Multiple sequence alignment - TraesCS3D01G333500

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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 TraesCS3D01G333500 chr3D 100.000 4601 0 0 1 4601 445626122 445630722 0.000000e+00 8497.0
1 TraesCS3D01G333500 chr3D 100.000 2147 0 0 4964 7110 445631085 445633231 0.000000e+00 3965.0
2 TraesCS3D01G333500 chr3D 97.222 72 1 1 6373 6444 22679079 22679149 3.480000e-23 121.0
3 TraesCS3D01G333500 chr3D 97.222 72 1 1 6373 6444 22767879 22767809 3.480000e-23 121.0
4 TraesCS3D01G333500 chr3D 98.507 67 1 0 6373 6439 436676919 436676985 1.250000e-22 119.0
5 TraesCS3D01G333500 chr3B 95.937 4529 140 19 63 4558 584538914 584543431 0.000000e+00 7304.0
6 TraesCS3D01G333500 chr3B 97.233 2132 47 7 4983 7110 584543694 584545817 0.000000e+00 3600.0
7 TraesCS3D01G333500 chr3A 97.961 2158 28 4 4966 7110 587400484 587402638 0.000000e+00 3727.0
8 TraesCS3D01G333500 chr3A 91.192 2509 157 18 608 3088 587396299 587398771 0.000000e+00 3350.0
9 TraesCS3D01G333500 chr3A 94.007 1435 59 15 3181 4601 587398768 587400189 0.000000e+00 2148.0
10 TraesCS3D01G333500 chr3A 89.071 549 58 1 63 609 587395647 587396195 0.000000e+00 680.0
11 TraesCS3D01G333500 chr3A 89.231 65 6 1 4436 4500 346425573 346425636 5.910000e-11 80.5
12 TraesCS3D01G333500 chr3A 100.000 29 0 0 5658 5686 26149356 26149328 4.000000e-03 54.7
13 TraesCS3D01G333500 chr2A 94.667 75 4 0 6373 6447 202840541 202840615 4.510000e-22 117.0
14 TraesCS3D01G333500 chr7D 97.015 67 2 0 6373 6439 95129455 95129521 5.830000e-21 113.0
15 TraesCS3D01G333500 chr4A 91.566 83 5 2 6373 6455 379041013 379040933 5.830000e-21 113.0
16 TraesCS3D01G333500 chr5D 91.463 82 4 1 6361 6439 290384303 290384384 7.540000e-20 110.0
17 TraesCS3D01G333500 chr6D 96.875 32 1 0 5655 5686 29771779 29771810 4.000000e-03 54.7
18 TraesCS3D01G333500 chr6A 100.000 29 0 0 5658 5686 32898019 32897991 4.000000e-03 54.7


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 TraesCS3D01G333500 chr3D 445626122 445633231 7109 False 6231.00 8497 100.00000 1 7110 2 chr3D.!!$F3 7109
1 TraesCS3D01G333500 chr3B 584538914 584545817 6903 False 5452.00 7304 96.58500 63 7110 2 chr3B.!!$F1 7047
2 TraesCS3D01G333500 chr3A 587395647 587402638 6991 False 2476.25 3727 93.05775 63 7110 4 chr3A.!!$F2 7047

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
799 909 0.108615 CCCGCCAGTACAACTCAGAG 60.109 60.000 0.0 0.0 0.00 3.35 F
2087 2206 0.482446 ACAGGCCCAATGGACAGAAA 59.518 50.000 0.0 0.0 45.14 2.52 F
3639 3799 1.037579 GGTGCTATTTCCTGCCCCAC 61.038 60.000 0.0 0.0 0.00 4.61 F
3750 3910 0.321653 GACATGACAAGCCCCGAGTT 60.322 55.000 0.0 0.0 0.00 3.01 F
5503 5666 2.028130 ACGCAAAAGGGACATGTTTCA 58.972 42.857 0.0 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2215 3.527533 TGTACGAGGTTCATATTGGCAC 58.472 45.455 0.00 0.0 0.00 5.01 R
3676 3836 1.378762 GAAGGGGGTAGTGCAAGCA 59.621 57.895 0.00 0.0 0.00 3.91 R
5470 5633 2.882927 TTTGCGTGTCAGACACTAGT 57.117 45.000 27.42 0.0 46.46 2.57 R
5740 5903 2.105128 GCGGTCCTGATCTCACGG 59.895 66.667 0.00 0.0 0.00 4.94 R
6934 7113 4.886489 ACGTAGGGACTAGAGTTATTGACC 59.114 45.833 0.00 0.0 44.14 4.02 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
40 41 5.130292 CAATGCCTGCTAATAATTCCCTG 57.870 43.478 0.00 0.00 0.00 4.45
41 42 4.729552 ATGCCTGCTAATAATTCCCTGA 57.270 40.909 0.00 0.00 0.00 3.86
42 43 4.518278 TGCCTGCTAATAATTCCCTGAA 57.482 40.909 0.00 0.00 0.00 3.02
43 44 4.464008 TGCCTGCTAATAATTCCCTGAAG 58.536 43.478 0.00 0.00 0.00 3.02
44 45 3.254411 GCCTGCTAATAATTCCCTGAAGC 59.746 47.826 0.00 0.00 0.00 3.86
45 46 4.464008 CCTGCTAATAATTCCCTGAAGCA 58.536 43.478 0.00 0.00 37.03 3.91
46 47 4.889409 CCTGCTAATAATTCCCTGAAGCAA 59.111 41.667 0.00 0.00 37.97 3.91
47 48 5.009410 CCTGCTAATAATTCCCTGAAGCAAG 59.991 44.000 0.00 0.00 37.97 4.01
48 49 4.339247 TGCTAATAATTCCCTGAAGCAAGC 59.661 41.667 0.00 0.00 35.70 4.01
49 50 4.582240 GCTAATAATTCCCTGAAGCAAGCT 59.418 41.667 0.00 0.00 0.00 3.74
50 51 5.068329 GCTAATAATTCCCTGAAGCAAGCTT 59.932 40.000 7.07 7.07 39.23 3.74
51 52 6.406288 GCTAATAATTCCCTGAAGCAAGCTTT 60.406 38.462 8.91 0.00 36.26 3.51
52 53 6.364568 AATAATTCCCTGAAGCAAGCTTTT 57.635 33.333 8.91 0.25 36.26 2.27
53 54 4.694760 AATTCCCTGAAGCAAGCTTTTT 57.305 36.364 8.91 0.00 36.26 1.94
107 108 6.586344 TGGTTTTATTTGAATGGCTGTTTGA 58.414 32.000 0.00 0.00 0.00 2.69
134 135 4.394729 CCTGGCTTTGTTACTAACCTCAA 58.605 43.478 0.00 0.00 0.00 3.02
173 174 1.249407 GGTACCTGATAGCTCCTCCG 58.751 60.000 4.06 0.00 0.00 4.63
174 175 0.599060 GTACCTGATAGCTCCTCCGC 59.401 60.000 0.00 0.00 0.00 5.54
175 176 0.185175 TACCTGATAGCTCCTCCGCA 59.815 55.000 0.00 0.00 0.00 5.69
178 179 1.071385 CCTGATAGCTCCTCCGCAAAT 59.929 52.381 0.00 0.00 0.00 2.32
202 203 3.152951 GCCAATTGGGTAGGCTTTTCCT 61.153 50.000 25.73 0.00 44.92 3.36
220 221 5.414789 TTCCTACAAGAACATCCATCGAA 57.585 39.130 0.00 0.00 0.00 3.71
222 223 5.175859 TCCTACAAGAACATCCATCGAAAC 58.824 41.667 0.00 0.00 0.00 2.78
225 226 3.189287 ACAAGAACATCCATCGAAACTGC 59.811 43.478 0.00 0.00 0.00 4.40
240 241 1.299541 ACTGCTTCTGGTTTGACGTG 58.700 50.000 0.00 0.00 0.00 4.49
242 243 2.146342 CTGCTTCTGGTTTGACGTGAT 58.854 47.619 0.00 0.00 0.00 3.06
263 264 1.491274 TTGATCTGCTGTGGAGGCCA 61.491 55.000 5.01 0.00 0.00 5.36
265 266 2.605854 GATCTGCTGTGGAGGCCAGG 62.606 65.000 5.01 0.00 32.34 4.45
268 269 3.640407 GCTGTGGAGGCCAGGACA 61.640 66.667 5.01 2.70 32.34 4.02
269 270 3.160585 CTGTGGAGGCCAGGACAA 58.839 61.111 5.01 0.00 32.34 3.18
276 277 4.643387 GGCCAGGACAACACGGCT 62.643 66.667 0.00 0.00 44.27 5.52
280 281 1.069765 CAGGACAACACGGCTGAGT 59.930 57.895 0.00 0.00 0.00 3.41
282 283 1.961277 GGACAACACGGCTGAGTGG 60.961 63.158 0.00 0.00 45.80 4.00
283 284 2.591715 ACAACACGGCTGAGTGGC 60.592 61.111 0.00 0.00 45.80 5.01
342 343 1.447489 CTTCAGTCAGGCTCCAGCG 60.447 63.158 0.00 0.00 43.26 5.18
382 385 3.058432 GGTAAGCCAGTCCTTCGTTTTTC 60.058 47.826 0.00 0.00 34.09 2.29
412 416 5.715279 GGGTTAATAGGAAGAAAGTTGCCTT 59.285 40.000 0.00 0.00 32.04 4.35
418 422 5.268118 AGGAAGAAAGTTGCCTTCTTTTG 57.732 39.130 14.29 0.00 38.92 2.44
421 425 4.926140 AGAAAGTTGCCTTCTTTTGAGG 57.074 40.909 0.00 0.00 35.62 3.86
423 427 5.143369 AGAAAGTTGCCTTCTTTTGAGGAT 58.857 37.500 0.00 0.00 35.62 3.24
428 432 5.707764 AGTTGCCTTCTTTTGAGGATAAGTC 59.292 40.000 0.00 0.00 0.00 3.01
435 439 2.961526 TTGAGGATAAGTCGCTCACC 57.038 50.000 0.00 0.00 33.94 4.02
560 565 8.557592 AAATATCAGCATCATGGTAGTATGTG 57.442 34.615 0.00 0.00 0.00 3.21
577 582 7.078249 AGTATGTGGCATCAAGATTATGGTA 57.922 36.000 0.00 0.00 0.00 3.25
578 583 7.517320 AGTATGTGGCATCAAGATTATGGTAA 58.483 34.615 0.00 0.00 0.00 2.85
579 584 7.998383 AGTATGTGGCATCAAGATTATGGTAAA 59.002 33.333 0.00 0.00 0.00 2.01
581 586 6.186957 TGTGGCATCAAGATTATGGTAAAGT 58.813 36.000 0.00 0.00 0.00 2.66
585 590 8.592809 TGGCATCAAGATTATGGTAAAGTTTTT 58.407 29.630 0.00 0.00 0.00 1.94
598 603 6.039493 TGGTAAAGTTTTTCAATTCGGTAGCA 59.961 34.615 0.00 0.00 0.00 3.49
602 607 8.742554 AAAGTTTTTCAATTCGGTAGCATTAG 57.257 30.769 0.00 0.00 0.00 1.73
604 609 7.305474 AGTTTTTCAATTCGGTAGCATTAGTG 58.695 34.615 0.00 0.00 0.00 2.74
609 719 6.408035 TCAATTCGGTAGCATTAGTGGTTAA 58.592 36.000 0.00 0.00 37.28 2.01
612 722 6.528537 TTCGGTAGCATTAGTGGTTAACTA 57.471 37.500 5.42 0.00 40.56 2.24
620 730 6.771267 AGCATTAGTGGTTAACTATTAAGCCC 59.229 38.462 11.54 4.27 41.10 5.19
624 734 8.570068 TTAGTGGTTAACTATTAAGCCCTTTG 57.430 34.615 5.42 0.00 41.10 2.77
626 736 7.692172 AGTGGTTAACTATTAAGCCCTTTGTA 58.308 34.615 5.42 0.00 41.61 2.41
630 740 9.404848 GGTTAACTATTAAGCCCTTTGTAATCT 57.595 33.333 5.42 0.00 37.59 2.40
744 854 7.445945 GTGCTAATGTATGGAGAAATAGGTCT 58.554 38.462 0.00 0.00 0.00 3.85
747 857 7.816995 GCTAATGTATGGAGAAATAGGTCTCAG 59.183 40.741 4.71 0.00 45.03 3.35
758 868 7.569240 AGAAATAGGTCTCAGGATAAAAGGTG 58.431 38.462 0.00 0.00 0.00 4.00
768 878 7.228706 TCTCAGGATAAAAGGTGAAACTGAAAC 59.771 37.037 0.00 0.00 36.74 2.78
772 882 9.362151 AGGATAAAAGGTGAAACTGAAACAATA 57.638 29.630 0.00 0.00 36.74 1.90
795 905 1.066430 TCATTCCCGCCAGTACAACTC 60.066 52.381 0.00 0.00 0.00 3.01
799 909 0.108615 CCCGCCAGTACAACTCAGAG 60.109 60.000 0.00 0.00 0.00 3.35
857 967 9.549078 CTTATCTTGCATGCTCTATGATGATAT 57.451 33.333 20.33 0.00 39.21 1.63
869 979 8.819015 GCTCTATGATGATATTTGCATCTACTG 58.181 37.037 0.00 0.00 42.00 2.74
890 1000 7.932120 ACTGTCATACGATTAAGATTAGTGC 57.068 36.000 0.00 0.00 0.00 4.40
920 1030 9.948747 ATATGATCCATGATAGGAGTGAGATTA 57.051 33.333 0.00 0.00 41.90 1.75
947 1057 9.582648 AATTACTGGAGTTGTTGGTATTAAAGT 57.417 29.630 0.00 0.00 0.00 2.66
948 1058 6.877611 ACTGGAGTTGTTGGTATTAAAGTG 57.122 37.500 0.00 0.00 0.00 3.16
949 1059 6.362248 ACTGGAGTTGTTGGTATTAAAGTGT 58.638 36.000 0.00 0.00 0.00 3.55
1023 1133 2.214376 AGAATTGGCGGAATCAACCA 57.786 45.000 0.00 0.00 0.00 3.67
1278 1391 7.439056 TCATTGCTTCCTCAATTTCAAAAGAAC 59.561 33.333 0.00 0.00 34.68 3.01
1279 1392 6.469782 TGCTTCCTCAATTTCAAAAGAACT 57.530 33.333 0.00 0.00 0.00 3.01
1280 1393 6.507023 TGCTTCCTCAATTTCAAAAGAACTC 58.493 36.000 0.00 0.00 0.00 3.01
1281 1394 5.923114 GCTTCCTCAATTTCAAAAGAACTCC 59.077 40.000 0.00 0.00 0.00 3.85
1579 1696 2.288457 GGAGCAAAAGAAAAGACAGGGC 60.288 50.000 0.00 0.00 0.00 5.19
1714 1833 7.597743 AGAATTCACTGAAATTTCAATGCAGAC 59.402 33.333 21.72 13.77 34.65 3.51
1979 2098 5.112686 GTTGTACCTGCTCTAGAATGGAAG 58.887 45.833 11.01 0.00 0.00 3.46
2087 2206 0.482446 ACAGGCCCAATGGACAGAAA 59.518 50.000 0.00 0.00 45.14 2.52
2096 2215 5.291971 CCCAATGGACAGAAAACTTTTCAG 58.708 41.667 15.17 10.28 0.00 3.02
2384 2512 4.443034 GCCGACTAGACCATAACCAATTCT 60.443 45.833 0.00 0.00 0.00 2.40
2386 2514 6.214399 CCGACTAGACCATAACCAATTCTAC 58.786 44.000 0.00 0.00 0.00 2.59
2391 2519 3.275999 ACCATAACCAATTCTACGGTGC 58.724 45.455 0.00 0.00 35.08 5.01
2542 2670 5.560724 AGCTTAGCAAGTAACCAATTGAGA 58.439 37.500 7.12 0.00 0.00 3.27
2612 2740 3.944015 AGGCACAAACTAGATCAATGCTC 59.056 43.478 0.00 0.00 0.00 4.26
2844 2993 7.071698 AGCCATGAATAGAACCTTCAGATCTAA 59.928 37.037 0.00 0.00 36.16 2.10
3103 3255 5.670792 TTTCCTCGATACTCCAGCTAAAA 57.329 39.130 0.00 0.00 0.00 1.52
3104 3256 4.650754 TCCTCGATACTCCAGCTAAAAC 57.349 45.455 0.00 0.00 0.00 2.43
3105 3257 4.279145 TCCTCGATACTCCAGCTAAAACT 58.721 43.478 0.00 0.00 0.00 2.66
3119 3271 4.774200 AGCTAAAACTTTCTCCAATGCCAT 59.226 37.500 0.00 0.00 0.00 4.40
3593 3753 3.763897 ACTCAAGGAAAAACAGCAAGTGT 59.236 39.130 0.00 0.00 43.24 3.55
3639 3799 1.037579 GGTGCTATTTCCTGCCCCAC 61.038 60.000 0.00 0.00 0.00 4.61
3676 3836 4.487714 TCCAGAAACTTCACAGAACTGT 57.512 40.909 1.32 1.32 46.17 3.55
3750 3910 0.321653 GACATGACAAGCCCCGAGTT 60.322 55.000 0.00 0.00 0.00 3.01
3861 4021 6.997476 GGAGCTCCTCTAAAATTCAGATTGAT 59.003 38.462 26.25 0.00 0.00 2.57
3921 4081 9.868277 CTCAGAAGTTATAAGAATCAGTTCTGT 57.132 33.333 13.40 0.00 43.80 3.41
4047 4207 9.113838 TCTCTTTTATTTGATATGTCTCCAAGC 57.886 33.333 0.00 0.00 0.00 4.01
5025 5188 3.056607 ACAAAGGAAAGATTGCGAATGGG 60.057 43.478 0.00 0.00 0.00 4.00
5222 5385 2.304761 TCAGGGACAACTTGATGGGTAC 59.695 50.000 0.00 0.00 0.00 3.34
5470 5633 5.048991 GGTAGCTGATTTTGGTCTTTCGAAA 60.049 40.000 10.71 10.71 0.00 3.46
5503 5666 2.028130 ACGCAAAAGGGACATGTTTCA 58.972 42.857 0.00 0.00 0.00 2.69
5677 5840 6.238897 CCGAGAAGAGTGATGTCTATAGCTTT 60.239 42.308 0.00 0.00 0.00 3.51
5740 5903 7.210873 CCATAGAGAAGGGTAAGTACATTGTC 58.789 42.308 0.00 0.00 0.00 3.18
6263 6427 0.754472 AGCAGGCACTTGCAAATTGT 59.246 45.000 7.53 0.00 44.36 2.71
6571 6750 1.953559 TAGCGGATGCAATCTCAACC 58.046 50.000 0.00 0.00 44.71 3.77
6574 6753 1.934589 CGGATGCAATCTCAACCGTA 58.065 50.000 0.00 0.00 44.21 4.02
6575 6754 1.860950 CGGATGCAATCTCAACCGTAG 59.139 52.381 0.00 0.00 44.21 3.51
6739 6918 1.611491 CGTAAAGTGGTTGGCATTGGT 59.389 47.619 0.00 0.00 0.00 3.67
6934 7113 5.698832 TGCACTTTTCTTATTGGAACATCG 58.301 37.500 0.00 0.00 39.30 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.750850 TGCCTATCGGACTGCTTACC 59.249 55.000 0.00 0.00 0.00 2.85
1 2 2.596904 TTGCCTATCGGACTGCTTAC 57.403 50.000 0.00 0.00 0.00 2.34
2 3 2.806745 GCATTGCCTATCGGACTGCTTA 60.807 50.000 0.00 0.00 31.64 3.09
3 4 1.959042 CATTGCCTATCGGACTGCTT 58.041 50.000 0.00 0.00 0.00 3.91
4 5 0.533755 GCATTGCCTATCGGACTGCT 60.534 55.000 0.00 0.00 31.64 4.24
5 6 1.510480 GGCATTGCCTATCGGACTGC 61.510 60.000 20.66 0.00 46.69 4.40
6 7 2.621763 GGCATTGCCTATCGGACTG 58.378 57.895 20.66 0.00 46.69 3.51
18 19 4.828939 TCAGGGAATTATTAGCAGGCATTG 59.171 41.667 0.00 0.00 0.00 2.82
19 20 5.065613 TCAGGGAATTATTAGCAGGCATT 57.934 39.130 0.00 0.00 0.00 3.56
20 21 4.729552 TCAGGGAATTATTAGCAGGCAT 57.270 40.909 0.00 0.00 0.00 4.40
21 22 4.464008 CTTCAGGGAATTATTAGCAGGCA 58.536 43.478 0.00 0.00 0.00 4.75
22 23 3.254411 GCTTCAGGGAATTATTAGCAGGC 59.746 47.826 0.00 0.00 0.00 4.85
23 24 4.464008 TGCTTCAGGGAATTATTAGCAGG 58.536 43.478 0.00 0.00 33.64 4.85
24 25 5.506982 GCTTGCTTCAGGGAATTATTAGCAG 60.507 44.000 0.00 0.00 38.27 4.24
25 26 4.339247 GCTTGCTTCAGGGAATTATTAGCA 59.661 41.667 0.00 0.00 35.56 3.49
26 27 4.582240 AGCTTGCTTCAGGGAATTATTAGC 59.418 41.667 0.00 0.00 0.00 3.09
27 28 6.705863 AAGCTTGCTTCAGGGAATTATTAG 57.294 37.500 0.00 0.00 0.00 1.73
28 29 7.480760 AAAAGCTTGCTTCAGGGAATTATTA 57.519 32.000 8.39 0.00 0.00 0.98
29 30 6.364568 AAAAGCTTGCTTCAGGGAATTATT 57.635 33.333 8.39 0.00 0.00 1.40
30 31 6.364568 AAAAAGCTTGCTTCAGGGAATTAT 57.635 33.333 8.39 0.00 0.00 1.28
31 32 5.806654 AAAAAGCTTGCTTCAGGGAATTA 57.193 34.783 8.39 0.00 0.00 1.40
32 33 4.694760 AAAAAGCTTGCTTCAGGGAATT 57.305 36.364 8.39 0.00 0.00 2.17
59 60 9.006839 CCATCTCATATATAGCTTGCTTCAAAA 57.993 33.333 0.00 0.00 0.00 2.44
60 61 8.159447 ACCATCTCATATATAGCTTGCTTCAAA 58.841 33.333 0.00 0.00 0.00 2.69
61 62 7.683578 ACCATCTCATATATAGCTTGCTTCAA 58.316 34.615 0.00 0.00 0.00 2.69
90 91 4.456566 GGCAAATCAAACAGCCATTCAAAT 59.543 37.500 0.00 0.00 46.26 2.32
107 108 4.021456 GGTTAGTAACAAAGCCAGGCAAAT 60.021 41.667 15.80 0.00 0.00 2.32
144 145 2.457743 ATCAGGTACCAAACGGCGCA 62.458 55.000 15.94 0.00 0.00 6.09
194 195 5.447818 CGATGGATGTTCTTGTAGGAAAAGC 60.448 44.000 0.00 0.00 0.00 3.51
198 199 5.414789 TTCGATGGATGTTCTTGTAGGAA 57.585 39.130 0.00 0.00 0.00 3.36
202 203 4.391830 GCAGTTTCGATGGATGTTCTTGTA 59.608 41.667 0.00 0.00 0.00 2.41
220 221 1.670811 CACGTCAAACCAGAAGCAGTT 59.329 47.619 0.00 0.00 0.00 3.16
222 223 1.581934 TCACGTCAAACCAGAAGCAG 58.418 50.000 0.00 0.00 0.00 4.24
225 226 4.058124 TCAAGATCACGTCAAACCAGAAG 58.942 43.478 0.00 0.00 0.00 2.85
240 241 2.836262 CCTCCACAGCAGATCAAGATC 58.164 52.381 1.81 1.81 38.09 2.75
242 243 0.251354 GCCTCCACAGCAGATCAAGA 59.749 55.000 0.00 0.00 0.00 3.02
263 264 1.069765 CACTCAGCCGTGTTGTCCT 59.930 57.895 0.00 0.00 0.00 3.85
265 266 2.607892 GCCACTCAGCCGTGTTGTC 61.608 63.158 0.00 0.00 33.07 3.18
268 269 3.240134 ATCGCCACTCAGCCGTGTT 62.240 57.895 0.00 0.00 33.07 3.32
269 270 3.695606 ATCGCCACTCAGCCGTGT 61.696 61.111 0.00 0.00 33.07 4.49
276 277 2.046988 CCACTGCATCGCCACTCA 60.047 61.111 0.00 0.00 0.00 3.41
342 343 0.107654 CCATCTTGGGGGTTCGTCTC 60.108 60.000 0.00 0.00 32.67 3.36
382 385 8.462016 CAACTTTCTTCCTATTAACCCAATGAG 58.538 37.037 0.00 0.00 0.00 2.90
412 416 4.495422 GTGAGCGACTTATCCTCAAAAGA 58.505 43.478 0.00 0.00 35.33 2.52
418 422 1.002251 CTCGGTGAGCGACTTATCCTC 60.002 57.143 1.26 0.00 0.00 3.71
421 425 1.534175 CCACTCGGTGAGCGACTTATC 60.534 57.143 1.26 0.00 35.23 1.75
423 427 1.880894 CCACTCGGTGAGCGACTTA 59.119 57.895 1.26 0.00 35.23 2.24
428 432 3.958147 AATGGCCACTCGGTGAGCG 62.958 63.158 8.16 0.00 35.23 5.03
453 457 4.100373 ACTAATCTGGCTCACCTTCTTCT 58.900 43.478 0.00 0.00 36.63 2.85
509 514 9.667107 TTTTCTCTGTCGGAATTCATTATAAGT 57.333 29.630 7.93 0.00 0.00 2.24
538 543 5.569428 GCCACATACTACCATGATGCTGATA 60.569 44.000 0.00 0.00 0.00 2.15
560 565 9.087424 GAAAAACTTTACCATAATCTTGATGCC 57.913 33.333 0.00 0.00 0.00 4.40
577 582 8.357402 ACTAATGCTACCGAATTGAAAAACTTT 58.643 29.630 0.00 0.00 0.00 2.66
578 583 7.807907 CACTAATGCTACCGAATTGAAAAACTT 59.192 33.333 0.00 0.00 0.00 2.66
579 584 7.305474 CACTAATGCTACCGAATTGAAAAACT 58.695 34.615 0.00 0.00 0.00 2.66
581 586 6.207810 ACCACTAATGCTACCGAATTGAAAAA 59.792 34.615 0.00 0.00 0.00 1.94
585 590 4.481368 ACCACTAATGCTACCGAATTGA 57.519 40.909 0.00 0.00 0.00 2.57
595 600 6.771267 GGGCTTAATAGTTAACCACTAATGCT 59.229 38.462 0.88 0.00 41.56 3.79
598 603 9.185680 CAAAGGGCTTAATAGTTAACCACTAAT 57.814 33.333 0.88 0.00 41.56 1.73
602 607 6.829229 ACAAAGGGCTTAATAGTTAACCAC 57.171 37.500 0.88 0.00 0.00 4.16
604 609 9.404848 AGATTACAAAGGGCTTAATAGTTAACC 57.595 33.333 0.88 0.00 0.00 2.85
624 734 9.249844 GCGCAACAAATTGAATTTAAAGATTAC 57.750 29.630 0.30 0.00 38.15 1.89
626 736 8.086851 AGCGCAACAAATTGAATTTAAAGATT 57.913 26.923 11.47 0.00 38.15 2.40
630 740 6.926272 ACCTAGCGCAACAAATTGAATTTAAA 59.074 30.769 11.47 0.00 38.15 1.52
632 742 6.019779 ACCTAGCGCAACAAATTGAATTTA 57.980 33.333 11.47 0.00 38.15 1.40
634 744 4.519540 ACCTAGCGCAACAAATTGAATT 57.480 36.364 11.47 0.00 38.15 2.17
666 776 8.297470 ACTGTGCATTTGATCCATTATAGTTT 57.703 30.769 0.00 0.00 0.00 2.66
682 792 5.301551 TGTTTGATTTGACCTACTGTGCATT 59.698 36.000 0.00 0.00 0.00 3.56
685 795 4.829064 TGTTTGATTTGACCTACTGTGC 57.171 40.909 0.00 0.00 0.00 4.57
744 854 6.831353 TGTTTCAGTTTCACCTTTTATCCTGA 59.169 34.615 0.00 0.00 0.00 3.86
758 868 7.201435 GCGGGAATGAAATATTGTTTCAGTTTC 60.201 37.037 13.06 11.94 41.13 2.78
768 878 4.578516 TGTACTGGCGGGAATGAAATATTG 59.421 41.667 0.00 0.00 0.00 1.90
772 882 2.752903 GTTGTACTGGCGGGAATGAAAT 59.247 45.455 0.00 0.00 0.00 2.17
795 905 2.039613 AGGAGGCCTTCTTTGAACTCTG 59.960 50.000 8.16 0.00 0.00 3.35
799 909 3.491342 AGAAAGGAGGCCTTCTTTGAAC 58.509 45.455 38.62 25.43 43.92 3.18
857 967 8.194769 TCTTAATCGTATGACAGTAGATGCAAA 58.805 33.333 0.00 0.00 0.00 3.68
890 1000 8.544687 TCACTCCTATCATGGATCATATTAGG 57.455 38.462 0.00 0.00 35.30 2.69
946 1056 4.486090 TCAAGCGAACATTAGAGAGACAC 58.514 43.478 0.00 0.00 0.00 3.67
947 1057 4.783764 TCAAGCGAACATTAGAGAGACA 57.216 40.909 0.00 0.00 0.00 3.41
948 1058 7.254151 GGTTTATCAAGCGAACATTAGAGAGAC 60.254 40.741 0.00 0.00 0.00 3.36
949 1059 6.757010 GGTTTATCAAGCGAACATTAGAGAGA 59.243 38.462 0.00 0.00 0.00 3.10
1023 1133 3.965888 GGATCCTGTCCAGCTTTGT 57.034 52.632 3.84 0.00 46.96 2.83
1278 1391 8.738645 AAGCTTTTATTACTGTATGAAGGGAG 57.261 34.615 0.00 0.00 0.00 4.30
1279 1392 8.325787 TGAAGCTTTTATTACTGTATGAAGGGA 58.674 33.333 0.00 0.00 0.00 4.20
1280 1393 8.506168 TGAAGCTTTTATTACTGTATGAAGGG 57.494 34.615 0.00 0.00 0.00 3.95
1281 1394 9.167311 ACTGAAGCTTTTATTACTGTATGAAGG 57.833 33.333 0.00 0.00 0.00 3.46
1514 1631 5.995282 AGAAGAATGTTTTGTGTATGGTCGA 59.005 36.000 0.00 0.00 0.00 4.20
1579 1696 5.125100 ACCACACAATATGTCAGCTTTTG 57.875 39.130 0.00 0.00 40.64 2.44
2012 2131 5.548836 TGGATGGATGGATGAGACAATATGA 59.451 40.000 0.00 0.00 0.00 2.15
2018 2137 4.166531 TGAATTGGATGGATGGATGAGACA 59.833 41.667 0.00 0.00 0.00 3.41
2020 2139 5.391577 TTGAATTGGATGGATGGATGAGA 57.608 39.130 0.00 0.00 0.00 3.27
2087 2206 5.539955 AGGTTCATATTGGCACTGAAAAGTT 59.460 36.000 7.63 0.00 31.21 2.66
2096 2215 3.527533 TGTACGAGGTTCATATTGGCAC 58.472 45.455 0.00 0.00 0.00 5.01
2146 2265 6.096001 GGCATGAAAGAACAGAGGACATTAAT 59.904 38.462 0.00 0.00 0.00 1.40
2391 2519 4.154918 GGTTACCGATACTATCAGGTACCG 59.845 50.000 6.18 1.56 37.79 4.02
2844 2993 0.987294 ATGTAGGGCAAGAGTGTGCT 59.013 50.000 0.00 0.00 44.31 4.40
3103 3255 6.769822 CAGTTAGATATGGCATTGGAGAAAGT 59.230 38.462 4.78 0.00 0.00 2.66
3104 3256 6.994496 TCAGTTAGATATGGCATTGGAGAAAG 59.006 38.462 4.78 0.00 0.00 2.62
3105 3257 6.899089 TCAGTTAGATATGGCATTGGAGAAA 58.101 36.000 4.78 0.00 0.00 2.52
3152 3304 8.362639 ACACACAATTATTTCTCAAAATCTGCT 58.637 29.630 0.00 0.00 36.49 4.24
3412 3572 3.007635 AGCTTGGGTCAACGTTATTAGC 58.992 45.455 0.00 4.81 0.00 3.09
3548 3708 9.713740 GAGTGTGCAGAAATTGATATTTTCTAG 57.286 33.333 1.48 0.00 40.53 2.43
3593 3753 2.491086 GGCCTGGGCTAGTAGAGTATGA 60.491 54.545 13.80 0.00 41.60 2.15
3676 3836 1.378762 GAAGGGGGTAGTGCAAGCA 59.621 57.895 0.00 0.00 0.00 3.91
4047 4207 5.699458 ACTGAAATGGACAAGTTACGTAAGG 59.301 40.000 8.60 4.22 46.39 2.69
5025 5188 3.301133 CGCGTTTTATTGCAGCTATTTGC 60.301 43.478 0.00 0.00 44.33 3.68
5222 5385 9.515020 GAGATAGTTGTAAAGATGAAGAGAGTG 57.485 37.037 0.00 0.00 0.00 3.51
5470 5633 2.882927 TTTGCGTGTCAGACACTAGT 57.117 45.000 27.42 0.00 46.46 2.57
5503 5666 2.965147 CAATGTTCCCTTCACTTGGGTT 59.035 45.455 0.00 0.00 44.84 4.11
5677 5840 2.182827 AGCTCTAGCATGACAACTCCA 58.817 47.619 4.54 0.00 45.16 3.86
5740 5903 2.105128 GCGGTCCTGATCTCACGG 59.895 66.667 0.00 0.00 0.00 4.94
5900 6063 4.920999 TCCTTGACCACATCATTCATTGA 58.079 39.130 0.00 0.00 37.11 2.57
6739 6918 4.904853 TGTATTATATCTGCAGACCACCCA 59.095 41.667 20.97 7.36 0.00 4.51
6802 6981 9.588774 CACAATGCATCTTCTAATTTTGTTTTG 57.411 29.630 0.00 0.00 0.00 2.44
6934 7113 4.886489 ACGTAGGGACTAGAGTTATTGACC 59.114 45.833 0.00 0.00 44.14 4.02


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

AutoCloner maintained by Alex Coulton.