Multiple sequence alignment - TraesCS6D01G253800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G253800 chr6D 100.000 4047 0 0 1 4047 358220443 358216397 0.000000e+00 7474.0
1 TraesCS6D01G253800 chr6D 92.364 550 26 5 2852 3394 357872204 357871664 0.000000e+00 769.0
2 TraesCS6D01G253800 chr6D 86.528 193 15 4 2648 2830 357872478 357872287 6.860000e-48 202.0
3 TraesCS6D01G253800 chr6D 94.340 53 3 0 3835 3887 350205599 350205651 9.320000e-12 82.4
4 TraesCS6D01G253800 chr6D 100.000 31 0 0 3970 4000 350205723 350205753 1.570000e-04 58.4
5 TraesCS6D01G253800 chr6B 94.542 1814 76 17 32 1842 539619356 539617563 0.000000e+00 2780.0
6 TraesCS6D01G253800 chr6B 89.940 994 57 26 2418 3394 539616759 539615792 0.000000e+00 1242.0
7 TraesCS6D01G253800 chr6B 92.797 472 21 6 1853 2316 539617445 539616979 0.000000e+00 671.0
8 TraesCS6D01G253800 chr6B 89.840 187 13 1 3820 4000 530852720 530852906 6.760000e-58 235.0
9 TraesCS6D01G253800 chr6B 93.836 146 5 1 2314 2459 539616929 539616788 2.450000e-52 217.0
10 TraesCS6D01G253800 chr6B 100.000 50 0 0 3998 4047 530852931 530852980 4.310000e-15 93.5
11 TraesCS6D01G253800 chr6B 92.063 63 5 0 3835 3897 529773523 529773461 5.570000e-14 89.8
12 TraesCS6D01G253800 chr6A 92.830 1311 67 12 552 1843 499800142 499801444 0.000000e+00 1875.0
13 TraesCS6D01G253800 chr6A 87.134 956 78 29 2419 3364 499802858 499803778 0.000000e+00 1042.0
14 TraesCS6D01G253800 chr6A 86.885 488 20 9 1851 2313 499801563 499802031 1.300000e-139 507.0
15 TraesCS6D01G253800 chr6A 86.940 268 33 2 3394 3661 517901231 517900966 2.360000e-77 300.0
16 TraesCS6D01G253800 chr6A 92.063 63 5 0 3835 3897 493755764 493755702 5.570000e-14 89.8
17 TraesCS6D01G253800 chrUn 95.115 655 31 1 3393 4047 209272757 209272104 0.000000e+00 1031.0
18 TraesCS6D01G253800 chr7B 95.115 655 31 1 3393 4047 642232890 642232237 0.000000e+00 1031.0
19 TraesCS6D01G253800 chr3D 88.806 268 28 2 3394 3661 505454493 505454228 1.080000e-85 327.0
20 TraesCS6D01G253800 chr3D 87.786 262 31 1 3392 3653 505453550 505453810 5.080000e-79 305.0
21 TraesCS6D01G253800 chr2A 87.687 268 31 2 3394 3661 60003857 60003592 1.090000e-80 311.0
22 TraesCS6D01G253800 chr5D 87.739 261 29 3 3394 3653 459224333 459224591 6.570000e-78 302.0
23 TraesCS6D01G253800 chr3A 88.189 254 29 1 3394 3647 723331093 723331345 6.570000e-78 302.0
24 TraesCS6D01G253800 chr2B 86.617 269 32 4 3394 3661 45643218 45642953 1.100000e-75 294.0
25 TraesCS6D01G253800 chr2B 93.478 46 3 0 2919 2964 711166234 711166189 7.260000e-08 69.4
26 TraesCS6D01G253800 chr4B 94.857 175 9 0 3651 3825 91228306 91228480 1.430000e-69 274.0
27 TraesCS6D01G253800 chr4B 92.571 175 13 0 3651 3825 91328267 91328441 6.710000e-63 252.0
28 TraesCS6D01G253800 chr4D 93.714 175 11 0 3651 3825 61594117 61593943 3.100000e-66 263.0
29 TraesCS6D01G253800 chr4A 92.571 175 13 0 3651 3825 534791153 534790979 6.710000e-63 252.0


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 TraesCS6D01G253800 chr6D 358216397 358220443 4046 True 7474.000000 7474 100.000000 1 4047 1 chr6D.!!$R1 4046
1 TraesCS6D01G253800 chr6D 357871664 357872478 814 True 485.500000 769 89.446000 2648 3394 2 chr6D.!!$R2 746
2 TraesCS6D01G253800 chr6B 539615792 539619356 3564 True 1227.500000 2780 92.778750 32 3394 4 chr6B.!!$R2 3362
3 TraesCS6D01G253800 chr6A 499800142 499803778 3636 False 1141.333333 1875 88.949667 552 3364 3 chr6A.!!$F1 2812
4 TraesCS6D01G253800 chrUn 209272104 209272757 653 True 1031.000000 1031 95.115000 3393 4047 1 chrUn.!!$R1 654
5 TraesCS6D01G253800 chr7B 642232237 642232890 653 True 1031.000000 1031 95.115000 3393 4047 1 chr7B.!!$R1 654

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
654 657 0.044161 CAAGCTAACGTACGCGCATC 60.044 55.0 16.72 0.98 42.83 3.91 F
655 658 0.457166 AAGCTAACGTACGCGCATCA 60.457 50.0 16.72 0.00 42.83 3.07 F
2306 2482 0.544833 TCCCGTTAGGCAACCTACCA 60.545 55.0 0.00 0.00 35.63 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 3378 0.667993 CATGCCAACAAACACGGACT 59.332 50.0 0.00 0.0 0.0 3.85 R
2473 3530 1.892209 CCCATAACCGAGCATTACCC 58.108 55.0 0.00 0.0 0.0 3.69 R
3559 4709 0.039165 GCAAAAACGCCAGCTAGCTT 60.039 50.0 16.46 0.0 0.0 3.74 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
18 19 1.752833 GGTAGGCCCTATTGACCGG 59.247 63.158 0.00 0.00 0.00 5.28
19 20 1.070957 GTAGGCCCTATTGACCGGC 59.929 63.158 0.00 0.00 42.23 6.13
20 21 1.074775 TAGGCCCTATTGACCGGCT 60.075 57.895 0.00 0.00 42.58 5.52
21 22 1.119574 TAGGCCCTATTGACCGGCTC 61.120 60.000 0.00 0.00 42.58 4.70
22 23 2.444256 GGCCCTATTGACCGGCTCT 61.444 63.158 0.00 0.00 42.58 4.09
23 24 1.119574 GGCCCTATTGACCGGCTCTA 61.120 60.000 0.00 0.00 42.58 2.43
24 25 0.318762 GCCCTATTGACCGGCTCTAG 59.681 60.000 0.00 0.00 39.70 2.43
25 26 1.705873 CCCTATTGACCGGCTCTAGT 58.294 55.000 0.00 0.00 0.00 2.57
26 27 1.341531 CCCTATTGACCGGCTCTAGTG 59.658 57.143 0.00 0.00 0.00 2.74
27 28 2.307768 CCTATTGACCGGCTCTAGTGA 58.692 52.381 0.00 0.00 0.00 3.41
28 29 2.294791 CCTATTGACCGGCTCTAGTGAG 59.705 54.545 0.00 0.00 42.96 3.51
29 30 1.115467 ATTGACCGGCTCTAGTGAGG 58.885 55.000 0.00 0.95 40.53 3.86
30 31 0.970937 TTGACCGGCTCTAGTGAGGG 60.971 60.000 0.00 6.05 40.53 4.30
31 32 1.076923 GACCGGCTCTAGTGAGGGA 60.077 63.158 0.00 0.00 40.53 4.20
32 33 1.076632 ACCGGCTCTAGTGAGGGAG 60.077 63.158 0.00 0.00 40.53 4.30
33 34 1.076632 CCGGCTCTAGTGAGGGAGT 60.077 63.158 0.00 0.00 40.53 3.85
34 35 1.388065 CCGGCTCTAGTGAGGGAGTG 61.388 65.000 0.00 0.00 40.53 3.51
35 36 0.681564 CGGCTCTAGTGAGGGAGTGT 60.682 60.000 0.00 0.00 40.53 3.55
36 37 0.820871 GGCTCTAGTGAGGGAGTGTG 59.179 60.000 0.00 0.00 40.53 3.82
43 44 0.539051 GTGAGGGAGTGTGATGAGGG 59.461 60.000 0.00 0.00 0.00 4.30
49 50 0.320771 GAGTGTGATGAGGGCAACGT 60.321 55.000 0.00 0.00 37.60 3.99
79 80 9.596677 TTTAGTTTATTCCAACGTTTGTAATCG 57.403 29.630 0.00 0.00 0.00 3.34
104 105 3.556004 GCTAGTTGGTCCATAGATCTGGC 60.556 52.174 5.18 3.39 36.16 4.85
105 106 2.481441 AGTTGGTCCATAGATCTGGCA 58.519 47.619 5.18 0.00 36.16 4.92
253 254 9.635520 AGCATGACAATTTTTCTAATCTTTCAG 57.364 29.630 0.00 0.00 0.00 3.02
254 255 8.866956 GCATGACAATTTTTCTAATCTTTCAGG 58.133 33.333 0.00 0.00 0.00 3.86
255 256 9.362539 CATGACAATTTTTCTAATCTTTCAGGG 57.637 33.333 0.00 0.00 0.00 4.45
260 261 3.695830 TTCTAATCTTTCAGGGCGTGT 57.304 42.857 7.12 0.00 0.00 4.49
278 279 7.544217 AGGGCGTGTCATTTTTATAAATTTGTC 59.456 33.333 0.00 0.00 31.63 3.18
297 298 9.528018 AATTTGTCCGTATTTTATTGCTAATGG 57.472 29.630 0.00 0.00 0.00 3.16
346 347 8.268738 GCAGTTTTAAAGTTTAGCATGTCAAAG 58.731 33.333 0.00 0.00 0.00 2.77
352 353 7.573968 AAAGTTTAGCATGTCAAAGAAGTCT 57.426 32.000 0.00 0.00 0.00 3.24
365 366 5.941058 TCAAAGAAGTCTAGATCACTCGACT 59.059 40.000 0.00 0.00 46.37 4.18
406 407 6.721571 TTAACGTGGCATTTTTCAAACAAA 57.278 29.167 0.00 0.00 0.00 2.83
447 449 1.497309 TTTGGGTCAATCGGGGCTCT 61.497 55.000 0.00 0.00 0.00 4.09
448 450 1.910580 TTGGGTCAATCGGGGCTCTC 61.911 60.000 0.00 0.00 0.00 3.20
549 551 4.546674 CCAGTTATTGGGCCCTAAAGAAT 58.453 43.478 25.70 16.29 43.75 2.40
654 657 0.044161 CAAGCTAACGTACGCGCATC 60.044 55.000 16.72 0.98 42.83 3.91
655 658 0.457166 AAGCTAACGTACGCGCATCA 60.457 50.000 16.72 0.00 42.83 3.07
694 697 1.003928 CTAAACCCCACTAAACCCGCT 59.996 52.381 0.00 0.00 0.00 5.52
707 710 2.269241 CCGCTCCCTGTTCCTTCC 59.731 66.667 0.00 0.00 0.00 3.46
708 711 2.294078 CCGCTCCCTGTTCCTTCCT 61.294 63.158 0.00 0.00 0.00 3.36
726 729 0.679960 CTTGTTCCCGTTGGATCCCC 60.680 60.000 9.90 0.00 41.40 4.81
825 829 3.095278 CGACGTCACCGGTCGTTG 61.095 66.667 20.70 19.52 38.84 4.10
906 919 0.760572 TACTAATACAAGCCCGGCCC 59.239 55.000 5.55 0.00 0.00 5.80
1077 1094 4.873129 CTCCGCCCCATCGACGTG 62.873 72.222 0.00 0.00 0.00 4.49
1581 1604 3.245346 TCCGTGGTGGCCATGACA 61.245 61.111 9.72 6.12 42.73 3.58
1769 1796 7.011950 CAGTCAAACACACCTATGTCTAAAACA 59.988 37.037 0.00 0.00 43.51 2.83
1816 1843 8.565896 ACTGTTCATTAGCTAAATGTGAATGA 57.434 30.769 18.99 11.54 44.58 2.57
1847 1991 7.759489 TTGGAATTGACATAGTAGTTTTGCT 57.241 32.000 0.00 0.00 0.00 3.91
1849 1993 6.150976 TGGAATTGACATAGTAGTTTTGCTGG 59.849 38.462 0.00 0.00 0.00 4.85
1853 1997 5.381757 TGACATAGTAGTTTTGCTGGGTTT 58.618 37.500 0.00 0.00 0.00 3.27
1857 2001 6.097696 ACATAGTAGTTTTGCTGGGTTTGTTT 59.902 34.615 0.00 0.00 0.00 2.83
1884 2028 1.529226 TTGGGTGGTTAACTGATGCG 58.471 50.000 5.42 0.00 0.00 4.73
1893 2037 4.000988 GGTTAACTGATGCGGGTATATGG 58.999 47.826 5.42 0.00 0.00 2.74
1894 2038 4.262721 GGTTAACTGATGCGGGTATATGGA 60.263 45.833 5.42 0.00 0.00 3.41
1896 2040 3.616956 ACTGATGCGGGTATATGGATG 57.383 47.619 0.00 0.00 0.00 3.51
1897 2041 2.906389 ACTGATGCGGGTATATGGATGT 59.094 45.455 0.00 0.00 0.00 3.06
1898 2042 3.264947 CTGATGCGGGTATATGGATGTG 58.735 50.000 0.00 0.00 0.00 3.21
1997 2141 2.575532 ACATGGATGCAAAGATACCGG 58.424 47.619 0.00 0.00 0.00 5.28
2041 2185 3.509575 AGTGCCTTTGTTCAAGTCAAACA 59.490 39.130 0.00 0.00 34.93 2.83
2071 2215 8.529476 CAACACCTACTTAATAACACTCCTACT 58.471 37.037 0.00 0.00 0.00 2.57
2175 2337 3.804786 TTGCAAATATGGCACCATCAG 57.195 42.857 5.20 0.00 41.75 2.90
2180 2342 1.683943 ATATGGCACCATCAGCACAC 58.316 50.000 5.20 0.00 37.82 3.82
2228 2400 2.158856 TGCTCATCTAGGAACCATGCAG 60.159 50.000 0.00 0.00 0.00 4.41
2236 2408 2.519013 AGGAACCATGCAGACTTTTCC 58.481 47.619 0.00 0.00 33.96 3.13
2251 2423 7.301054 CAGACTTTTCCTTAAGCATGTTACTG 58.699 38.462 0.00 0.00 0.00 2.74
2273 2449 5.664457 TGTATCAATGAGTTGCCTCTGTAG 58.336 41.667 0.00 0.00 38.61 2.74
2306 2482 0.544833 TCCCGTTAGGCAACCTACCA 60.545 55.000 0.00 0.00 35.63 3.25
2355 3344 1.401905 CCATTTCTTTAGGGACTGCGC 59.598 52.381 0.00 0.00 41.52 6.09
2365 3354 2.719354 GACTGCGCCCGTGTTTTT 59.281 55.556 4.18 0.00 0.00 1.94
2388 3377 9.712305 TTTTTCTTGTTTGATTGAAACCAACTA 57.288 25.926 0.00 0.00 43.04 2.24
2389 3378 9.712305 TTTTCTTGTTTGATTGAAACCAACTAA 57.288 25.926 0.00 0.00 43.04 2.24
2470 3527 4.518249 GTCTCTATTCCAAGGAGGGTTTG 58.482 47.826 0.00 0.00 38.24 2.93
2473 3530 4.662278 TCTATTCCAAGGAGGGTTTGTTG 58.338 43.478 0.00 0.00 38.24 3.33
2508 3565 5.450550 GGTTATGGGCTTTAAATCTGTGCTC 60.451 44.000 0.00 0.00 0.00 4.26
2559 3616 2.092375 AGTGCTTGGGCCCTTAATCTAC 60.092 50.000 25.70 12.58 37.74 2.59
2600 3662 0.466124 CTAAGCTAGGCCACCACCTC 59.534 60.000 5.01 0.00 41.50 3.85
2659 3721 4.670347 GAGGAAGAAATGCTGCTGAATTC 58.330 43.478 0.00 0.00 0.00 2.17
2819 3897 1.836555 GTAAGCTTCTACGTACACGCG 59.163 52.381 3.53 3.53 44.43 6.01
2827 3947 0.110238 TACGTACACGCGTTCCAGTC 60.110 55.000 10.22 0.00 43.04 3.51
2866 4008 8.642020 GCAAAGTTTGACTATGAGCAAATTAAG 58.358 33.333 19.82 0.00 36.51 1.85
2914 4056 2.682494 ATTTGCAGGCAGCTGGGG 60.682 61.111 17.12 0.00 45.94 4.96
3125 4274 0.877213 AGCAAAGCAAAGGCAAAGCG 60.877 50.000 0.00 0.00 44.61 4.68
3170 4319 2.428902 CAACACGCACCGCATTGG 60.429 61.111 0.00 0.00 46.41 3.16
3210 4359 2.684881 CAACCCATGGATGTGAAGCTAC 59.315 50.000 15.22 0.00 0.00 3.58
3224 4373 5.361857 TGTGAAGCTACCCATTACTACTACC 59.638 44.000 0.00 0.00 0.00 3.18
3227 4376 3.887716 AGCTACCCATTACTACTACCACG 59.112 47.826 0.00 0.00 0.00 4.94
3228 4377 3.633986 GCTACCCATTACTACTACCACGT 59.366 47.826 0.00 0.00 0.00 4.49
3229 4378 4.821805 GCTACCCATTACTACTACCACGTA 59.178 45.833 0.00 0.00 0.00 3.57
3231 4380 3.954258 ACCCATTACTACTACCACGTACC 59.046 47.826 0.00 0.00 0.00 3.34
3338 4488 5.220416 CGATGTCGTTTTATTTCCTCCTGTC 60.220 44.000 0.00 0.00 34.11 3.51
3379 4529 5.801350 TGATGCTACTACATGACTTTTGC 57.199 39.130 0.00 0.00 0.00 3.68
3381 4531 3.920446 TGCTACTACATGACTTTTGCGA 58.080 40.909 0.00 0.00 0.00 5.10
3404 4554 1.994916 CGATTGTGGGCCAAAATCAC 58.005 50.000 36.59 20.08 37.81 3.06
3408 4558 1.327303 TGTGGGCCAAAATCACTGTC 58.673 50.000 8.40 0.00 33.04 3.51
3411 4561 1.707989 TGGGCCAAAATCACTGTCCTA 59.292 47.619 2.13 0.00 0.00 2.94
3418 4568 5.475564 GCCAAAATCACTGTCCTAACCTTTA 59.524 40.000 0.00 0.00 0.00 1.85
3419 4569 6.015772 GCCAAAATCACTGTCCTAACCTTTAA 60.016 38.462 0.00 0.00 0.00 1.52
3438 4588 9.150348 ACCTTTAAAACAATCTTTGTCACAAAG 57.850 29.630 22.39 22.39 44.59 2.77
3446 4596 4.857871 TCTTTGTCACAAAGTGAACTCG 57.142 40.909 26.10 3.16 44.49 4.18
3491 4641 2.032924 ACCTTTTTAGCAACGTCACAGC 59.967 45.455 0.00 0.00 0.00 4.40
3515 4665 4.116961 CGTGGCGTTTCTTCTCCATATAA 58.883 43.478 0.00 0.00 0.00 0.98
3521 4671 6.402875 GGCGTTTCTTCTCCATATAAAAACGT 60.403 38.462 15.86 0.00 45.35 3.99
3523 4673 6.892951 CGTTTCTTCTCCATATAAAAACGTCG 59.107 38.462 8.76 0.00 41.27 5.12
3559 4709 0.537143 AGCTCCACATTCAAACGCCA 60.537 50.000 0.00 0.00 0.00 5.69
3568 4718 0.874390 TTCAAACGCCAAGCTAGCTG 59.126 50.000 20.16 12.30 0.00 4.24
3569 4719 0.955428 TCAAACGCCAAGCTAGCTGG 60.955 55.000 20.16 21.29 0.00 4.85
3589 4739 3.181486 TGGCGTTTTTGCTCAACATGTAA 60.181 39.130 0.00 0.00 34.52 2.41
3600 4750 4.615912 GCTCAACATGTAAAACGCCAAGAT 60.616 41.667 0.00 0.00 0.00 2.40
3601 4751 5.391523 GCTCAACATGTAAAACGCCAAGATA 60.392 40.000 0.00 0.00 0.00 1.98
3602 4752 6.677920 GCTCAACATGTAAAACGCCAAGATAT 60.678 38.462 0.00 0.00 0.00 1.63
3650 4800 4.214980 CCATGAGCTTTGGCGTTTATAG 57.785 45.455 3.92 0.00 44.37 1.31
3790 4940 4.562425 ACCTGGTGCACGTGTGGG 62.562 66.667 18.38 13.78 0.00 4.61
3817 4967 1.374631 CACAAGCTCGGCTACTGCA 60.375 57.895 0.00 0.00 38.25 4.41
3841 4991 2.693591 CAGGGAGCTAATCGTTACCTCA 59.306 50.000 0.00 0.00 0.00 3.86
3842 4992 2.959707 AGGGAGCTAATCGTTACCTCAG 59.040 50.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.752833 CCGGTCAATAGGGCCTACC 59.247 63.158 17.19 14.47 40.67 3.18
6 7 1.341531 CACTAGAGCCGGTCAATAGGG 59.658 57.143 1.90 0.00 0.00 3.53
7 8 2.294791 CTCACTAGAGCCGGTCAATAGG 59.705 54.545 1.90 0.00 34.61 2.57
8 9 2.294791 CCTCACTAGAGCCGGTCAATAG 59.705 54.545 1.90 3.46 40.68 1.73
9 10 2.307768 CCTCACTAGAGCCGGTCAATA 58.692 52.381 1.90 0.00 40.68 1.90
10 11 1.115467 CCTCACTAGAGCCGGTCAAT 58.885 55.000 1.90 0.00 40.68 2.57
11 12 0.970937 CCCTCACTAGAGCCGGTCAA 60.971 60.000 1.90 0.00 40.68 3.18
12 13 1.379977 CCCTCACTAGAGCCGGTCA 60.380 63.158 1.90 0.00 40.68 4.02
13 14 1.076923 TCCCTCACTAGAGCCGGTC 60.077 63.158 1.90 0.00 40.68 4.79
14 15 1.076632 CTCCCTCACTAGAGCCGGT 60.077 63.158 1.90 0.00 40.68 5.28
15 16 1.076632 ACTCCCTCACTAGAGCCGG 60.077 63.158 0.00 0.00 40.68 6.13
16 17 0.681564 ACACTCCCTCACTAGAGCCG 60.682 60.000 0.00 0.00 40.68 5.52
17 18 0.820871 CACACTCCCTCACTAGAGCC 59.179 60.000 0.00 0.00 40.68 4.70
18 19 1.840737 TCACACTCCCTCACTAGAGC 58.159 55.000 0.00 0.00 40.68 4.09
19 20 3.625853 TCATCACACTCCCTCACTAGAG 58.374 50.000 0.00 0.00 41.72 2.43
20 21 3.625853 CTCATCACACTCCCTCACTAGA 58.374 50.000 0.00 0.00 0.00 2.43
21 22 2.692557 CCTCATCACACTCCCTCACTAG 59.307 54.545 0.00 0.00 0.00 2.57
22 23 2.624293 CCCTCATCACACTCCCTCACTA 60.624 54.545 0.00 0.00 0.00 2.74
23 24 1.566211 CCTCATCACACTCCCTCACT 58.434 55.000 0.00 0.00 0.00 3.41
24 25 0.539051 CCCTCATCACACTCCCTCAC 59.461 60.000 0.00 0.00 0.00 3.51
25 26 1.267574 GCCCTCATCACACTCCCTCA 61.268 60.000 0.00 0.00 0.00 3.86
26 27 1.267574 TGCCCTCATCACACTCCCTC 61.268 60.000 0.00 0.00 0.00 4.30
27 28 0.842030 TTGCCCTCATCACACTCCCT 60.842 55.000 0.00 0.00 0.00 4.20
28 29 0.678048 GTTGCCCTCATCACACTCCC 60.678 60.000 0.00 0.00 0.00 4.30
29 30 1.021390 CGTTGCCCTCATCACACTCC 61.021 60.000 0.00 0.00 0.00 3.85
30 31 0.320771 ACGTTGCCCTCATCACACTC 60.321 55.000 0.00 0.00 0.00 3.51
31 32 0.603707 CACGTTGCCCTCATCACACT 60.604 55.000 0.00 0.00 0.00 3.55
32 33 0.884704 ACACGTTGCCCTCATCACAC 60.885 55.000 0.00 0.00 0.00 3.82
33 34 0.602638 GACACGTTGCCCTCATCACA 60.603 55.000 0.00 0.00 0.00 3.58
34 35 0.320771 AGACACGTTGCCCTCATCAC 60.321 55.000 0.00 0.00 0.00 3.06
35 36 0.396435 AAGACACGTTGCCCTCATCA 59.604 50.000 0.00 0.00 0.00 3.07
36 37 1.523758 AAAGACACGTTGCCCTCATC 58.476 50.000 0.00 0.00 0.00 2.92
43 44 5.992729 TGGAATAAACTAAAGACACGTTGC 58.007 37.500 0.00 0.00 0.00 4.17
49 50 7.987649 ACAAACGTTGGAATAAACTAAAGACA 58.012 30.769 10.33 0.00 34.12 3.41
79 80 3.570550 AGATCTATGGACCAACTAGCGAC 59.429 47.826 0.00 0.00 0.00 5.19
144 145 6.073167 TCGATCTATTCCTAATCTGTCACGAC 60.073 42.308 0.00 0.00 0.00 4.34
184 185 8.964772 CATCCTCCACATAAGATTTTCTCTTTT 58.035 33.333 0.00 0.00 41.60 2.27
188 189 5.240403 GCCATCCTCCACATAAGATTTTCTC 59.760 44.000 0.00 0.00 0.00 2.87
190 191 4.889409 TGCCATCCTCCACATAAGATTTTC 59.111 41.667 0.00 0.00 0.00 2.29
201 202 6.152831 ACTTTATAAAAACTGCCATCCTCCAC 59.847 38.462 0.00 0.00 0.00 4.02
203 204 6.775594 ACTTTATAAAAACTGCCATCCTCC 57.224 37.500 0.00 0.00 0.00 4.30
241 242 2.565391 TGACACGCCCTGAAAGATTAGA 59.435 45.455 0.00 0.00 34.07 2.10
242 243 2.972625 TGACACGCCCTGAAAGATTAG 58.027 47.619 0.00 0.00 34.07 1.73
247 248 3.369546 AAAAATGACACGCCCTGAAAG 57.630 42.857 0.00 0.00 0.00 2.62
253 254 7.201487 GGACAAATTTATAAAAATGACACGCCC 60.201 37.037 16.24 7.06 35.46 6.13
254 255 7.462200 CGGACAAATTTATAAAAATGACACGCC 60.462 37.037 16.24 9.95 35.46 5.68
255 256 7.061326 ACGGACAAATTTATAAAAATGACACGC 59.939 33.333 16.24 2.76 35.46 5.34
306 307 9.959721 ACTTTAAAACTGCCATCTTCTAGATAA 57.040 29.630 0.00 0.00 32.12 1.75
426 427 0.611896 AGCCCCGATTGACCCAAAAG 60.612 55.000 0.00 0.00 0.00 2.27
474 476 0.252103 TCCTAGCGACCCTTTCTGGT 60.252 55.000 0.00 0.00 42.79 4.00
527 529 3.662759 TCTTTAGGGCCCAATAACTGG 57.337 47.619 27.56 7.75 45.97 4.00
539 541 8.028938 CACACTTTGGACATAAATTCTTTAGGG 58.971 37.037 0.00 0.00 31.62 3.53
654 657 4.478206 AGTGATCTACCACAATCCACTG 57.522 45.455 0.00 0.00 39.42 3.66
655 658 6.407202 GTTTAGTGATCTACCACAATCCACT 58.593 40.000 0.00 0.00 39.42 4.00
694 697 1.423921 GGAACAAGGAAGGAACAGGGA 59.576 52.381 0.00 0.00 0.00 4.20
726 729 0.534652 GGATAGGGCAGCAGCAAGAG 60.535 60.000 2.65 0.00 44.61 2.85
906 919 2.549754 AGTGTTTGAATTCGGAGCAGTG 59.450 45.455 0.04 0.00 0.00 3.66
917 930 1.317613 TGCGGCTCAAGTGTTTGAAT 58.682 45.000 0.00 0.00 42.48 2.57
1230 1253 2.364317 TTCCTCCTCCTGCTCCCG 60.364 66.667 0.00 0.00 0.00 5.14
1745 1768 7.012044 AGTGTTTTAGACATAGGTGTGTTTGAC 59.988 37.037 0.00 0.00 41.10 3.18
1750 1773 8.999431 CATTTAGTGTTTTAGACATAGGTGTGT 58.001 33.333 0.00 0.00 41.10 3.72
1842 1869 1.280457 ACCCAAACAAACCCAGCAAA 58.720 45.000 0.00 0.00 0.00 3.68
1843 1870 2.035632 CTACCCAAACAAACCCAGCAA 58.964 47.619 0.00 0.00 0.00 3.91
1847 1991 2.766828 CCAAACTACCCAAACAAACCCA 59.233 45.455 0.00 0.00 0.00 4.51
1849 1993 2.767394 ACCCAAACTACCCAAACAAACC 59.233 45.455 0.00 0.00 0.00 3.27
1853 1997 1.288335 ACCACCCAAACTACCCAAACA 59.712 47.619 0.00 0.00 0.00 2.83
1857 2001 2.784682 AGTTAACCACCCAAACTACCCA 59.215 45.455 0.88 0.00 31.84 4.51
1884 2028 5.451798 CCAAAGCAAACACATCCATATACCC 60.452 44.000 0.00 0.00 0.00 3.69
1893 2037 4.232221 CTCATCACCAAAGCAAACACATC 58.768 43.478 0.00 0.00 0.00 3.06
1894 2038 3.638160 ACTCATCACCAAAGCAAACACAT 59.362 39.130 0.00 0.00 0.00 3.21
1896 2040 3.715628 ACTCATCACCAAAGCAAACAC 57.284 42.857 0.00 0.00 0.00 3.32
1897 2041 3.820467 CCTACTCATCACCAAAGCAAACA 59.180 43.478 0.00 0.00 0.00 2.83
1898 2042 3.366374 GCCTACTCATCACCAAAGCAAAC 60.366 47.826 0.00 0.00 0.00 2.93
1997 2141 2.420372 GCTTACTTACCTGCTGGAAAGC 59.580 50.000 17.64 16.52 37.04 3.51
2041 2185 7.174426 GGAGTGTTATTAAGTAGGTGTTGCTTT 59.826 37.037 0.00 0.00 33.49 3.51
2175 2337 2.361757 TGCCATGCATATAAAGGTGTGC 59.638 45.455 0.00 0.00 38.05 4.57
2228 2400 7.203255 ACAGTAACATGCTTAAGGAAAAGTC 57.797 36.000 0.00 0.00 0.00 3.01
2236 2408 9.102757 ACTCATTGATACAGTAACATGCTTAAG 57.897 33.333 0.00 0.00 0.00 1.85
2273 2449 2.165319 ACGGGAGCAAAGTCACTAAC 57.835 50.000 0.00 0.00 0.00 2.34
2306 2482 6.319048 ACAGTCATTCCTATCTTGGTCAAT 57.681 37.500 0.00 0.00 0.00 2.57
2365 3354 8.527810 ACTTAGTTGGTTTCAATCAAACAAGAA 58.472 29.630 11.60 0.00 45.66 2.52
2375 3364 4.457466 ACACGGACTTAGTTGGTTTCAAT 58.543 39.130 0.00 0.00 35.10 2.57
2376 3365 3.876341 ACACGGACTTAGTTGGTTTCAA 58.124 40.909 0.00 0.00 0.00 2.69
2377 3366 3.547054 ACACGGACTTAGTTGGTTTCA 57.453 42.857 0.00 0.00 0.00 2.69
2378 3367 4.095334 ACAAACACGGACTTAGTTGGTTTC 59.905 41.667 0.00 0.00 0.00 2.78
2388 3377 1.066908 CATGCCAACAAACACGGACTT 59.933 47.619 0.00 0.00 0.00 3.01
2389 3378 0.667993 CATGCCAACAAACACGGACT 59.332 50.000 0.00 0.00 0.00 3.85
2470 3527 2.616842 CCATAACCGAGCATTACCCAAC 59.383 50.000 0.00 0.00 0.00 3.77
2473 3530 1.892209 CCCATAACCGAGCATTACCC 58.108 55.000 0.00 0.00 0.00 3.69
2508 3565 4.522971 GCTTTAGAGCCCACGGAG 57.477 61.111 0.00 0.00 43.29 4.63
2528 3585 2.825836 CAAGCACTCGGCCCATCC 60.826 66.667 0.00 0.00 46.50 3.51
2693 3758 6.366877 CAGCAATTCCGTTTCATTTTCAGAAT 59.633 34.615 0.00 0.00 0.00 2.40
2704 3769 0.729140 CACGCCAGCAATTCCGTTTC 60.729 55.000 0.00 0.00 0.00 2.78
2819 3897 1.108776 ATGCATGCATGGACTGGAAC 58.891 50.000 31.74 9.08 35.03 3.62
2845 3965 6.961554 CCGACTTAATTTGCTCATAGTCAAAC 59.038 38.462 0.00 0.00 35.34 2.93
2846 3966 6.653320 ACCGACTTAATTTGCTCATAGTCAAA 59.347 34.615 0.00 0.00 36.72 2.69
2866 4008 1.332904 CGTCAGCTTTGTTTCACCGAC 60.333 52.381 0.00 0.00 0.00 4.79
3125 4274 2.203294 AACGTTGACAGGCCACCC 60.203 61.111 5.01 0.00 0.00 4.61
3170 4319 1.487976 TGACCTCTCCAGGCAATCATC 59.512 52.381 0.00 0.00 45.05 2.92
3210 4359 3.953612 TGGTACGTGGTAGTAGTAATGGG 59.046 47.826 0.00 0.00 0.00 4.00
3224 4373 1.065701 CCTAGCAGCTAGTGGTACGTG 59.934 57.143 25.03 6.24 38.14 4.49
3227 4376 3.889520 AAACCTAGCAGCTAGTGGTAC 57.110 47.619 25.03 0.00 38.14 3.34
3228 4377 4.346730 TGTAAACCTAGCAGCTAGTGGTA 58.653 43.478 25.03 12.36 38.14 3.25
3229 4378 3.170717 TGTAAACCTAGCAGCTAGTGGT 58.829 45.455 25.03 16.47 40.92 4.16
3231 4380 3.430929 CCCTGTAAACCTAGCAGCTAGTG 60.431 52.174 25.03 18.82 32.62 2.74
3314 4463 4.630069 ACAGGAGGAAATAAAACGACATCG 59.370 41.667 0.00 0.00 46.33 3.84
3319 4468 3.585732 AGGGACAGGAGGAAATAAAACGA 59.414 43.478 0.00 0.00 0.00 3.85
3338 4488 1.067516 CAAAGCAAACAGTCACCAGGG 59.932 52.381 0.00 0.00 0.00 4.45
3379 4529 4.160635 GGCCCACAATCGCGTTCG 62.161 66.667 5.77 0.00 0.00 3.95
3381 4531 1.739338 TTTTGGCCCACAATCGCGTT 61.739 50.000 5.77 0.00 39.21 4.84
3404 4554 9.463443 CAAAGATTGTTTTAAAGGTTAGGACAG 57.537 33.333 0.00 0.00 0.00 3.51
3408 4558 9.244799 GTGACAAAGATTGTTTTAAAGGTTAGG 57.755 33.333 0.00 0.00 45.52 2.69
3411 4561 9.495572 TTTGTGACAAAGATTGTTTTAAAGGTT 57.504 25.926 6.66 0.00 45.52 3.50
3418 4568 7.872483 AGTTCACTTTGTGACAAAGATTGTTTT 59.128 29.630 36.37 15.42 45.52 2.43
3419 4569 7.378181 AGTTCACTTTGTGACAAAGATTGTTT 58.622 30.769 36.37 16.08 45.52 2.83
3438 4588 7.117241 TGAAATACTTTCATGTCGAGTTCAC 57.883 36.000 0.00 0.00 44.21 3.18
3461 4611 5.107220 ACGTTGCTAAAAAGGTTAGATCGTG 60.107 40.000 0.00 0.00 0.00 4.35
3469 4619 3.488553 GCTGTGACGTTGCTAAAAAGGTT 60.489 43.478 0.00 0.00 0.00 3.50
3477 4627 2.048597 CGGGCTGTGACGTTGCTA 60.049 61.111 0.00 0.00 0.00 3.49
3491 4641 2.033194 GGAGAAGAAACGCCACGGG 61.033 63.158 0.00 0.00 0.00 5.28
3504 4654 7.594015 GCTATCTCGACGTTTTTATATGGAGAA 59.406 37.037 0.00 0.00 33.52 2.87
3523 4673 0.849579 GCTGAAACGCGAGCTATCTC 59.150 55.000 15.93 0.00 35.99 2.75
3533 4683 0.874390 TGAATGTGGAGCTGAAACGC 59.126 50.000 0.00 0.00 0.00 4.84
3559 4709 0.039165 GCAAAAACGCCAGCTAGCTT 60.039 50.000 16.46 0.00 0.00 3.74
3568 4718 1.851658 ACATGTTGAGCAAAAACGCC 58.148 45.000 0.00 0.00 0.00 5.68
3569 4719 5.187480 GTTTTACATGTTGAGCAAAAACGC 58.813 37.500 2.30 0.00 30.14 4.84
3710 4860 0.541863 GAACACCGGGACCATGATCT 59.458 55.000 6.32 0.00 0.00 2.75
3790 4940 2.328099 CGAGCTTGTGGTTGAGGCC 61.328 63.158 0.00 0.00 0.00 5.19
3897 5047 3.568853 ACTTACGCTTCCGCTAGACATAT 59.431 43.478 0.00 0.00 38.22 1.78
3915 5065 7.385205 GCTCAAGCTTCATTCGGATATTACTTA 59.615 37.037 0.00 0.00 38.21 2.24


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

AutoCloner maintained by Alex Coulton.