Multiple sequence alignment - TraesCS6D01G145200

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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 TraesCS6D01G145200 chr6D 100.000 6099 0 0 1 6099 115550930 115544832 0.000000e+00 11263.0
1 TraesCS6D01G145200 chr6D 95.918 245 10 0 4373 4617 162229148 162228904 1.230000e-106 398.0
2 TraesCS6D01G145200 chr6D 84.884 172 18 8 3255 3423 285745702 285745536 3.780000e-37 167.0
3 TraesCS6D01G145200 chr6D 97.561 41 1 0 4588 4628 62117753 62117793 3.050000e-08 71.3
4 TraesCS6D01G145200 chr6A 96.072 2902 81 17 801 3688 143969829 143966947 0.000000e+00 4697.0
5 TraesCS6D01G145200 chr6A 95.345 1869 55 12 3616 5480 143966946 143965106 0.000000e+00 2940.0
6 TraesCS6D01G145200 chr6A 97.611 586 14 0 5514 6099 143965109 143964524 0.000000e+00 1005.0
7 TraesCS6D01G145200 chr6A 89.877 326 27 5 84 406 143972600 143972278 1.220000e-111 414.0
8 TraesCS6D01G145200 chr6A 91.440 257 18 4 554 808 143970913 143970659 3.500000e-92 350.0
9 TraesCS6D01G145200 chr6A 97.561 41 1 0 4588 4628 79271070 79271110 3.050000e-08 71.3
10 TraesCS6D01G145200 chr6A 97.561 41 1 0 4588 4628 79341161 79341201 3.050000e-08 71.3
11 TraesCS6D01G145200 chr6B 92.520 2206 92 34 777 2928 204927963 204925777 0.000000e+00 3092.0
12 TraesCS6D01G145200 chr6B 94.893 1958 68 12 4146 6099 204924583 204922654 0.000000e+00 3033.0
13 TraesCS6D01G145200 chr6B 93.683 1124 48 11 2955 4067 204925694 204924583 0.000000e+00 1661.0
14 TraesCS6D01G145200 chr6B 97.561 41 1 0 4588 4628 135862343 135862383 3.050000e-08 71.3
15 TraesCS6D01G145200 chr6B 100.000 37 0 0 2914 2950 204925752 204925716 1.100000e-07 69.4
16 TraesCS6D01G145200 chr2A 83.529 170 21 6 3257 3425 613475878 613476041 1.060000e-32 152.0
17 TraesCS6D01G145200 chr1B 81.818 176 25 5 3250 3425 22073220 22073388 2.290000e-29 141.0
18 TraesCS6D01G145200 chr7B 87.179 117 13 2 3310 3425 685245058 685244943 1.380000e-26 132.0
19 TraesCS6D01G145200 chr5D 84.348 115 15 3 1 114 89483703 89483815 6.460000e-20 110.0
20 TraesCS6D01G145200 chr3A 91.803 61 5 0 3363 3423 557963473 557963533 1.090000e-12 86.1
21 TraesCS6D01G145200 chr5A 95.349 43 2 0 3562 3604 646358248 646358206 1.100000e-07 69.4
22 TraesCS6D01G145200 chr4D 91.489 47 4 0 3379 3425 123099038 123099084 1.420000e-06 65.8
23 TraesCS6D01G145200 chr4A 95.000 40 1 1 492 531 628635071 628635033 1.840000e-05 62.1
24 TraesCS6D01G145200 chrUn 92.857 42 2 1 492 533 51239449 51239489 6.600000e-05 60.2


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 TraesCS6D01G145200 chr6D 115544832 115550930 6098 True 11263.00 11263 100.000 1 6099 1 chr6D.!!$R1 6098
1 TraesCS6D01G145200 chr6A 143964524 143972600 8076 True 1881.20 4697 94.069 84 6099 5 chr6A.!!$R1 6015
2 TraesCS6D01G145200 chr6B 204922654 204927963 5309 True 1963.85 3092 95.274 777 6099 4 chr6B.!!$R1 5322

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
21 22 0.095245 CTTATGTGTGCCGCTCAACG 59.905 55.000 0.0 0.0 43.15 4.10 F
1445 3520 0.107993 TTCTGCGATTGCCCTCTCTG 60.108 55.000 1.5 0.0 41.78 3.35 F
2239 4369 0.182299 TTGCACTCCACACCACATCA 59.818 50.000 0.0 0.0 0.00 3.07 F
3317 5521 2.264005 TCAGCCCGCTTTTTCACTTA 57.736 45.000 0.0 0.0 0.00 2.24 F
3364 5568 0.329596 GGTGCATTCCTCCTTCTGGT 59.670 55.000 0.0 0.0 34.23 4.00 F
3424 5628 1.074405 AGCTCTCCTGCCAACATTCAA 59.926 47.619 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
1687 3797 0.529119 GTACCCGCACAGGATAACCG 60.529 60.000 0.00 0.0 45.00 4.44 R
3258 5462 0.955905 GGGCGAAAACCTAAACAGCA 59.044 50.000 0.00 0.0 0.00 4.41 R
3364 5568 1.145571 AGGGGCCTTACAAGAACACA 58.854 50.000 0.84 0.0 0.00 3.72 R
4770 7059 2.125552 CGAACTGAGGCGATGGCA 60.126 61.111 1.01 0.0 42.47 4.92 R
5027 7316 3.118956 TGGTTTCAAAACGAGCCAACAAT 60.119 39.130 0.00 0.0 39.77 2.71 R
5404 7693 1.732259 CTAACGCGAGCTGTTTGGATT 59.268 47.619 15.93 0.0 0.00 3.01 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
19 20 2.401583 ATCTTATGTGTGCCGCTCAA 57.598 45.000 0.00 0.00 0.00 3.02
20 21 1.438651 TCTTATGTGTGCCGCTCAAC 58.561 50.000 0.00 0.00 0.00 3.18
21 22 0.095245 CTTATGTGTGCCGCTCAACG 59.905 55.000 0.00 0.00 43.15 4.10
31 32 1.497278 CGCTCAACGGTTGTGATGG 59.503 57.895 22.89 9.83 38.44 3.51
32 33 1.227999 CGCTCAACGGTTGTGATGGT 61.228 55.000 22.89 0.00 38.44 3.55
33 34 0.951558 GCTCAACGGTTGTGATGGTT 59.048 50.000 22.89 0.00 0.00 3.67
34 35 1.336755 GCTCAACGGTTGTGATGGTTT 59.663 47.619 22.89 0.00 0.00 3.27
35 36 2.223711 GCTCAACGGTTGTGATGGTTTT 60.224 45.455 22.89 0.00 0.00 2.43
36 37 3.736740 GCTCAACGGTTGTGATGGTTTTT 60.737 43.478 22.89 0.00 0.00 1.94
70 71 7.461182 TTTCATAATTAACTGGACAACCTGG 57.539 36.000 0.00 0.00 39.06 4.45
71 72 6.134535 TCATAATTAACTGGACAACCTGGT 57.865 37.500 0.00 0.00 39.06 4.00
72 73 6.548321 TCATAATTAACTGGACAACCTGGTT 58.452 36.000 6.18 6.18 39.06 3.67
73 74 7.007723 TCATAATTAACTGGACAACCTGGTTT 58.992 34.615 9.90 1.56 39.06 3.27
74 75 7.507616 TCATAATTAACTGGACAACCTGGTTTT 59.492 33.333 9.90 3.03 39.06 2.43
75 76 5.784578 ATTAACTGGACAACCTGGTTTTC 57.215 39.130 15.71 15.71 39.06 2.29
76 77 2.818751 ACTGGACAACCTGGTTTTCA 57.181 45.000 23.09 14.37 39.06 2.69
77 78 2.375146 ACTGGACAACCTGGTTTTCAC 58.625 47.619 23.09 14.58 39.06 3.18
78 79 2.025321 ACTGGACAACCTGGTTTTCACT 60.025 45.455 23.09 5.83 39.06 3.41
79 80 2.618709 CTGGACAACCTGGTTTTCACTC 59.381 50.000 23.09 9.85 37.04 3.51
80 81 1.602377 GGACAACCTGGTTTTCACTCG 59.398 52.381 23.09 8.34 0.00 4.18
81 82 1.602377 GACAACCTGGTTTTCACTCGG 59.398 52.381 18.39 4.58 0.00 4.63
82 83 0.951558 CAACCTGGTTTTCACTCGGG 59.048 55.000 9.90 0.00 0.00 5.14
88 89 2.025898 TGGTTTTCACTCGGGTTTTCC 58.974 47.619 0.00 0.00 39.75 3.13
99 100 5.123344 CACTCGGGTTTTCCTAATTAACTGG 59.877 44.000 0.00 0.00 40.46 4.00
100 101 4.011698 TCGGGTTTTCCTAATTAACTGGC 58.988 43.478 0.00 0.00 40.46 4.85
101 102 3.759618 CGGGTTTTCCTAATTAACTGGCA 59.240 43.478 0.00 0.00 40.46 4.92
103 104 5.475719 GGGTTTTCCTAATTAACTGGCAAC 58.524 41.667 0.00 0.00 40.46 4.17
104 105 5.245301 GGGTTTTCCTAATTAACTGGCAACT 59.755 40.000 0.00 0.00 40.46 3.16
105 106 6.387465 GGTTTTCCTAATTAACTGGCAACTC 58.613 40.000 0.00 0.00 36.94 3.01
111 112 6.433093 TCCTAATTAACTGGCAACTCCTTTTC 59.567 38.462 0.00 0.00 35.26 2.29
120 121 7.231467 ACTGGCAACTCCTTTTCTTCTTAATA 58.769 34.615 0.00 0.00 35.26 0.98
124 125 9.358872 GGCAACTCCTTTTCTTCTTAATAAATG 57.641 33.333 0.00 0.00 0.00 2.32
125 126 8.864024 GCAACTCCTTTTCTTCTTAATAAATGC 58.136 33.333 0.00 0.00 0.00 3.56
144 145 7.571080 AAATGCAAAAATCCTGTCATTTTGT 57.429 28.000 10.70 0.00 42.89 2.83
151 152 9.108284 CAAAAATCCTGTCATTTTGTAAAAGGT 57.892 29.630 2.28 0.00 38.56 3.50
152 153 9.679661 AAAAATCCTGTCATTTTGTAAAAGGTT 57.320 25.926 2.28 0.00 36.33 3.50
176 177 6.957631 TGTGGAATAAGAGCCTTTTGATCTA 58.042 36.000 0.00 0.00 0.00 1.98
248 249 6.183360 TGTGTAGGTTGTTCAATTTGCAGAAT 60.183 34.615 0.00 0.00 0.00 2.40
293 295 1.851658 ACGAATTGCAGTTGCCAAAC 58.148 45.000 0.00 0.00 41.18 2.93
296 298 2.865551 CGAATTGCAGTTGCCAAACTTT 59.134 40.909 0.00 0.00 44.47 2.66
345 347 9.995003 TGACTATGCACATATACATATTCAACA 57.005 29.630 0.00 0.00 36.25 3.33
406 408 8.819015 TGCGATTCTTAGCGTTTAAATTATACA 58.181 29.630 0.00 0.00 35.17 2.29
407 409 9.640974 GCGATTCTTAGCGTTTAAATTATACAA 57.359 29.630 0.00 0.00 35.17 2.41
412 414 9.101655 TCTTAGCGTTTAAATTATACAACTCCC 57.898 33.333 0.00 0.00 0.00 4.30
413 415 9.106070 CTTAGCGTTTAAATTATACAACTCCCT 57.894 33.333 0.00 0.00 0.00 4.20
414 416 7.549615 AGCGTTTAAATTATACAACTCCCTC 57.450 36.000 0.00 0.00 0.00 4.30
427 429 6.652205 ACAACTCCCTCCATTCCTAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
428 430 6.663734 ACAACTCCCTCCATTCCTAAATAAG 58.336 40.000 0.00 0.00 0.00 1.73
430 432 7.129504 ACAACTCCCTCCATTCCTAAATAAGAT 59.870 37.037 0.00 0.00 0.00 2.40
434 436 9.105844 CTCCCTCCATTCCTAAATAAGATTCTA 57.894 37.037 0.00 0.00 0.00 2.10
435 437 8.881262 TCCCTCCATTCCTAAATAAGATTCTAC 58.119 37.037 0.00 0.00 0.00 2.59
436 438 8.885346 CCCTCCATTCCTAAATAAGATTCTACT 58.115 37.037 0.00 0.00 0.00 2.57
490 492 8.936864 ACTAGAGTACATGTTCACTTATTTTGC 58.063 33.333 2.30 0.00 0.00 3.68
493 512 7.119846 AGAGTACATGTTCACTTATTTTGCTCC 59.880 37.037 2.30 0.00 0.00 4.70
494 513 6.714810 AGTACATGTTCACTTATTTTGCTCCA 59.285 34.615 2.30 0.00 0.00 3.86
501 520 9.237187 TGTTCACTTATTTTGCTCCATATGTAA 57.763 29.630 1.24 0.00 0.00 2.41
551 570 8.716674 ACTTATACTCCGTATTTAGGAATGGA 57.283 34.615 0.00 0.00 37.32 3.41
552 571 9.151177 ACTTATACTCCGTATTTAGGAATGGAA 57.849 33.333 0.00 0.00 37.32 3.53
566 1791 3.714798 GGAATGGAAGGAGTACATGGGTA 59.285 47.826 0.00 0.00 0.00 3.69
571 1796 3.118371 GGAAGGAGTACATGGGTAAGGTG 60.118 52.174 0.00 0.00 0.00 4.00
583 1808 6.101734 ACATGGGTAAGGTGTATGAGAATGAT 59.898 38.462 0.00 0.00 0.00 2.45
584 1809 6.575244 TGGGTAAGGTGTATGAGAATGATT 57.425 37.500 0.00 0.00 0.00 2.57
649 1875 7.707624 AAAATGAAGCAACTTGGAGATCATA 57.292 32.000 0.00 0.00 0.00 2.15
705 1932 4.769345 TTCCTTTTGGCCAAAATCAGTT 57.231 36.364 37.05 0.00 39.29 3.16
816 2880 4.101585 TCCAGCTATCCACAATCCACTTAG 59.898 45.833 0.00 0.00 0.00 2.18
853 2917 5.535753 AGAAAAATGGTGGGAAAGAACAG 57.464 39.130 0.00 0.00 0.00 3.16
1354 3428 2.561037 GCCGGTGGGTGTTTCTTGG 61.561 63.158 1.90 0.00 34.97 3.61
1364 3438 2.742372 TTTCTTGGCGCTCCGAGC 60.742 61.111 10.59 10.59 42.61 5.03
1445 3520 0.107993 TTCTGCGATTGCCCTCTCTG 60.108 55.000 1.50 0.00 41.78 3.35
1456 3531 1.199615 CCCTCTCTGTTTCTCCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
1462 3537 1.433199 TCTGTTTCTCCCTCCCTCTCA 59.567 52.381 0.00 0.00 0.00 3.27
1646 3756 4.087510 TCGTTCGTCGTCAGTTGATTAT 57.912 40.909 0.00 0.00 40.80 1.28
1647 3757 5.220557 TCGTTCGTCGTCAGTTGATTATA 57.779 39.130 0.00 0.00 40.80 0.98
1664 3774 5.689031 TGATTATAATCCGGGAACCTTGTGG 60.689 44.000 20.29 0.00 39.19 4.17
1687 3797 1.092921 TGTGTGTGTCCGGAAACTGC 61.093 55.000 25.12 17.54 0.00 4.40
2014 4144 0.681175 GGTTTTGCTGATTGCCTGGT 59.319 50.000 0.00 0.00 42.00 4.00
2022 4152 2.867647 GCTGATTGCCTGGTTTTTGGTC 60.868 50.000 0.00 0.00 35.15 4.02
2224 4354 4.815269 CGGGATTTGTATTTTTCCTTGCA 58.185 39.130 0.00 0.00 0.00 4.08
2239 4369 0.182299 TTGCACTCCACACCACATCA 59.818 50.000 0.00 0.00 0.00 3.07
2256 4386 7.817478 CACCACATCATACTGAAACTACTGTTA 59.183 37.037 0.00 0.00 34.96 2.41
2275 4406 8.292444 ACTGTTATTTATGCTTAATTGGCTGA 57.708 30.769 6.75 0.00 0.00 4.26
2288 4419 5.733620 AATTGGCTGATTGTGAGTTGAAT 57.266 34.783 0.00 0.00 0.00 2.57
2585 4723 4.331168 CCGCAAGTGAAGGAAATAAGAGAG 59.669 45.833 0.00 0.00 0.00 3.20
3258 5462 6.361768 AAGCTTACTTTGAACTAGCTAGGT 57.638 37.500 24.35 19.20 41.05 3.08
3317 5521 2.264005 TCAGCCCGCTTTTTCACTTA 57.736 45.000 0.00 0.00 0.00 2.24
3364 5568 0.329596 GGTGCATTCCTCCTTCTGGT 59.670 55.000 0.00 0.00 34.23 4.00
3365 5569 1.457346 GTGCATTCCTCCTTCTGGTG 58.543 55.000 0.00 0.00 34.23 4.17
3424 5628 1.074405 AGCTCTCCTGCCAACATTCAA 59.926 47.619 0.00 0.00 0.00 2.69
3425 5629 2.097825 GCTCTCCTGCCAACATTCAAT 58.902 47.619 0.00 0.00 0.00 2.57
3426 5630 2.098770 GCTCTCCTGCCAACATTCAATC 59.901 50.000 0.00 0.00 0.00 2.67
4047 6331 9.897744 ACATCACACATTTAAAACTACAATCAG 57.102 29.630 0.00 0.00 0.00 2.90
4084 6368 5.463724 GGTTAGACAGCTCTGTATTGCATAC 59.536 44.000 2.07 0.00 45.05 2.39
4169 6454 4.148079 TGGTGTCATGGCAATACTTTTGA 58.852 39.130 0.00 0.00 0.00 2.69
4205 6493 6.552932 AGTAAGCTTAGGAACTCCCAAATTT 58.447 36.000 6.38 0.00 41.75 1.82
4282 6570 4.202040 TGAGTTTCATGCCTCAAAACAGTG 60.202 41.667 8.99 0.00 34.88 3.66
4411 6699 6.308766 GCAATACTGCTCAATTGTTTTCGATT 59.691 34.615 5.13 0.00 45.74 3.34
4468 6756 5.483811 TGTTCGTTCACCTTTGCAGATATA 58.516 37.500 0.00 0.00 0.00 0.86
4608 6897 1.219124 GAGCACCGGATCTTCAGCA 59.781 57.895 9.46 0.00 0.00 4.41
4770 7059 2.671070 CGAAGGACAGCCCATGGT 59.329 61.111 11.73 0.00 37.41 3.55
4828 7117 2.648059 GCCAGCAGTGGTTATGAATCT 58.352 47.619 0.00 0.00 46.96 2.40
4863 7152 1.750193 AACCGGATGAATTGATGCGT 58.250 45.000 16.59 3.55 35.58 5.24
4865 7154 1.298602 CCGGATGAATTGATGCGTGA 58.701 50.000 16.59 0.00 35.58 4.35
4886 7175 1.140407 GACGCACGAGCATCTGTACC 61.140 60.000 5.50 0.00 42.27 3.34
4943 7232 4.218852 AGAACTGCTCCTGTCAACTACTAC 59.781 45.833 0.00 0.00 0.00 2.73
4977 7266 9.167311 GAAAATCTCACTGTTCATGTTACCTAT 57.833 33.333 0.00 0.00 0.00 2.57
5027 7316 0.106469 TTGTACAACCCTGCTGCCAA 60.106 50.000 3.59 0.00 0.00 4.52
5155 7444 1.754803 TCTCCATTACTGATTCGCGGT 59.245 47.619 6.13 0.00 39.97 5.68
5272 7561 3.843999 CAGGCAGAAGAGAACAGTCTAC 58.156 50.000 0.00 0.00 32.80 2.59
5288 7577 3.073062 AGTCTACTTTGACTTGCCCACAT 59.927 43.478 0.00 0.00 44.01 3.21
5289 7578 4.286032 AGTCTACTTTGACTTGCCCACATA 59.714 41.667 0.00 0.00 44.01 2.29
5301 7590 8.779303 TGACTTGCCCACATATTAAATTATACG 58.221 33.333 0.00 0.00 0.00 3.06
5302 7591 8.911918 ACTTGCCCACATATTAAATTATACGA 57.088 30.769 0.00 0.00 0.00 3.43
5303 7592 8.999431 ACTTGCCCACATATTAAATTATACGAG 58.001 33.333 0.00 0.00 0.00 4.18
5345 7634 4.715896 GTGCACACACATACATCAAAGAG 58.284 43.478 13.17 0.00 46.61 2.85
5404 7693 2.172505 TCCTGTCTCCTCAAAGCAAACA 59.827 45.455 0.00 0.00 0.00 2.83
5444 7733 4.955811 AGGACACACAAGATGTAGAACA 57.044 40.909 0.00 0.00 40.64 3.18
5616 7905 6.883756 TGAAGTGTCACCATGATTAGCATAAA 59.116 34.615 0.00 0.00 34.82 1.40
5724 8013 2.394632 ACCGCAATATAGTGTCCAGGA 58.605 47.619 1.67 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.009774 GTTGAGCGGCACACATAAGAT 58.990 47.619 1.45 0.00 0.00 2.40
1 2 1.438651 GTTGAGCGGCACACATAAGA 58.561 50.000 1.45 0.00 0.00 2.10
2 3 0.095245 CGTTGAGCGGCACACATAAG 59.905 55.000 1.45 0.00 36.85 1.73
3 4 2.158300 CGTTGAGCGGCACACATAA 58.842 52.632 1.45 0.00 36.85 1.90
4 5 3.869187 CGTTGAGCGGCACACATA 58.131 55.556 1.45 0.00 36.85 2.29
13 14 1.227999 ACCATCACAACCGTTGAGCG 61.228 55.000 18.19 6.09 40.95 5.03
14 15 0.951558 AACCATCACAACCGTTGAGC 59.048 50.000 18.19 0.00 0.00 4.26
15 16 3.708563 AAAACCATCACAACCGTTGAG 57.291 42.857 18.19 10.22 0.00 3.02
44 45 8.364142 CCAGGTTGTCCAGTTAATTATGAAAAA 58.636 33.333 0.00 0.00 35.89 1.94
45 46 7.507616 ACCAGGTTGTCCAGTTAATTATGAAAA 59.492 33.333 0.00 0.00 35.89 2.29
46 47 7.007723 ACCAGGTTGTCCAGTTAATTATGAAA 58.992 34.615 0.00 0.00 35.89 2.69
47 48 6.548321 ACCAGGTTGTCCAGTTAATTATGAA 58.452 36.000 0.00 0.00 35.89 2.57
48 49 6.134535 ACCAGGTTGTCCAGTTAATTATGA 57.865 37.500 0.00 0.00 35.89 2.15
49 50 6.834168 AACCAGGTTGTCCAGTTAATTATG 57.166 37.500 3.18 0.00 32.97 1.90
50 51 7.507616 TGAAAACCAGGTTGTCCAGTTAATTAT 59.492 33.333 18.66 0.00 33.89 1.28
51 52 6.834451 TGAAAACCAGGTTGTCCAGTTAATTA 59.166 34.615 18.66 0.00 33.89 1.40
52 53 5.659079 TGAAAACCAGGTTGTCCAGTTAATT 59.341 36.000 18.66 0.00 33.89 1.40
53 54 5.068591 GTGAAAACCAGGTTGTCCAGTTAAT 59.931 40.000 18.66 0.00 33.89 1.40
54 55 4.399934 GTGAAAACCAGGTTGTCCAGTTAA 59.600 41.667 18.66 0.00 33.89 2.01
55 56 3.949113 GTGAAAACCAGGTTGTCCAGTTA 59.051 43.478 18.66 0.00 33.89 2.24
56 57 2.758423 GTGAAAACCAGGTTGTCCAGTT 59.242 45.455 18.66 2.28 35.12 3.16
57 58 2.025321 AGTGAAAACCAGGTTGTCCAGT 60.025 45.455 18.66 10.71 29.33 4.00
58 59 2.618709 GAGTGAAAACCAGGTTGTCCAG 59.381 50.000 18.66 0.00 29.33 3.86
59 60 2.650322 GAGTGAAAACCAGGTTGTCCA 58.350 47.619 18.66 8.46 29.33 4.02
60 61 1.602377 CGAGTGAAAACCAGGTTGTCC 59.398 52.381 18.66 10.62 29.33 4.02
61 62 1.602377 CCGAGTGAAAACCAGGTTGTC 59.398 52.381 15.11 15.11 30.98 3.18
62 63 1.675552 CCGAGTGAAAACCAGGTTGT 58.324 50.000 5.30 0.00 0.00 3.32
63 64 0.951558 CCCGAGTGAAAACCAGGTTG 59.048 55.000 5.30 0.00 0.00 3.77
64 65 0.549469 ACCCGAGTGAAAACCAGGTT 59.451 50.000 0.00 0.00 0.00 3.50
65 66 0.549469 AACCCGAGTGAAAACCAGGT 59.451 50.000 0.00 0.00 0.00 4.00
66 67 1.687563 AAACCCGAGTGAAAACCAGG 58.312 50.000 0.00 0.00 0.00 4.45
67 68 2.034179 GGAAAACCCGAGTGAAAACCAG 59.966 50.000 0.00 0.00 0.00 4.00
68 69 2.025898 GGAAAACCCGAGTGAAAACCA 58.974 47.619 0.00 0.00 0.00 3.67
69 70 2.304092 AGGAAAACCCGAGTGAAAACC 58.696 47.619 0.00 0.00 40.87 3.27
70 71 5.700722 ATTAGGAAAACCCGAGTGAAAAC 57.299 39.130 0.00 0.00 40.87 2.43
71 72 7.503230 AGTTAATTAGGAAAACCCGAGTGAAAA 59.497 33.333 0.00 0.00 40.87 2.29
72 73 6.999871 AGTTAATTAGGAAAACCCGAGTGAAA 59.000 34.615 0.00 0.00 40.87 2.69
73 74 6.428771 CAGTTAATTAGGAAAACCCGAGTGAA 59.571 38.462 0.00 0.00 40.87 3.18
74 75 5.935789 CAGTTAATTAGGAAAACCCGAGTGA 59.064 40.000 0.00 0.00 40.87 3.41
75 76 5.123344 CCAGTTAATTAGGAAAACCCGAGTG 59.877 44.000 0.00 0.00 40.87 3.51
76 77 5.250982 CCAGTTAATTAGGAAAACCCGAGT 58.749 41.667 0.00 0.00 40.87 4.18
77 78 4.095932 GCCAGTTAATTAGGAAAACCCGAG 59.904 45.833 0.00 0.00 40.87 4.63
78 79 4.011698 GCCAGTTAATTAGGAAAACCCGA 58.988 43.478 0.00 0.00 40.87 5.14
79 80 3.759618 TGCCAGTTAATTAGGAAAACCCG 59.240 43.478 0.00 0.00 40.87 5.28
80 81 5.245301 AGTTGCCAGTTAATTAGGAAAACCC 59.755 40.000 0.00 0.00 0.00 4.11
81 82 6.340962 AGTTGCCAGTTAATTAGGAAAACC 57.659 37.500 0.00 0.00 0.00 3.27
82 83 6.208797 AGGAGTTGCCAGTTAATTAGGAAAAC 59.791 38.462 0.00 0.00 40.02 2.43
88 89 7.454260 AGAAAAGGAGTTGCCAGTTAATTAG 57.546 36.000 0.00 0.00 40.02 1.73
99 100 8.864024 GCATTTATTAAGAAGAAAAGGAGTTGC 58.136 33.333 0.00 0.00 0.00 4.17
100 101 9.912634 TGCATTTATTAAGAAGAAAAGGAGTTG 57.087 29.630 0.00 0.00 0.00 3.16
120 121 7.571080 ACAAAATGACAGGATTTTTGCATTT 57.429 28.000 10.49 0.00 41.69 2.32
124 125 8.069574 CCTTTTACAAAATGACAGGATTTTTGC 58.930 33.333 10.49 0.00 41.69 3.68
125 126 9.108284 ACCTTTTACAAAATGACAGGATTTTTG 57.892 29.630 9.42 9.42 42.93 2.44
127 128 9.108284 CAACCTTTTACAAAATGACAGGATTTT 57.892 29.630 0.00 0.00 36.21 1.82
128 129 8.264347 ACAACCTTTTACAAAATGACAGGATTT 58.736 29.630 0.00 0.00 0.00 2.17
136 137 9.757227 CTTATTCCACAACCTTTTACAAAATGA 57.243 29.630 0.00 0.00 0.00 2.57
142 143 5.475564 GGCTCTTATTCCACAACCTTTTACA 59.524 40.000 0.00 0.00 0.00 2.41
143 144 5.710567 AGGCTCTTATTCCACAACCTTTTAC 59.289 40.000 0.00 0.00 0.00 2.01
144 145 5.887754 AGGCTCTTATTCCACAACCTTTTA 58.112 37.500 0.00 0.00 0.00 1.52
151 152 6.248433 AGATCAAAAGGCTCTTATTCCACAA 58.752 36.000 0.00 0.00 0.00 3.33
152 153 5.819991 AGATCAAAAGGCTCTTATTCCACA 58.180 37.500 0.00 0.00 0.00 4.17
220 221 6.166279 TGCAAATTGAACAACCTACACAAAA 58.834 32.000 0.00 0.00 0.00 2.44
224 225 5.181690 TCTGCAAATTGAACAACCTACAC 57.818 39.130 0.00 0.00 0.00 2.90
228 229 8.729805 TTAAAATTCTGCAAATTGAACAACCT 57.270 26.923 0.00 0.00 0.00 3.50
261 262 9.988350 CAACTGCAATTCGTAATAAGTAGAAAT 57.012 29.630 0.00 0.00 0.00 2.17
263 264 7.413657 GGCAACTGCAATTCGTAATAAGTAGAA 60.414 37.037 3.76 0.00 44.36 2.10
265 266 6.183360 TGGCAACTGCAATTCGTAATAAGTAG 60.183 38.462 3.76 0.00 44.36 2.57
296 298 8.092687 GTCATGGACTAAGTAGGAGTTACAAAA 58.907 37.037 0.00 0.00 34.56 2.44
387 389 9.106070 AGGGAGTTGTATAATTTAAACGCTAAG 57.894 33.333 0.00 0.00 0.00 2.18
392 394 7.852971 TGGAGGGAGTTGTATAATTTAAACG 57.147 36.000 0.00 0.00 0.00 3.60
406 408 7.713704 ATCTTATTTAGGAATGGAGGGAGTT 57.286 36.000 0.00 0.00 0.00 3.01
407 409 7.574372 AGAATCTTATTTAGGAATGGAGGGAGT 59.426 37.037 0.00 0.00 0.00 3.85
408 410 7.983363 AGAATCTTATTTAGGAATGGAGGGAG 58.017 38.462 0.00 0.00 0.00 4.30
409 411 7.954539 AGAATCTTATTTAGGAATGGAGGGA 57.045 36.000 0.00 0.00 0.00 4.20
410 412 8.885346 AGTAGAATCTTATTTAGGAATGGAGGG 58.115 37.037 0.00 0.00 0.00 4.30
464 466 8.936864 GCAAAATAAGTGAACATGTACTCTAGT 58.063 33.333 0.00 0.00 0.00 2.57
465 467 9.155975 AGCAAAATAAGTGAACATGTACTCTAG 57.844 33.333 0.00 0.00 0.00 2.43
466 468 9.151471 GAGCAAAATAAGTGAACATGTACTCTA 57.849 33.333 0.00 0.00 0.00 2.43
467 469 7.119846 GGAGCAAAATAAGTGAACATGTACTCT 59.880 37.037 0.00 0.00 0.00 3.24
468 470 7.094805 TGGAGCAAAATAAGTGAACATGTACTC 60.095 37.037 0.00 0.00 0.00 2.59
470 472 6.908825 TGGAGCAAAATAAGTGAACATGTAC 58.091 36.000 0.00 0.00 0.00 2.90
471 473 7.701539 ATGGAGCAAAATAAGTGAACATGTA 57.298 32.000 0.00 0.00 0.00 2.29
472 474 6.594788 ATGGAGCAAAATAAGTGAACATGT 57.405 33.333 0.00 0.00 0.00 3.21
473 475 8.192774 ACATATGGAGCAAAATAAGTGAACATG 58.807 33.333 7.80 0.00 0.00 3.21
475 477 7.701539 ACATATGGAGCAAAATAAGTGAACA 57.298 32.000 7.80 0.00 0.00 3.18
532 551 8.078989 TACTCCTTCCATTCCTAAATACGGAGT 61.079 40.741 0.00 0.00 46.47 3.85
533 552 5.070580 ACTCCTTCCATTCCTAAATACGGAG 59.929 44.000 0.00 0.00 40.00 4.63
534 553 4.966805 ACTCCTTCCATTCCTAAATACGGA 59.033 41.667 0.00 0.00 0.00 4.69
535 554 5.291905 ACTCCTTCCATTCCTAAATACGG 57.708 43.478 0.00 0.00 0.00 4.02
538 557 7.202186 CCCATGTACTCCTTCCATTCCTAAATA 60.202 40.741 0.00 0.00 0.00 1.40
539 558 6.410853 CCCATGTACTCCTTCCATTCCTAAAT 60.411 42.308 0.00 0.00 0.00 1.40
540 559 5.104109 CCCATGTACTCCTTCCATTCCTAAA 60.104 44.000 0.00 0.00 0.00 1.85
541 560 4.412199 CCCATGTACTCCTTCCATTCCTAA 59.588 45.833 0.00 0.00 0.00 2.69
542 561 3.973973 CCCATGTACTCCTTCCATTCCTA 59.026 47.826 0.00 0.00 0.00 2.94
543 562 2.780010 CCCATGTACTCCTTCCATTCCT 59.220 50.000 0.00 0.00 0.00 3.36
545 564 3.933861 ACCCATGTACTCCTTCCATTC 57.066 47.619 0.00 0.00 0.00 2.67
547 566 3.716872 CCTTACCCATGTACTCCTTCCAT 59.283 47.826 0.00 0.00 0.00 3.41
548 567 3.112263 CCTTACCCATGTACTCCTTCCA 58.888 50.000 0.00 0.00 0.00 3.53
551 570 3.527937 ACACCTTACCCATGTACTCCTT 58.472 45.455 0.00 0.00 0.00 3.36
552 571 3.200958 ACACCTTACCCATGTACTCCT 57.799 47.619 0.00 0.00 0.00 3.69
628 1854 6.204301 CGAATATGATCTCCAAGTTGCTTCAT 59.796 38.462 0.00 5.53 0.00 2.57
649 1875 7.449086 TCTGGATAAAGTAAACAAAACCCGAAT 59.551 33.333 0.00 0.00 0.00 3.34
749 1976 7.119699 CACAACTTATTTTGGATGCTCTGTCTA 59.880 37.037 0.00 0.00 0.00 2.59
750 1977 6.006449 ACAACTTATTTTGGATGCTCTGTCT 58.994 36.000 0.00 0.00 0.00 3.41
751 1978 6.072508 TCACAACTTATTTTGGATGCTCTGTC 60.073 38.462 0.00 0.00 0.00 3.51
752 1979 5.769662 TCACAACTTATTTTGGATGCTCTGT 59.230 36.000 0.00 0.00 0.00 3.41
753 1980 6.258230 TCACAACTTATTTTGGATGCTCTG 57.742 37.500 0.00 0.00 0.00 3.35
816 2880 1.185315 TTTCTATGCTTGGCTTGCCC 58.815 50.000 9.35 0.00 0.00 5.36
853 2917 5.810095 TCTCTCTCTCATTTTTCCCTTTCC 58.190 41.667 0.00 0.00 0.00 3.13
1364 3438 0.661020 AACAAACTCCGGCGAACAAG 59.339 50.000 9.30 2.50 0.00 3.16
1407 3482 0.668535 AGTCAAAGAAAAGCACGGCC 59.331 50.000 0.00 0.00 0.00 6.13
1445 3520 1.552792 CAGTGAGAGGGAGGGAGAAAC 59.447 57.143 0.00 0.00 0.00 2.78
1456 3531 0.887836 TGCAGCTTTGCAGTGAGAGG 60.888 55.000 0.00 0.00 40.23 3.69
1488 3595 4.248859 GAGTAGAGCAAGAGCAATCACAA 58.751 43.478 0.00 0.00 45.49 3.33
1491 3598 2.159184 CGGAGTAGAGCAAGAGCAATCA 60.159 50.000 0.00 0.00 45.49 2.57
1625 3735 2.410785 AATCAACTGACGACGAACGA 57.589 45.000 0.00 0.00 45.77 3.85
1664 3774 2.162809 AGTTTCCGGACACACACAAAAC 59.837 45.455 22.24 12.04 0.00 2.43
1687 3797 0.529119 GTACCCGCACAGGATAACCG 60.529 60.000 0.00 0.00 45.00 4.44
1851 3976 1.299316 CAGCCCAAAAGTGCACACG 60.299 57.895 21.04 3.68 36.20 4.49
1873 3998 2.154462 GTAGCCACAGCACAACAGAAT 58.846 47.619 0.00 0.00 43.56 2.40
1914 4039 8.263640 AGTATGCATACACAGAAGAGAAATCTT 58.736 33.333 32.69 8.28 35.74 2.40
2014 4144 4.502950 GCATGGAACCTTGATGACCAAAAA 60.503 41.667 10.28 0.00 33.76 1.94
2022 4152 0.099968 CAGCGCATGGAACCTTGATG 59.900 55.000 11.47 0.00 0.00 3.07
2105 4235 4.021925 GTCCGGCTGTGGCTTCCT 62.022 66.667 0.00 0.00 38.73 3.36
2224 4354 3.173151 TCAGTATGATGTGGTGTGGAGT 58.827 45.455 0.00 0.00 42.56 3.85
2256 4386 7.784037 TCACAATCAGCCAATTAAGCATAAAT 58.216 30.769 2.79 0.00 0.00 1.40
2585 4723 6.757897 TGAACTTGTCCATTGATTGATACC 57.242 37.500 0.00 0.00 0.00 2.73
2795 4937 5.938125 TCAAAGAGGCCTACATTACAAAGAC 59.062 40.000 4.42 0.00 0.00 3.01
3258 5462 0.955905 GGGCGAAAACCTAAACAGCA 59.044 50.000 0.00 0.00 0.00 4.41
3364 5568 1.145571 AGGGGCCTTACAAGAACACA 58.854 50.000 0.84 0.00 0.00 3.72
3365 5569 2.287977 AAGGGGCCTTACAAGAACAC 57.712 50.000 0.84 0.00 34.05 3.32
3636 5843 8.636213 CCTGATTCTTAAATGTAAAGCCATCAT 58.364 33.333 0.00 0.00 29.94 2.45
3925 6208 2.224426 TGTAGGTGCAAGTTGTTCCGAT 60.224 45.455 4.48 0.00 0.00 4.18
3927 6210 1.588674 TGTAGGTGCAAGTTGTTCCG 58.411 50.000 4.48 0.00 0.00 4.30
4005 6288 7.421599 TGTGTGATGTTCGTTGTTATCAAAAT 58.578 30.769 0.00 0.00 35.20 1.82
4047 6331 4.865365 GCTGTCTAACCACAAGATCACTAC 59.135 45.833 0.00 0.00 0.00 2.73
4246 6534 7.831193 AGGCATGAAACTCAACAGTCTATTATT 59.169 33.333 0.00 0.00 29.93 1.40
4247 6535 7.341805 AGGCATGAAACTCAACAGTCTATTAT 58.658 34.615 0.00 0.00 29.93 1.28
4248 6536 6.711277 AGGCATGAAACTCAACAGTCTATTA 58.289 36.000 0.00 0.00 29.93 0.98
4411 6699 9.038803 GCTCATATGCATTCGAGATATATTTCA 57.961 33.333 22.56 0.00 0.00 2.69
4608 6897 2.428171 GCTGACAGAAGAGAGAGAGCAT 59.572 50.000 6.65 0.00 0.00 3.79
4770 7059 2.125552 CGAACTGAGGCGATGGCA 60.126 61.111 1.01 0.00 42.47 4.92
4819 7108 5.657474 ACGCCGAAGAAAGTAGATTCATAA 58.343 37.500 0.00 0.00 0.00 1.90
4886 7175 3.889815 TCCTGGCTGTAGATCCAAAATG 58.110 45.455 0.00 0.00 30.98 2.32
4943 7232 4.013267 ACAGTGAGATTTTCCACTCTGG 57.987 45.455 0.00 0.00 41.26 3.86
4990 7279 9.968870 GTTGTACAATGGAAAAATAACAAGGTA 57.031 29.630 12.26 0.00 0.00 3.08
5027 7316 3.118956 TGGTTTCAAAACGAGCCAACAAT 60.119 39.130 0.00 0.00 39.77 2.71
5404 7693 1.732259 CTAACGCGAGCTGTTTGGATT 59.268 47.619 15.93 0.00 0.00 3.01
5616 7905 4.422073 TCACTGTCACTTGATCCAAAGT 57.578 40.909 0.00 0.00 41.08 2.66
5695 7984 7.601130 TGGACACTATATTGCGGTTCATAATAC 59.399 37.037 0.00 0.00 0.00 1.89
5724 8013 2.925724 TGATTTCTGTGGTGTCGGTTT 58.074 42.857 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.