00 0.00 0.00 2.52 R
4878 6703 0.533308 CTACTCGCCGAGCTCCTAGT 60.533 60.000 15.20 8.90 32.04 2.57 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
35 36 4.590487 GTTGGCCTCGACGATGAA 57.410 55.556 3.32 0.00 0.00 2.57
36 37 2.079049 GTTGGCCTCGACGATGAAC 58.921 57.895 3.32 0.00 0.00 3.18
37 38 0.669318 GTTGGCCTCGACGATGAACA 60.669 55.000 3.32 0.00 0.00 3.18
38 39 0.249120 TTGGCCTCGACGATGAACAT 59.751 50.000 3.32 0.00 0.00 2.71
39 40 0.179111 TGGCCTCGACGATGAACATC 60.179 55.000 3.32 4.88 34.56 3.06
40 41 0.179111 GGCCTCGACGATGAACATCA 60.179 55.000 13.92 0.00 37.69 3.07
41 42 0.924090 GCCTCGACGATGAACATCAC 59.076 55.000 13.92 7.10 37.69 3.06
42 43 1.191944 CCTCGACGATGAACATCACG 58.808 55.000 13.92 16.10 37.69 4.35
43 44 1.202143 CCTCGACGATGAACATCACGA 60.202 52.381 21.66 21.66 40.76 4.35
44 45 1.840741 CTCGACGATGAACATCACGAC 59.159 52.381 20.33 8.27 39.42 4.34
45 46 1.198178 TCGACGATGAACATCACGACA 59.802 47.619 20.33 8.29 39.42 4.35
46 47 1.579361 CGACGATGAACATCACGACAG 59.421 52.381 18.43 5.16 38.52 3.51
47 48 1.920574 GACGATGAACATCACGACAGG 59.079 52.381 13.92 0.32 37.69 4.00
48 49 1.280982 CGATGAACATCACGACAGGG 58.719 55.000 13.92 0.00 37.69 4.45
49 50 1.656652 GATGAACATCACGACAGGGG 58.343 55.000 9.54 0.00 37.74 4.79
50 51 1.207089 GATGAACATCACGACAGGGGA 59.793 52.381 9.54 0.00 37.74 4.81
51 52 1.275666 TGAACATCACGACAGGGGAT 58.724 50.000 0.00 0.00 0.00 3.85
52 53 1.066215 TGAACATCACGACAGGGGATG 60.066 52.381 4.49 4.49 43.08 3.51
53 54 0.392998 AACATCACGACAGGGGATGC 60.393 55.000 5.89 0.00 41.58 3.91
54 55 1.524621 CATCACGACAGGGGATGCC 60.525 63.158 0.00 0.00 32.87 4.40
55 56 3.094062 ATCACGACAGGGGATGCCG 62.094 63.158 0.00 0.00 0.00 5.69
56 57 4.838152 CACGACAGGGGATGCCGG 62.838 72.222 0.00 0.00 0.00 6.13
66 67 3.161450 GATGCCGGGGACTGCCTA 61.161 66.667 2.18 0.00 40.23 3.93
67 68 3.462199 GATGCCGGGGACTGCCTAC 62.462 68.421 2.18 0.00 40.23 3.18
74 75 1.514553 GGGACTGCCTACCGTACAC 59.485 63.158 0.00 0.00 0.00 2.90
157 1905 2.526046 CCCCGACCTCCACCTTGTT 61.526 63.158 0.00 0.00 0.00 2.83
207 1955 1.766059 ACCAGCACACTCTCCACCA 60.766 57.895 0.00 0.00 0.00 4.17
210 1958 0.107456 CAGCACACTCTCCACCAACT 59.893 55.000 0.00 0.00 0.00 3.16
226 1974 4.816385 CACCAACTTTCTGCTTCTTGAGTA 59.184 41.667 0.00 0.00 0.00 2.59
269 2017 1.300481 TTGACACGACGATTTTGCCA 58.700 45.000 0.00 0.00 0.00 4.92
270 2018 0.865111 TGACACGACGATTTTGCCAG 59.135 50.000 0.00 0.00 0.00 4.85
276 2024 2.098298 CGATTTTGCCAGGTCGCG 59.902 61.111 0.00 0.00 0.00 5.87
345 2093 4.361971 TCCGGCGTGGTCTCCTCT 62.362 66.667 6.01 0.00 39.52 3.69
350 2098 2.584391 GCGTGGTCTCCTCTGGGTT 61.584 63.158 0.00 0.00 0.00 4.11
366 2114 1.964373 GTTCATGGGTCAACGGCGT 60.964 57.895 6.77 6.77 0.00 5.68
436 2186 4.804108 CGAGATGAAAGAAGTGAGTGAGT 58.196 43.478 0.00 0.00 0.00 3.41
437 2187 5.620205 GCGAGATGAAAGAAGTGAGTGAGTA 60.620 44.000 0.00 0.00 0.00 2.59
448 2198 4.890088 AGTGAGTGAGTAATTTTACCGCA 58.110 39.130 0.00 0.00 34.19 5.69
464 2214 1.468908 CCGCAAAAACAGTGCAGACAA 60.469 47.619 0.00 0.00 42.33 3.18
480 2230 0.816421 ACAACTACAAAAGCGCGGGT 60.816 50.000 8.83 1.24 0.00 5.28
508 2260 0.250513 AGTTTCTGATGAGTCGGGGC 59.749 55.000 0.00 0.00 0.00 5.80
509 2261 0.036388 GTTTCTGATGAGTCGGGGCA 60.036 55.000 0.00 0.00 0.00 5.36
519 2271 1.448540 GTCGGGGCATGTCAGAGTG 60.449 63.158 0.00 0.00 0.00 3.51
524 2276 0.250234 GGGCATGTCAGAGTGCTACA 59.750 55.000 0.00 0.00 41.04 2.74
553 2305 2.901192 TGTCCAGATTCCGGTAAAGTCA 59.099 45.455 0.00 0.00 0.00 3.41
557 2309 3.262420 CAGATTCCGGTAAAGTCACCAG 58.738 50.000 0.00 0.00 38.61 4.00
587 2341 7.719689 TTCGACTTTGCGAAAAATTATGATC 57.280 32.000 0.00 0.00 46.07 2.92
589 2343 5.169561 CGACTTTGCGAAAAATTATGATCCG 59.830 40.000 0.00 0.00 0.00 4.18
616 2370 1.822371 TCAACGGATCGATGAGGTCAA 59.178 47.619 0.54 0.00 34.04 3.18
618 2372 1.182667 ACGGATCGATGAGGTCAACA 58.817 50.000 0.54 0.00 0.00 3.33
626 2380 4.831107 TCGATGAGGTCAACATTGAATGA 58.169 39.130 12.80 0.00 39.21 2.57
627 2381 5.430886 TCGATGAGGTCAACATTGAATGAT 58.569 37.500 12.80 0.00 39.21 2.45
639 2393 2.488204 TGAATGATTTGCGGAGTCCA 57.512 45.000 10.49 0.00 0.00 4.02
651 2405 1.005630 GAGTCCAGACAGCTGCGTT 60.006 57.895 15.27 0.00 40.91 4.84
666 2420 3.833706 CGTTCGGACGGATACCTAC 57.166 57.895 8.83 0.00 45.32 3.18
667 2421 1.016627 CGTTCGGACGGATACCTACA 58.983 55.000 8.83 0.00 45.32 2.74
679 2433 4.679905 CGGATACCTACAGTTTGAGGGTTC 60.680 50.000 0.00 0.00 37.14 3.62
680 2434 2.833631 ACCTACAGTTTGAGGGTTCG 57.166 50.000 0.00 0.00 37.14 3.95
681 2435 1.270678 ACCTACAGTTTGAGGGTTCGC 60.271 52.381 0.00 0.00 37.14 4.70
682 2436 1.068474 CTACAGTTTGAGGGTTCGCG 58.932 55.000 0.00 0.00 0.00 5.87
683 2437 0.390124 TACAGTTTGAGGGTTCGCGT 59.610 50.000 5.77 0.00 0.00 6.01
684 2438 0.463116 ACAGTTTGAGGGTTCGCGTT 60.463 50.000 5.77 0.00 0.00 4.84
690 2444 1.005394 GAGGGTTCGCGTTGGAGAA 60.005 57.895 5.77 0.00 0.00 2.87
693 2447 1.959226 GGTTCGCGTTGGAGAAGCA 60.959 57.895 5.77 0.00 45.80 3.91
694 2448 1.493311 GTTCGCGTTGGAGAAGCAG 59.507 57.895 5.77 0.00 32.42 4.24
696 2450 0.315886 TTCGCGTTGGAGAAGCAGTA 59.684 50.000 5.77 0.00 0.00 2.74
707 2461 2.258580 GAAGCAGTAAAGCGCCTGGC 62.259 60.000 9.11 9.11 44.05 4.85
716 2470 3.440415 GCGCCTGGCTGTAAACCC 61.440 66.667 17.92 0.00 39.11 4.11
720 2474 1.078426 CCTGGCTGTAAACCCGGAG 60.078 63.158 0.73 0.00 0.00 4.63
794 2548 3.384927 GACGATCCAACGGCGAAG 58.615 61.111 16.62 4.94 37.61 3.79
1005 2763 0.914417 TCCACAGTCAATCCCCTCCC 60.914 60.000 0.00 0.00 0.00 4.30
1019 2777 1.541672 CTCCCCTCCTCTCCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
1462 3225 3.878699 CCCTCCTCTAAAGACGTCTACTC 59.121 52.174 20.39 0.00 0.00 2.59
1532 3295 3.679389 TCCTCTCAGCTCCAATTGTTTC 58.321 45.455 4.43 0.00 0.00 2.78
1553 3316 7.337184 TGTTTCTTTCATGCCCGTGTATAATTA 59.663 33.333 0.00 0.00 0.00 1.40
1569 3332 7.272515 GTGTATAATTATTTTTGCGTGTGCTGT 59.727 33.333 2.68 0.00 43.34 4.40
1843 3606 2.547855 CGGCGATCATAGGTGATTCCAA 60.548 50.000 0.00 0.00 44.96 3.53
1912 3675 2.979814 TAATCATGCTAGGTGTGCGT 57.020 45.000 0.00 0.00 0.00 5.24
1918 3681 1.153353 TGCTAGGTGTGCGTTTAAGC 58.847 50.000 0.00 0.00 37.71 3.09
1936 3699 3.444703 AGCGCAACTAGGTGAGATAAG 57.555 47.619 16.41 0.00 0.00 1.73
1940 3703 2.120232 CAACTAGGTGAGATAAGCGCG 58.880 52.381 0.00 0.00 0.00 6.86
2162 3926 5.478407 ACAGCATTTTTAATTACCTGCACC 58.522 37.500 9.23 0.00 32.18 5.01
2249 4014 1.444895 CATGCCAAAGCTTGACCGC 60.445 57.895 0.00 0.00 44.78 5.68
2374 4139 7.189079 TGGGGTTTTAATTTTCAAGTCAAGT 57.811 32.000 0.00 0.00 0.00 3.16
2466 4231 8.197592 ACCAATATAGGGTAACGACATAATGA 57.802 34.615 0.00 0.00 36.72 2.57
2468 4233 8.932791 CCAATATAGGGTAACGACATAATGAAC 58.067 37.037 0.00 0.00 37.60 3.18
2527 4292 6.049149 TCCGAGCTAGAAAATTGGATTGTAG 58.951 40.000 0.00 0.00 0.00 2.74
2603 4368 0.387202 TTGACATTTGTTGCACCCCG 59.613 50.000 0.00 0.00 0.00 5.73
2604 4369 1.288752 GACATTTGTTGCACCCCGG 59.711 57.895 0.00 0.00 0.00 5.73
2686 4453 3.438781 TGCGGTGATGAATTTACCAGTTC 59.561 43.478 0.00 0.00 34.10 3.01
2863 4639 7.175347 TCAGTTTCTGTATAGCTTGAGATGT 57.825 36.000 0.00 0.00 32.61 3.06
2877 4654 2.912956 TGAGATGTTAAGCCCTTCCTGT 59.087 45.455 0.00 0.00 0.00 4.00
2908 4685 2.035193 TGCAACGTTTTATGTGCCATGT 59.965 40.909 0.00 0.00 0.00 3.21
2979 4756 2.286365 TCGGAGGTTTTTGCTTGGAT 57.714 45.000 0.00 0.00 0.00 3.41
2984 4761 3.062042 GAGGTTTTTGCTTGGATTGCAG 58.938 45.455 0.00 0.00 41.71 4.41
3011 4788 1.000896 AAAGGGTGATTGGCGAGGG 60.001 57.895 0.00 0.00 0.00 4.30
3155 4932 2.224161 GCCTGATGAGGTAGGTTGCTAG 60.224 54.545 0.00 0.00 42.15 3.42
3205 4982 4.333926 GTGGCATAACTTGACCTGATTCTC 59.666 45.833 0.00 0.00 29.16 2.87
3291 5103 1.806542 GTGTAGTGTTGCATGGACAGG 59.193 52.381 0.00 0.00 0.00 4.00
3386 5198 6.529125 ACGGTATCTTGTGTATTTTACAGTCG 59.471 38.462 0.00 0.00 39.77 4.18
3401 5213 4.974438 TCGGACCTGCCACCCCTT 62.974 66.667 0.00 0.00 35.94 3.95
3434 5246 2.441001 AGAACCTGAGGCCCAGATATTG 59.559 50.000 19.43 7.55 45.78 1.90
3653 5465 2.507058 TGGAGATGATCTTGGACAAGGG 59.493 50.000 11.76 0.00 38.88 3.95
3680 5492 2.106338 TGAGATTGTGAAGCCTGTTCCA 59.894 45.455 0.00 0.00 0.00 3.53
3728 5540 0.700564 ATGAACTGGTGGGCATGTCT 59.299 50.000 0.00 0.00 0.00 3.41
4083 5896 2.834549 CTGATCTCCAGGGTTGTACTGT 59.165 50.000 0.00 0.00 39.23 3.55
4158 5971 4.122143 AGCTCTGCTCATTCTGTTCTAC 57.878 45.455 0.00 0.00 30.62 2.59
4164 5977 5.871524 TCTGCTCATTCTGTTCTACACAATC 59.128 40.000 0.00 0.00 33.87 2.67
4206 6019 4.389374 TCAGTGTCTTCAGATTTTGTCCC 58.611 43.478 0.00 0.00 0.00 4.46
4316 6129 9.341078 TGACTGCTGCATGATTTTATTCTTATA 57.659 29.630 1.31 0.00 0.00 0.98
4372 6185 3.252215 TGTGGCAAGAACAAACGGATTAG 59.748 43.478 0.00 0.00 0.00 1.73
4395 6208 2.436173 GGATTCTCCTTCGGGACAGATT 59.564 50.000 0.00 0.00 39.58 2.40
4646 6460 5.687780 TGATGCATAATCAGACAATCCAGT 58.312 37.500 0.00 0.00 40.50 4.00
4673 6496 6.711194 CCTCTGAGAGACGGTTCACTTATATA 59.289 42.308 11.82 0.00 0.00 0.86
4848 6673 5.830991 TGTACTATGTTTTTCCTTGCAGGTT 59.169 36.000 0.00 0.00 36.53 3.50
4871 6696 7.273381 GGTTTGATGGAAATACATTCAAGTTCG 59.727 37.037 0.00 0.00 39.98 3.95
4878 6703 6.148811 GGAAATACATTCAAGTTCGGAAGTCA 59.851 38.462 0.00 0.00 39.98 3.41
4896 6721 0.814410 CACTAGGAGCTCGGCGAGTA 60.814 60.000 34.41 19.48 31.39 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.554692 CATCGTCGAGGCCAACGC 61.555 66.667 17.48 11.64 38.72 4.84
17 18 1.445410 TTCATCGTCGAGGCCAACG 60.445 57.895 16.51 16.51 40.17 4.10
18 19 0.669318 TGTTCATCGTCGAGGCCAAC 60.669 55.000 5.01 3.43 0.00 3.77
19 20 0.249120 ATGTTCATCGTCGAGGCCAA 59.751 50.000 5.01 0.00 0.00 4.52
20 21 0.179111 GATGTTCATCGTCGAGGCCA 60.179 55.000 5.01 1.91 0.00 5.36
21 22 0.179111 TGATGTTCATCGTCGAGGCC 60.179 55.000 1.15 0.00 35.01 5.19
22 23 0.924090 GTGATGTTCATCGTCGAGGC 59.076 55.000 1.15 0.00 35.01 4.70
23 24 1.191944 CGTGATGTTCATCGTCGAGG 58.808 55.000 17.66 0.00 35.01 4.63
24 25 1.840741 GTCGTGATGTTCATCGTCGAG 59.159 52.381 21.99 8.62 35.01 4.04
25 26 1.198178 TGTCGTGATGTTCATCGTCGA 59.802 47.619 19.60 19.60 35.01 4.20
26 27 1.579361 CTGTCGTGATGTTCATCGTCG 59.421 52.381 16.97 16.97 35.01 5.12
27 28 1.920574 CCTGTCGTGATGTTCATCGTC 59.079 52.381 8.04 3.87 0.00 4.20
28 29 1.404181 CCCTGTCGTGATGTTCATCGT 60.404 52.381 8.04 0.00 0.00 3.73
29 30 1.280982 CCCTGTCGTGATGTTCATCG 58.719 55.000 8.04 0.00 0.00 3.84
30 31 1.207089 TCCCCTGTCGTGATGTTCATC 59.793 52.381 5.91 5.91 0.00 2.92
31 32 1.275666 TCCCCTGTCGTGATGTTCAT 58.724 50.000 0.00 0.00 0.00 2.57
32 33 1.066215 CATCCCCTGTCGTGATGTTCA 60.066 52.381 0.00 0.00 32.98 3.18
33 34 1.656652 CATCCCCTGTCGTGATGTTC 58.343 55.000 0.00 0.00 32.98 3.18
34 35 0.392998 GCATCCCCTGTCGTGATGTT 60.393 55.000 0.00 0.00 38.47 2.71
35 36 1.221840 GCATCCCCTGTCGTGATGT 59.778 57.895 0.00 0.00 38.47 3.06
36 37 1.524621 GGCATCCCCTGTCGTGATG 60.525 63.158 0.00 0.00 39.07 3.07
37 38 2.911143 GGCATCCCCTGTCGTGAT 59.089 61.111 0.00 0.00 0.00 3.06
49 50 3.161450 TAGGCAGTCCCCGGCATC 61.161 66.667 0.00 0.00 32.95 3.91
50 51 3.480133 GTAGGCAGTCCCCGGCAT 61.480 66.667 0.00 0.00 32.95 4.40
54 55 2.440796 TACGGTAGGCAGTCCCCG 60.441 66.667 0.00 0.00 41.26 5.73
55 56 1.683365 TGTACGGTAGGCAGTCCCC 60.683 63.158 0.00 0.00 0.00 4.81
56 57 1.514553 GTGTACGGTAGGCAGTCCC 59.485 63.158 0.00 0.00 0.00 4.46
57 58 1.138247 CGTGTACGGTAGGCAGTCC 59.862 63.158 0.00 0.00 35.37 3.85
58 59 4.779819 CGTGTACGGTAGGCAGTC 57.220 61.111 0.00 0.00 35.37 3.51
68 69 1.717194 ACATTACAAGGCCGTGTACG 58.283 50.000 28.22 23.32 33.73 3.67
74 75 1.708822 GCCAAAACATTACAAGGCCG 58.291 50.000 0.00 0.00 36.17 6.13
103 104 2.034879 CCTCACCGACCATGCACAC 61.035 63.158 0.00 0.00 0.00 3.82
105 106 1.741770 GACCTCACCGACCATGCAC 60.742 63.158 0.00 0.00 0.00 4.57
207 1955 7.001073 AGGAAATACTCAAGAAGCAGAAAGTT 58.999 34.615 0.00 0.00 0.00 2.66
210 1958 5.940470 GGAGGAAATACTCAAGAAGCAGAAA 59.060 40.000 0.00 0.00 39.27 2.52
226 1974 0.251787 AAGGCCGCAAAGGAGGAAAT 60.252 50.000 0.00 0.00 45.00 2.17
269 2017 0.173708 GAAGATCAACTCCGCGACCT 59.826 55.000 8.23 0.00 0.00 3.85
270 2018 0.806492 GGAAGATCAACTCCGCGACC 60.806 60.000 8.23 0.00 0.00 4.79
276 2024 1.521681 CGCCCGGAAGATCAACTCC 60.522 63.158 0.73 0.00 0.00 3.85
334 2082 1.065854 CATGAACCCAGAGGAGACCAC 60.066 57.143 0.00 0.00 36.73 4.16
335 2083 1.279496 CATGAACCCAGAGGAGACCA 58.721 55.000 0.00 0.00 36.73 4.02
345 2093 1.074072 CCGTTGACCCATGAACCCA 59.926 57.895 0.00 0.00 0.00 4.51
350 2098 2.358125 CACGCCGTTGACCCATGA 60.358 61.111 0.00 0.00 0.00 3.07
366 2114 1.553417 CCCCACTCTCTTCTTCCCTCA 60.553 57.143 0.00 0.00 0.00 3.86
436 2186 5.348986 TGCACTGTTTTTGCGGTAAAATTA 58.651 33.333 4.85 0.00 43.34 1.40
437 2187 4.184629 TGCACTGTTTTTGCGGTAAAATT 58.815 34.783 4.85 0.00 43.34 1.82
448 2198 5.637006 TTGTAGTTGTCTGCACTGTTTTT 57.363 34.783 0.00 0.00 36.13 1.94
464 2214 1.232621 GGAACCCGCGCTTTTGTAGT 61.233 55.000 5.56 0.00 0.00 2.73
480 2230 3.260884 ACTCATCAGAAACTAAGGCGGAA 59.739 43.478 0.00 0.00 0.00 4.30
488 2240 1.480954 GCCCCGACTCATCAGAAACTA 59.519 52.381 0.00 0.00 0.00 2.24
508 2260 1.067565 ACCGTGTAGCACTCTGACATG 60.068 52.381 0.00 0.00 31.34 3.21
509 2261 1.257743 ACCGTGTAGCACTCTGACAT 58.742 50.000 0.00 0.00 31.34 3.06
524 2276 0.037605 GGAATCTGGACACGAACCGT 60.038 55.000 0.00 0.00 42.36 4.83
553 2305 2.477189 CGCAAAGTCGAAACAAACTGGT 60.477 45.455 0.00 0.00 0.00 4.00
580 2332 3.317149 CCGTTGAGTAGTCCGGATCATAA 59.683 47.826 7.81 0.00 43.01 1.90
587 2341 0.029035 CGATCCGTTGAGTAGTCCGG 59.971 60.000 8.51 8.51 41.75 5.14
589 2343 2.617308 TCATCGATCCGTTGAGTAGTCC 59.383 50.000 0.00 0.00 31.91 3.85
614 2368 4.487948 ACTCCGCAAATCATTCAATGTTG 58.512 39.130 0.00 0.00 0.00 3.33
616 2370 3.129287 GGACTCCGCAAATCATTCAATGT 59.871 43.478 0.00 0.00 0.00 2.71
618 2372 3.355378 TGGACTCCGCAAATCATTCAAT 58.645 40.909 0.00 0.00 0.00 2.57
626 2380 0.674895 GCTGTCTGGACTCCGCAAAT 60.675 55.000 2.38 0.00 0.00 2.32
627 2381 1.301716 GCTGTCTGGACTCCGCAAA 60.302 57.895 2.38 0.00 0.00 3.68
639 2393 2.049063 GTCCGAACGCAGCTGTCT 60.049 61.111 16.64 0.00 0.00 3.41
651 2405 2.424601 CAAACTGTAGGTATCCGTCCGA 59.575 50.000 0.00 0.00 0.00 4.55
664 2418 0.390124 ACGCGAACCCTCAAACTGTA 59.610 50.000 15.93 0.00 0.00 2.74
666 2420 0.041312 CAACGCGAACCCTCAAACTG 60.041 55.000 15.93 0.00 0.00 3.16
667 2421 1.164041 CCAACGCGAACCCTCAAACT 61.164 55.000 15.93 0.00 0.00 2.66
679 2433 1.126846 CTTTACTGCTTCTCCAACGCG 59.873 52.381 3.53 3.53 0.00 6.01
680 2434 1.135944 GCTTTACTGCTTCTCCAACGC 60.136 52.381 0.00 0.00 0.00 4.84
681 2435 1.126846 CGCTTTACTGCTTCTCCAACG 59.873 52.381 0.00 0.00 0.00 4.10
682 2436 1.135944 GCGCTTTACTGCTTCTCCAAC 60.136 52.381 0.00 0.00 0.00 3.77
683 2437 1.156736 GCGCTTTACTGCTTCTCCAA 58.843 50.000 0.00 0.00 0.00 3.53
684 2438 0.673644 GGCGCTTTACTGCTTCTCCA 60.674 55.000 7.64 0.00 0.00 3.86
690 2444 2.747855 GCCAGGCGCTTTACTGCT 60.748 61.111 7.64 0.00 33.43 4.24
707 2461 1.405661 GCTTCTCCTCCGGGTTTACAG 60.406 57.143 0.00 0.00 0.00 2.74
716 2470 4.636249 AGCTAATTAATGCTTCTCCTCCG 58.364 43.478 0.00 0.00 35.86 4.63
720 2474 5.106752 GCAGCTAGCTAATTAATGCTTCTCC 60.107 44.000 18.86 0.00 40.35 3.71
757 2511 3.006003 GTCGGATCTCCTATTCCTGTTCC 59.994 52.174 0.00 0.00 0.00 3.62
768 2522 1.033574 GTTGGATCGTCGGATCTCCT 58.966 55.000 4.30 0.00 46.77 3.69
794 2548 2.506438 CGGTCGCCTCCTTTCGTC 60.506 66.667 0.00 0.00 0.00 4.20
1005 2763 1.541672 GAGGGGAGAGGAGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1019 2777 3.151022 GCAGAGGAGACGGGAGGG 61.151 72.222 0.00 0.00 0.00 4.30
1532 3295 9.528018 AAAAATAATTATACACGGGCATGAAAG 57.472 29.630 0.00 0.00 0.00 2.62
1553 3316 1.032014 AGGACAGCACACGCAAAAAT 58.968 45.000 0.00 0.00 42.27 1.82
1569 3332 6.071221 CCATCTCAATCAAAAATTGGACAGGA 60.071 38.462 0.00 0.00 0.00 3.86
1912 3675 3.671008 TCTCACCTAGTTGCGCTTAAA 57.329 42.857 9.73 0.00 0.00 1.52
1918 3681 2.120232 CGCTTATCTCACCTAGTTGCG 58.880 52.381 0.00 0.00 35.22 4.85
1922 3685 1.604755 CTCGCGCTTATCTCACCTAGT 59.395 52.381 5.56 0.00 0.00 2.57
2140 3904 4.562394 CGGTGCAGGTAATTAAAAATGCTG 59.438 41.667 11.45 0.00 34.80 4.41
2162 3926 4.093998 ACATCTTTCTTGCAGAATGTAGCG 59.906 41.667 9.79 0.00 39.31 4.26
2224 3989 2.293122 TCAAGCTTTGGCATGTGTACAC 59.707 45.455 19.36 19.36 41.70 2.90
2344 4109 7.406916 ACTTGAAAATTAAAACCCCAACCTTT 58.593 30.769 0.00 0.00 0.00 3.11
2374 4139 5.301551 TGCTTTGAAGAATTTCCAGCTGTAA 59.698 36.000 13.81 6.97 38.51 2.41
2448 4213 9.537192 CTAAATGTTCATTATGTCGTTACCCTA 57.463 33.333 0.00 0.00 0.00 3.53
2461 4226 6.162777 GCAAAGGGCAACTAAATGTTCATTA 58.837 36.000 0.00 0.00 43.97 1.90
2603 4368 3.733443 ACAATGAAGCCAGACAAAACC 57.267 42.857 0.00 0.00 0.00 3.27
2604 4369 5.108517 TGAAACAATGAAGCCAGACAAAAC 58.891 37.500 0.00 0.00 0.00 2.43
2741 4508 8.964476 AGGAGTGTATTATCACCACATTAAAG 57.036 34.615 0.00 0.00 38.91 1.85
2809 4584 3.308866 ACGACTTACAAACAGAAGCACAC 59.691 43.478 0.00 0.00 0.00 3.82
2863 4639 2.729028 GCCATACAGGAAGGGCTTAA 57.271 50.000 0.00 0.00 43.09 1.85
2877 4654 1.313772 AAACGTTGCACACAGCCATA 58.686 45.000 0.00 0.00 44.83 2.74
2908 4685 5.337491 GCCAAAAAGCCATCTTAATCAGGAA 60.337 40.000 0.00 0.00 31.02 3.36
2979 4756 1.331214 CCCTTTCCAAGCTTCTGCAA 58.669 50.000 0.00 0.00 42.74 4.08
2984 4761 2.232208 CCAATCACCCTTTCCAAGCTTC 59.768 50.000 0.00 0.00 0.00 3.86
3011 4788 6.100004 TGAGACCACAAAATTACGAGAGATC 58.900 40.000 0.00 0.00 0.00 2.75
3270 5082 1.460743 CTGTCCATGCAACACTACACG 59.539 52.381 0.00 0.00 0.00 4.49
3291 5103 0.304098 GCGAGATGAGAACTGCATGC 59.696 55.000 11.82 11.82 0.00 4.06
3298 5110 5.755375 TCCTAATGAAATGCGAGATGAGAAC 59.245 40.000 0.00 0.00 0.00 3.01
3350 5162 4.386049 CACAAGATACCGTTCAGTTCTGAC 59.614 45.833 1.72 0.00 0.00 3.51
3386 5198 4.048470 GGAAGGGGTGGCAGGTCC 62.048 72.222 0.00 0.00 0.00 4.46
3401 5213 3.519510 CCTCAGGTTCTTGATTACCAGGA 59.480 47.826 0.00 0.00 36.87 3.86
3434 5246 2.241176 TGGAGGTAATGGTGGGTGATTC 59.759 50.000 0.00 0.00 0.00 2.52
3680 5492 7.232127 ACATTGATTGGACTCTTTGAATGAACT 59.768 33.333 0.00 0.00 0.00 3.01
3728 5540 3.182152 GGGATCCCCTATGCTTAGCTTA 58.818 50.000 21.42 2.48 41.34 3.09
4031 5844 7.255569 ACATTAATGATTCTGTCAACATGCAG 58.744 34.615 22.16 0.00 40.97 4.41
4187 6000 3.399330 TCGGGACAAAATCTGAAGACAC 58.601 45.455 0.00 0.00 0.00 3.67
4206 6019 3.313526 CCAGCTCCAAATTTCCAGTATCG 59.686 47.826 0.00 0.00 0.00 2.92
4316 6129 4.141181 ACCATATAGACACATGCCAACCAT 60.141 41.667 0.00 0.00 33.39 3.55
4813 6638 9.888878 GGAAAAACATAGTACAGGACTTTAAAC 57.111 33.333 0.00 0.00 39.81 2.01
4814 6639 9.856162 AGGAAAAACATAGTACAGGACTTTAAA 57.144 29.630 0.00 0.00 39.81 1.52
4820 6645 5.472137 TGCAAGGAAAAACATAGTACAGGAC 59.528 40.000 0.00 0.00 0.00 3.85
4848 6673 6.657117 TCCGAACTTGAATGTATTTCCATCAA 59.343 34.615 0.00 0.00 33.04 2.57
4871 6696 0.741915 CCGAGCTCCTAGTGACTTCC 59.258 60.000 8.47 0.00 0.00 3.46
4878 6703 0.533308 CTACTCGCCGAGCTCCTAGT 60.533 60.000 15.20 8.90 32.04 2.57


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

AutoCloner maintained by Alex Coulton.