Multiple sequence alignment - TraesCS3A01G532000

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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 TraesCS3A01G532000 chr3A 100.000 3323 0 0 1 3323 744878055 744881377 0.000000e+00 6137.0
1 TraesCS3A01G532000 chr3A 80.758 686 74 32 1457 2140 750298761 750298132 1.790000e-132 483.0
2 TraesCS3A01G532000 chr3A 85.263 95 5 4 828 922 744941595 744941510 4.570000e-14 89.8
3 TraesCS3A01G532000 chr3A 85.263 95 5 4 828 922 745014522 745014437 4.570000e-14 89.8
4 TraesCS3A01G532000 chr3A 85.263 95 5 4 828 922 745081331 745081246 4.570000e-14 89.8
5 TraesCS3A01G532000 chr3A 85.263 95 5 4 828 922 745194533 745194448 4.570000e-14 89.8
6 TraesCS3A01G532000 chr3A 95.652 46 2 0 878 923 744792707 744792662 1.280000e-09 75.0
7 TraesCS3A01G532000 chr3D 93.413 2854 105 31 4 2808 610542582 610545401 0.000000e+00 4152.0
8 TraesCS3A01G532000 chr3D 77.650 1217 130 64 989 2140 613806607 613805468 7.880000e-171 610.0
9 TraesCS3A01G532000 chr3D 78.821 1001 136 40 1184 2164 610697546 610696602 3.670000e-169 604.0
10 TraesCS3A01G532000 chr3D 86.898 519 54 7 2806 3319 610545430 610545939 1.340000e-158 569.0
11 TraesCS3A01G532000 chr3D 77.193 684 127 18 1650 2331 610685057 610684401 4.050000e-99 372.0
12 TraesCS3A01G532000 chr3D 83.721 129 9 6 797 922 610629492 610629373 9.750000e-21 111.0
13 TraesCS3A01G532000 chr3D 86.000 100 8 2 823 922 610597833 610597740 5.870000e-18 102.0
14 TraesCS3A01G532000 chr3D 82.353 85 13 2 3206 3288 522191376 522191460 4.600000e-09 73.1
15 TraesCS3A01G532000 chr3B 92.389 2733 123 33 127 2808 828110100 828112798 0.000000e+00 3816.0
16 TraesCS3A01G532000 chr3B 77.645 1087 189 36 1263 2331 828254038 828252988 2.190000e-171 612.0
17 TraesCS3A01G532000 chr3B 87.938 514 51 5 2807 3319 828112828 828113331 2.210000e-166 595.0
18 TraesCS3A01G532000 chr3B 77.131 927 101 55 852 1700 823130598 823129705 5.090000e-118 435.0
19 TraesCS3A01G532000 chr3B 93.000 100 6 1 6 104 828110007 828110106 9.610000e-31 145.0
20 TraesCS3A01G532000 chr3B 90.217 92 9 0 986 1077 828256077 828255986 1.620000e-23 121.0
21 TraesCS3A01G532000 chr3B 85.149 101 9 3 829 923 827864139 827864239 7.590000e-17 99.0
22 TraesCS3A01G532000 chr1D 91.358 243 18 3 1457 1699 17169115 17168876 2.470000e-86 329.0
23 TraesCS3A01G532000 chr1A 91.358 243 18 3 1457 1699 18461769 18461530 2.470000e-86 329.0


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 TraesCS3A01G532000 chr3A 744878055 744881377 3322 False 6137.000000 6137 100.0000 1 3323 1 chr3A.!!$F1 3322
1 TraesCS3A01G532000 chr3A 750298132 750298761 629 True 483.000000 483 80.7580 1457 2140 1 chr3A.!!$R6 683
2 TraesCS3A01G532000 chr3D 610542582 610545939 3357 False 2360.500000 4152 90.1555 4 3319 2 chr3D.!!$F2 3315
3 TraesCS3A01G532000 chr3D 613805468 613806607 1139 True 610.000000 610 77.6500 989 2140 1 chr3D.!!$R5 1151
4 TraesCS3A01G532000 chr3D 610696602 610697546 944 True 604.000000 604 78.8210 1184 2164 1 chr3D.!!$R4 980
5 TraesCS3A01G532000 chr3D 610684401 610685057 656 True 372.000000 372 77.1930 1650 2331 1 chr3D.!!$R3 681
6 TraesCS3A01G532000 chr3B 828110007 828113331 3324 False 1518.666667 3816 91.1090 6 3319 3 chr3B.!!$F2 3313
7 TraesCS3A01G532000 chr3B 823129705 823130598 893 True 435.000000 435 77.1310 852 1700 1 chr3B.!!$R1 848
8 TraesCS3A01G532000 chr3B 828252988 828256077 3089 True 366.500000 612 83.9310 986 2331 2 chr3B.!!$R2 1345

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
737 754 1.302832 GTTGTGCTGCTACCTGGCT 60.303 57.895 0.00 0.0 0.00 4.75 F
1389 3249 0.258774 AAGGATTAATGGCCACGGCT 59.741 50.000 8.16 0.0 41.60 5.52 F
2172 4065 1.303309 GCGATGATGGAGGAAACCAG 58.697 55.000 0.00 0.0 43.49 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 4108 0.746923 TAATCCTGCTGCTGCTGCTG 60.747 55.0 27.67 25.97 40.48 4.41 R
2210 4109 0.747283 GTAATCCTGCTGCTGCTGCT 60.747 55.0 27.67 12.94 40.48 4.24 R
3023 4973 1.698506 ACCAGCCCACGAAATTGAAA 58.301 45.0 0.00 0.00 0.00 2.69 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 5.351740 GGTCTCTTTTTCCTTTAGGACATCG 59.648 44.000 0.00 0.00 45.39 3.84
43 44 4.478206 AGGACATCGACATCTCAACATT 57.522 40.909 0.00 0.00 0.00 2.71
62 63 6.775594 ACATTAAAATTGGACTAAGCTCCC 57.224 37.500 0.00 0.00 0.00 4.30
100 101 1.347050 TGGAACCGTGGGATTACGAAA 59.653 47.619 0.00 0.00 46.46 3.46
104 105 3.062122 ACCGTGGGATTACGAAAACAT 57.938 42.857 0.00 0.00 46.46 2.71
125 126 7.902920 ACATGGAAATAGGAAAGCACATAAT 57.097 32.000 0.00 0.00 0.00 1.28
180 181 4.582701 TTCATTGGAAGAAAACGCATGT 57.417 36.364 0.00 0.00 0.00 3.21
228 229 4.763793 ACTTCTCCATGAGATGTTGGTTTG 59.236 41.667 6.78 0.00 41.96 2.93
231 232 3.499338 TCCATGAGATGTTGGTTTGCTT 58.501 40.909 0.00 0.00 34.48 3.91
232 233 3.256383 TCCATGAGATGTTGGTTTGCTTG 59.744 43.478 0.00 0.00 34.48 4.01
234 235 4.482386 CATGAGATGTTGGTTTGCTTGAG 58.518 43.478 0.00 0.00 0.00 3.02
261 264 8.465273 ACTACTAGGAAAAATTTCAAAGCTGT 57.535 30.769 8.06 4.64 38.92 4.40
263 266 7.346751 ACTAGGAAAAATTTCAAAGCTGTGA 57.653 32.000 1.21 1.21 38.92 3.58
273 276 9.777575 AAATTTCAAAGCTGTGATTTTCTTTTG 57.222 25.926 7.60 0.00 0.00 2.44
290 293 6.978343 TCTTTTGGTGTAATCCAAGTATCG 57.022 37.500 0.00 0.00 46.27 2.92
299 302 7.709613 GGTGTAATCCAAGTATCGAAAGTGTAT 59.290 37.037 0.00 0.00 0.00 2.29
300 303 8.540492 GTGTAATCCAAGTATCGAAAGTGTATG 58.460 37.037 0.00 0.00 0.00 2.39
302 305 9.309516 GTAATCCAAGTATCGAAAGTGTATGAA 57.690 33.333 0.00 0.00 0.00 2.57
364 367 2.549778 CCACCATTGTTCCCGCAAAAAT 60.550 45.455 0.00 0.00 31.63 1.82
473 486 4.651778 TGGGCTGGTATTGACTATTATGC 58.348 43.478 0.00 0.00 0.00 3.14
496 509 4.438608 CGGCTGCAAATCAACTATAGCAAA 60.439 41.667 0.50 0.00 30.90 3.68
562 575 1.460504 CAACACTGCATCCATCAGCT 58.539 50.000 0.00 0.00 35.04 4.24
580 593 1.717032 CTAGGTAGCATGGGTAGCCA 58.283 55.000 17.55 17.55 35.04 4.75
655 668 6.275335 AGGAAAACAACAACAAGATGATGTG 58.725 36.000 0.00 0.00 36.57 3.21
737 754 1.302832 GTTGTGCTGCTACCTGGCT 60.303 57.895 0.00 0.00 0.00 4.75
980 998 3.333980 TCCTCTCCCAACAACTCTCTCTA 59.666 47.826 0.00 0.00 0.00 2.43
981 999 4.090090 CCTCTCCCAACAACTCTCTCTAA 58.910 47.826 0.00 0.00 0.00 2.10
1089 1145 2.763249 GCATCCTTGCGGTCAATTAG 57.237 50.000 0.00 0.00 39.49 1.73
1093 1149 2.432444 TCCTTGCGGTCAATTAGTTGG 58.568 47.619 0.00 0.00 35.99 3.77
1095 1151 2.095263 CCTTGCGGTCAATTAGTTGGTG 60.095 50.000 0.00 0.00 35.99 4.17
1389 3249 0.258774 AAGGATTAATGGCCACGGCT 59.741 50.000 8.16 0.00 41.60 5.52
1413 3282 1.536418 TGGAGGAGGTGGTGGTGAG 60.536 63.158 0.00 0.00 0.00 3.51
2172 4065 1.303309 GCGATGATGGAGGAAACCAG 58.697 55.000 0.00 0.00 43.49 4.00
2208 4107 1.602771 GGCCAAGAGGGACTACCAC 59.397 63.158 0.00 0.00 43.78 4.16
2209 4108 1.602771 GCCAAGAGGGACTACCACC 59.397 63.158 0.00 0.00 41.55 4.61
2210 4109 1.198759 GCCAAGAGGGACTACCACCA 61.199 60.000 0.00 0.00 41.55 4.17
2211 4110 0.905357 CCAAGAGGGACTACCACCAG 59.095 60.000 0.00 0.00 41.55 4.00
2212 4111 0.250513 CAAGAGGGACTACCACCAGC 59.749 60.000 0.00 0.00 41.55 4.85
2213 4112 0.178903 AAGAGGGACTACCACCAGCA 60.179 55.000 0.00 0.00 41.55 4.41
2355 4257 5.482908 TCTAGCTAGCTTTGTTCTTCCAAG 58.517 41.667 24.88 9.46 0.00 3.61
2384 4286 0.325860 ATGCATGGTGAAATGGGGCT 60.326 50.000 0.00 0.00 0.00 5.19
2410 4312 7.720957 TGGGGATGTATAAAATCTTCATCACTG 59.279 37.037 0.00 0.00 38.50 3.66
2502 4405 8.851145 TGCATACACAAGAATGTTAACCTTTTA 58.149 29.630 2.48 0.00 37.82 1.52
2547 4450 9.998106 ACTATGGCCTTAATTTGTAGTACTATG 57.002 33.333 5.75 0.00 0.00 2.23
2548 4451 9.998106 CTATGGCCTTAATTTGTAGTACTATGT 57.002 33.333 5.75 0.00 0.00 2.29
2588 4495 3.944055 AGCACCTAAGTGTAGTGTCTG 57.056 47.619 0.00 0.00 46.35 3.51
2589 4496 3.231818 AGCACCTAAGTGTAGTGTCTGT 58.768 45.455 0.00 0.00 46.35 3.41
2590 4497 3.641906 AGCACCTAAGTGTAGTGTCTGTT 59.358 43.478 0.00 0.00 46.35 3.16
2591 4498 4.831155 AGCACCTAAGTGTAGTGTCTGTTA 59.169 41.667 0.00 0.00 46.35 2.41
2592 4499 5.047943 AGCACCTAAGTGTAGTGTCTGTTAG 60.048 44.000 0.00 0.00 46.35 2.34
2593 4500 5.278858 GCACCTAAGTGTAGTGTCTGTTAGT 60.279 44.000 0.00 0.00 46.35 2.24
2594 4501 6.072286 GCACCTAAGTGTAGTGTCTGTTAGTA 60.072 42.308 0.00 0.00 46.35 1.82
2595 4502 7.528307 CACCTAAGTGTAGTGTCTGTTAGTAG 58.472 42.308 0.00 0.00 39.30 2.57
2600 4507 4.946157 GTGTAGTGTCTGTTAGTAGCCCTA 59.054 45.833 0.00 0.00 0.00 3.53
2615 4522 2.374504 AGCCCTACATATGCATGCTCTT 59.625 45.455 20.33 6.43 35.39 2.85
2644 4551 8.966868 GGATCTTTCCCATTGAGTTTTATTACA 58.033 33.333 0.00 0.00 35.84 2.41
2690 4597 4.595986 GGTATGTACCAATGTCCCACTTT 58.404 43.478 4.34 0.00 45.73 2.66
2695 4602 5.636123 TGTACCAATGTCCCACTTTTACAT 58.364 37.500 0.00 0.00 35.40 2.29
2710 4617 7.867403 CCACTTTTACATTGTGCTAGTTTCATT 59.133 33.333 0.00 0.00 0.00 2.57
2753 4660 5.923733 ATCAGGTTCGTCTCTTTGTATCT 57.076 39.130 0.00 0.00 0.00 1.98
2783 4700 4.136517 TCGCGTGAAGGTTTTTCATAAC 57.863 40.909 5.77 0.00 0.00 1.89
2805 4722 2.930682 GGTTTTACTGAGTCTCGGATGC 59.069 50.000 15.88 1.25 0.00 3.91
2812 4761 1.474478 TGAGTCTCGGATGCTGAGAAC 59.526 52.381 7.49 6.25 45.88 3.01
2838 4787 4.114794 CAATATGACTGTGAGATGCGTGA 58.885 43.478 0.00 0.00 0.00 4.35
2839 4788 2.290531 ATGACTGTGAGATGCGTGAG 57.709 50.000 0.00 0.00 0.00 3.51
2843 4792 3.257393 GACTGTGAGATGCGTGAGAAAT 58.743 45.455 0.00 0.00 0.00 2.17
2849 4798 5.106712 TGTGAGATGCGTGAGAAATTTAACC 60.107 40.000 0.00 0.00 0.00 2.85
2910 4860 8.621532 TTTCTGCACTAGATGAACAAAATACT 57.378 30.769 0.00 0.00 34.80 2.12
2916 4866 7.898309 GCACTAGATGAACAAAATACTACAACG 59.102 37.037 0.00 0.00 0.00 4.10
2919 4869 7.197071 AGATGAACAAAATACTACAACGCAA 57.803 32.000 0.00 0.00 0.00 4.85
2927 4877 8.175069 ACAAAATACTACAACGCAATGACTATG 58.825 33.333 0.00 0.00 0.00 2.23
2967 4917 8.833231 TGAACAATTTTGTAAAACAGGTTGAA 57.167 26.923 0.00 0.00 41.31 2.69
2984 4934 8.624776 ACAGGTTGAAACTTAAGAAAATCTCAG 58.375 33.333 10.09 0.00 0.00 3.35
2998 4948 5.661056 AAATCTCAGTTGACTATCGACCA 57.339 39.130 0.00 0.00 31.00 4.02
3012 4962 3.692791 TCGACCATCGTCTTAGATGTG 57.307 47.619 1.05 0.17 44.76 3.21
3019 4969 3.247006 TCGTCTTAGATGTGGCCTTTC 57.753 47.619 3.32 0.00 0.00 2.62
3040 4990 2.995258 CCATTTTCAATTTCGTGGGCTG 59.005 45.455 0.00 0.00 0.00 4.85
3077 5027 4.942761 AAGTTGTACTCCGTTAAGGTGA 57.057 40.909 0.00 0.00 41.99 4.02
3146 5096 9.618890 ACTTATGTATTCAGTCATGCAAGTTAT 57.381 29.630 0.00 0.00 0.00 1.89
3150 5100 7.977904 TGTATTCAGTCATGCAAGTTATTCTG 58.022 34.615 0.00 0.00 0.00 3.02
3160 5110 6.185852 TGCAAGTTATTCTGATGTGTCATG 57.814 37.500 0.00 0.00 32.98 3.07
3161 5111 5.706833 TGCAAGTTATTCTGATGTGTCATGT 59.293 36.000 0.00 0.00 32.98 3.21
3162 5112 6.128200 TGCAAGTTATTCTGATGTGTCATGTC 60.128 38.462 0.00 0.00 32.98 3.06
3178 5128 4.629634 GTCATGTCGTTGTTGGATGTATCA 59.370 41.667 0.00 0.00 0.00 2.15
3235 5185 8.164070 TCTTTAAATTTAGAGGAGGATATGGCC 58.836 37.037 14.03 0.00 0.00 5.36
3253 5207 2.433239 GGCCGAGTATCCTTTAGTGGAA 59.567 50.000 0.00 0.00 39.85 3.53
3254 5208 3.492829 GGCCGAGTATCCTTTAGTGGAAG 60.493 52.174 0.00 0.00 39.85 3.46
3279 5233 3.492102 TTGCTCCTCTAAACAAGTGCT 57.508 42.857 0.00 0.00 0.00 4.40
3280 5234 4.617253 TTGCTCCTCTAAACAAGTGCTA 57.383 40.909 0.00 0.00 0.00 3.49
3282 5236 4.759782 TGCTCCTCTAAACAAGTGCTATC 58.240 43.478 0.00 0.00 0.00 2.08
3289 5243 7.616150 TCCTCTAAACAAGTGCTATCTCTAACT 59.384 37.037 0.00 0.00 0.00 2.24
3290 5244 7.704472 CCTCTAAACAAGTGCTATCTCTAACTG 59.296 40.741 0.00 0.00 0.00 3.16
3298 5252 7.744087 AGTGCTATCTCTAACTGATCTACTG 57.256 40.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.124617 CCTAAAGGAAAAAGAGACCATGCTC 59.875 44.000 0.00 0.00 37.39 4.26
1 2 5.012893 CCTAAAGGAAAAAGAGACCATGCT 58.987 41.667 0.00 0.00 37.39 3.79
43 44 5.249780 TGTGGGAGCTTAGTCCAATTTTA 57.750 39.130 0.00 0.00 38.52 1.52
62 63 2.644299 TCCATGGAGGCCCTATAATGTG 59.356 50.000 11.44 0.00 37.29 3.21
100 101 7.716799 TTATGTGCTTTCCTATTTCCATGTT 57.283 32.000 0.00 0.00 0.00 2.71
131 132 8.991026 CAACCATTTAATCTCAAAATTCTTGCA 58.009 29.630 0.00 0.00 0.00 4.08
132 133 7.959109 GCAACCATTTAATCTCAAAATTCTTGC 59.041 33.333 0.00 0.00 33.45 4.01
135 136 9.428097 GAAGCAACCATTTAATCTCAAAATTCT 57.572 29.630 0.00 0.00 0.00 2.40
154 155 3.182372 GCGTTTTCTTCCAATGAAGCAAC 59.818 43.478 0.00 3.28 46.28 4.17
175 176 5.292345 TCAATTTTGAATGCAGCATACATGC 59.708 36.000 8.75 6.06 43.30 4.06
180 181 6.689554 TCACTTCAATTTTGAATGCAGCATA 58.310 32.000 8.75 0.00 45.26 3.14
184 185 7.473027 AAGTTCACTTCAATTTTGAATGCAG 57.527 32.000 6.21 0.00 45.26 4.41
228 229 8.784043 TGAAATTTTTCCTAGTAGTTCTCAAGC 58.216 33.333 0.00 0.00 36.36 4.01
232 233 9.613957 GCTTTGAAATTTTTCCTAGTAGTTCTC 57.386 33.333 0.00 0.00 36.36 2.87
234 235 9.399403 CAGCTTTGAAATTTTTCCTAGTAGTTC 57.601 33.333 0.00 0.00 36.36 3.01
273 276 5.873164 ACACTTTCGATACTTGGATTACACC 59.127 40.000 0.00 0.00 0.00 4.16
318 321 3.957497 TGCAGTCCTAAGCCAAAGAAAAA 59.043 39.130 0.00 0.00 0.00 1.94
319 322 3.561143 TGCAGTCCTAAGCCAAAGAAAA 58.439 40.909 0.00 0.00 0.00 2.29
320 323 3.222173 TGCAGTCCTAAGCCAAAGAAA 57.778 42.857 0.00 0.00 0.00 2.52
327 330 1.383523 GTGGATTGCAGTCCTAAGCC 58.616 55.000 26.57 5.46 39.12 4.35
379 384 3.714798 AGACTCCAAGTTCAACCAACCTA 59.285 43.478 0.00 0.00 35.28 3.08
387 392 5.496556 TCACTTTTGAGACTCCAAGTTCAA 58.503 37.500 12.41 2.50 0.00 2.69
436 449 9.520515 AATACCAGCCCATAGAGTTAAATAATG 57.479 33.333 0.00 0.00 0.00 1.90
439 452 8.154856 GTCAATACCAGCCCATAGAGTTAAATA 58.845 37.037 0.00 0.00 0.00 1.40
473 486 2.613595 TGCTATAGTTGATTTGCAGCCG 59.386 45.455 0.84 0.00 0.00 5.52
562 575 3.959387 TGGCTACCCATGCTACCTA 57.041 52.632 0.00 0.00 35.79 3.08
580 593 0.987081 AGTGCTGATGGGGCTGAGAT 60.987 55.000 0.00 0.00 0.00 2.75
655 668 0.105778 CGATTTGGAGGAGGGAGAGC 59.894 60.000 0.00 0.00 0.00 4.09
737 754 5.015178 AGAGGAGAGAGAAAAAGGAGAGAGA 59.985 44.000 0.00 0.00 0.00 3.10
980 998 0.179081 GGCCGGCGATCTAGACTTTT 60.179 55.000 22.54 0.00 0.00 2.27
981 999 1.327690 TGGCCGGCGATCTAGACTTT 61.328 55.000 22.54 0.00 0.00 2.66
1089 1145 5.743872 GTGAACAAAATCTTGAGACACCAAC 59.256 40.000 0.00 0.00 36.33 3.77
1093 1149 5.879237 TGTGTGAACAAAATCTTGAGACAC 58.121 37.500 0.00 0.00 38.49 3.67
1095 1151 6.785191 TCTTGTGTGAACAAAATCTTGAGAC 58.215 36.000 0.00 0.00 36.33 3.36
1128 1824 7.723616 AGCTTAGCTAGAACATATTCTCTCTCA 59.276 37.037 4.30 0.00 41.63 3.27
1285 3139 6.150641 GGAGTAGTAGTGACATGAGTGTTACA 59.849 42.308 0.00 0.00 44.70 2.41
1858 3748 2.106332 CGCCGGGTCGAAGCTATT 59.894 61.111 2.18 0.00 0.00 1.73
1947 3837 4.960866 TGGTGGTGCTGCTGCTGG 62.961 66.667 17.00 0.00 40.48 4.85
1956 3846 4.974721 CCCTGGTGGTGGTGGTGC 62.975 72.222 0.00 0.00 0.00 5.01
1962 3852 4.344865 CCGTTCCCCTGGTGGTGG 62.345 72.222 0.00 0.00 0.00 4.61
2076 3966 1.546589 CCATTGTGGTGGGCATTGCT 61.547 55.000 8.82 0.00 35.55 3.91
2172 4065 3.758931 GGCGGGTGGTGGAATTGC 61.759 66.667 0.00 0.00 0.00 3.56
2208 4107 3.997400 ATCCTGCTGCTGCTGCTGG 62.997 63.158 35.27 35.27 44.29 4.85
2209 4108 0.746923 TAATCCTGCTGCTGCTGCTG 60.747 55.000 27.67 25.97 40.48 4.41
2210 4109 0.747283 GTAATCCTGCTGCTGCTGCT 60.747 55.000 27.67 12.94 40.48 4.24
2211 4110 1.722636 GGTAATCCTGCTGCTGCTGC 61.723 60.000 22.51 22.51 40.48 5.25
2212 4111 1.099879 GGGTAATCCTGCTGCTGCTG 61.100 60.000 17.00 15.58 40.48 4.41
2213 4112 1.225704 GGGTAATCCTGCTGCTGCT 59.774 57.895 17.00 0.00 40.48 4.24
2351 4253 2.557056 CCATGCATCAATCTAGGCTTGG 59.443 50.000 0.00 0.00 42.54 3.61
2355 4257 2.854963 TCACCATGCATCAATCTAGGC 58.145 47.619 0.00 0.00 0.00 3.93
2384 4286 7.720957 CAGTGATGAAGATTTTATACATCCCCA 59.279 37.037 0.00 0.00 37.23 4.96
2410 4312 6.403333 TCGAGTTCTTGTAACACATATTGC 57.597 37.500 0.00 0.00 0.00 3.56
2572 4479 6.404513 GGCTACTAACAGACACTACACTTAGG 60.405 46.154 0.00 0.00 0.00 2.69
2586 4493 5.468540 TGCATATGTAGGGCTACTAACAG 57.531 43.478 4.29 0.00 37.00 3.16
2588 4495 4.631813 GCATGCATATGTAGGGCTACTAAC 59.368 45.833 14.21 0.00 36.65 2.34
2589 4496 4.532126 AGCATGCATATGTAGGGCTACTAA 59.468 41.667 21.98 0.00 36.65 2.24
2590 4497 4.096681 AGCATGCATATGTAGGGCTACTA 58.903 43.478 21.98 0.00 36.65 1.82
2591 4498 2.909006 AGCATGCATATGTAGGGCTACT 59.091 45.455 21.98 0.42 36.65 2.57
2592 4499 3.055530 AGAGCATGCATATGTAGGGCTAC 60.056 47.826 21.98 13.27 36.65 3.58
2593 4500 3.176411 AGAGCATGCATATGTAGGGCTA 58.824 45.455 21.98 0.00 36.65 3.93
2594 4501 1.983691 AGAGCATGCATATGTAGGGCT 59.016 47.619 21.98 18.31 36.65 5.19
2595 4502 2.486472 AGAGCATGCATATGTAGGGC 57.514 50.000 21.98 9.40 36.65 5.19
2600 4507 3.301794 TCCCAAAGAGCATGCATATGT 57.698 42.857 21.98 0.00 36.65 2.29
2644 4551 9.683870 ACCCACAAATTAAATGCATGATAAAAT 57.316 25.926 0.00 0.00 0.00 1.82
2649 4556 7.794041 ACATACCCACAAATTAAATGCATGAT 58.206 30.769 0.00 0.00 0.00 2.45
2650 4557 7.180322 ACATACCCACAAATTAAATGCATGA 57.820 32.000 0.00 0.00 0.00 3.07
2651 4558 7.437862 GGTACATACCCACAAATTAAATGCATG 59.562 37.037 0.00 0.00 40.53 4.06
2652 4559 7.124901 TGGTACATACCCACAAATTAAATGCAT 59.875 33.333 5.62 0.00 45.87 3.96
2653 4560 6.437477 TGGTACATACCCACAAATTAAATGCA 59.563 34.615 5.62 0.00 45.87 3.96
2654 4561 6.868622 TGGTACATACCCACAAATTAAATGC 58.131 36.000 5.62 0.00 45.87 3.56
2655 4562 9.311916 CATTGGTACATACCCACAAATTAAATG 57.688 33.333 5.62 2.51 45.87 2.32
2656 4563 9.041354 ACATTGGTACATACCCACAAATTAAAT 57.959 29.630 5.62 0.00 45.87 1.40
2657 4564 8.423906 ACATTGGTACATACCCACAAATTAAA 57.576 30.769 5.62 0.00 45.87 1.52
2733 4640 5.060662 TCAGATACAAAGAGACGAACCTG 57.939 43.478 0.00 0.00 0.00 4.00
2734 4641 5.654650 AGATCAGATACAAAGAGACGAACCT 59.345 40.000 0.00 0.00 0.00 3.50
2735 4642 5.897050 AGATCAGATACAAAGAGACGAACC 58.103 41.667 0.00 0.00 0.00 3.62
2736 4643 7.699566 AGTAGATCAGATACAAAGAGACGAAC 58.300 38.462 0.00 0.00 0.00 3.95
2737 4644 7.867305 AGTAGATCAGATACAAAGAGACGAA 57.133 36.000 0.00 0.00 0.00 3.85
2738 4645 7.254488 CGAAGTAGATCAGATACAAAGAGACGA 60.254 40.741 0.00 0.00 0.00 4.20
2739 4646 6.848800 CGAAGTAGATCAGATACAAAGAGACG 59.151 42.308 0.00 0.00 0.00 4.18
2740 4647 6.635239 GCGAAGTAGATCAGATACAAAGAGAC 59.365 42.308 0.00 0.00 0.00 3.36
2753 4660 1.816835 ACCTTCACGCGAAGTAGATCA 59.183 47.619 15.93 0.00 46.19 2.92
2783 4700 3.179830 CATCCGAGACTCAGTAAAACCG 58.820 50.000 2.82 0.00 0.00 4.44
2886 4836 9.151471 GTAGTATTTTGTTCATCTAGTGCAGAA 57.849 33.333 0.00 0.00 36.67 3.02
2887 4837 8.311109 TGTAGTATTTTGTTCATCTAGTGCAGA 58.689 33.333 0.00 0.00 37.79 4.26
2888 4838 8.479313 TGTAGTATTTTGTTCATCTAGTGCAG 57.521 34.615 0.00 0.00 0.00 4.41
2889 4839 8.717821 GTTGTAGTATTTTGTTCATCTAGTGCA 58.282 33.333 0.00 0.00 0.00 4.57
2907 4857 6.627243 AGAACATAGTCATTGCGTTGTAGTA 58.373 36.000 0.00 0.00 0.00 1.82
2908 4858 5.479306 AGAACATAGTCATTGCGTTGTAGT 58.521 37.500 0.00 0.00 0.00 2.73
2910 4860 7.892778 TTAAGAACATAGTCATTGCGTTGTA 57.107 32.000 0.00 0.00 0.00 2.41
2998 4948 3.432326 GGAAAGGCCACATCTAAGACGAT 60.432 47.826 5.01 0.00 36.34 3.73
3012 4962 4.152223 CACGAAATTGAAAATGGAAAGGCC 59.848 41.667 0.00 0.00 37.10 5.19
3019 4969 2.995258 CAGCCCACGAAATTGAAAATGG 59.005 45.455 0.00 0.00 0.00 3.16
3023 4973 1.698506 ACCAGCCCACGAAATTGAAA 58.301 45.000 0.00 0.00 0.00 2.69
3032 4982 2.027460 GCAACAAACCAGCCCACG 59.973 61.111 0.00 0.00 0.00 4.94
3040 4990 5.544136 ACAACTTTTGATTGCAACAAACC 57.456 34.783 19.81 3.23 37.05 3.27
3077 5027 6.258507 GCATTTTCAGACAAAACAATGAACCT 59.741 34.615 0.00 0.00 31.72 3.50
3119 5069 7.312657 ACTTGCATGACTGAATACATAAGTG 57.687 36.000 6.60 0.00 29.74 3.16
3135 5085 6.185852 TGACACATCAGAATAACTTGCATG 57.814 37.500 0.00 0.00 0.00 4.06
3137 5087 5.706833 ACATGACACATCAGAATAACTTGCA 59.293 36.000 0.00 0.00 38.57 4.08
3140 5090 6.166279 ACGACATGACACATCAGAATAACTT 58.834 36.000 0.00 0.00 38.57 2.66
3146 5096 3.727726 ACAACGACATGACACATCAGAA 58.272 40.909 0.00 0.00 38.57 3.02
3150 5100 2.805671 TCCAACAACGACATGACACATC 59.194 45.455 0.00 0.00 0.00 3.06
3160 5110 6.844696 ATACATGATACATCCAACAACGAC 57.155 37.500 0.00 0.00 0.00 4.34
3161 5111 7.117667 GCATATACATGATACATCCAACAACGA 59.882 37.037 0.00 0.00 33.67 3.85
3162 5112 7.118245 AGCATATACATGATACATCCAACAACG 59.882 37.037 0.00 0.00 33.67 4.10
3211 5161 6.940298 CGGCCATATCCTCCTCTAAATTTAAA 59.060 38.462 2.24 0.00 0.00 1.52
3213 5163 5.783360 TCGGCCATATCCTCCTCTAAATTTA 59.217 40.000 2.24 0.00 0.00 1.40
3221 5171 2.217510 TACTCGGCCATATCCTCCTC 57.782 55.000 2.24 0.00 0.00 3.71
3253 5207 6.317391 GCACTTGTTTAGAGGAGCAAATATCT 59.683 38.462 0.00 0.00 0.00 1.98
3254 5208 6.317391 AGCACTTGTTTAGAGGAGCAAATATC 59.683 38.462 0.00 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.