Multiple sequence alignment - TraesCS1B01G250100

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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 TraesCS1B01G250100 chr1B 100.000 6199 0 0 572 6770 442181680 442175482 0.000000e+00 11448.0
1 TraesCS1B01G250100 chr1B 100.000 282 0 0 1 282 442182251 442181970 7.780000e-144 521.0
2 TraesCS1B01G250100 chr1B 93.548 93 6 0 585 677 562470630 562470538 9.160000e-29 139.0
3 TraesCS1B01G250100 chr1B 91.304 69 5 1 2031 2098 399622557 399622489 7.230000e-15 93.5
4 TraesCS1B01G250100 chr1D 96.833 4137 101 20 2201 6326 328101709 328097592 0.000000e+00 6887.0
5 TraesCS1B01G250100 chr1D 94.545 1540 61 6 677 2200 328103278 328101746 0.000000e+00 2357.0
6 TraesCS1B01G250100 chr1D 88.571 70 5 2 4547 4616 480394137 480394203 1.560000e-11 82.4
7 TraesCS1B01G250100 chr1A 94.708 2872 123 17 3905 6769 407325830 407322981 0.000000e+00 4434.0
8 TraesCS1B01G250100 chr1A 94.702 1491 48 8 738 2200 407329257 407327770 0.000000e+00 2287.0
9 TraesCS1B01G250100 chr1A 96.692 1179 31 5 2201 3371 407327733 407326555 0.000000e+00 1954.0
10 TraesCS1B01G250100 chr1A 97.043 541 15 1 3358 3898 407326536 407325997 0.000000e+00 909.0
11 TraesCS1B01G250100 chr1A 75.532 376 49 24 6385 6756 456326284 456326620 1.970000e-30 145.0
12 TraesCS1B01G250100 chr1A 91.919 99 7 1 583 680 58277348 58277250 3.290000e-28 137.0
13 TraesCS1B01G250100 chr1A 90.000 70 5 2 4546 4614 538407231 538407299 9.350000e-14 89.8
14 TraesCS1B01G250100 chr5B 97.872 282 5 1 1 282 106355344 106355064 2.840000e-133 486.0
15 TraesCS1B01G250100 chr5B 95.390 282 13 0 1 282 344238151 344238432 3.720000e-122 449.0
16 TraesCS1B01G250100 chr5B 81.472 394 53 8 6367 6760 75220130 75220503 8.530000e-79 305.0
17 TraesCS1B01G250100 chr5B 93.377 151 10 0 4985 5135 98663178 98663328 2.460000e-54 224.0
18 TraesCS1B01G250100 chr5B 93.750 96 5 1 583 678 106354592 106354498 7.080000e-30 143.0
19 TraesCS1B01G250100 chr5B 80.153 131 24 2 4487 4615 21728255 21728385 5.590000e-16 97.1
20 TraesCS1B01G250100 chr7B 95.745 282 11 1 1 282 395639940 395639660 2.880000e-123 453.0
21 TraesCS1B01G250100 chr7B 93.421 152 9 1 4985 5135 453623443 453623292 2.460000e-54 224.0
22 TraesCS1B01G250100 chr7B 94.845 97 4 1 583 679 395639240 395639145 4.230000e-32 150.0
23 TraesCS1B01G250100 chr7B 94.681 94 5 0 585 678 568483837 568483930 5.470000e-31 147.0
24 TraesCS1B01G250100 chr4A 95.035 282 14 0 1 282 656817510 656817791 1.730000e-120 444.0
25 TraesCS1B01G250100 chr4A 93.972 282 16 1 1 282 436436636 436436916 6.280000e-115 425.0
26 TraesCS1B01G250100 chr4A 93.750 96 6 0 585 680 654845676 654845771 1.970000e-30 145.0
27 TraesCS1B01G250100 chr3A 94.681 282 15 0 1 282 41105213 41104932 8.060000e-119 438.0
28 TraesCS1B01G250100 chr3A 79.562 137 22 5 4488 4620 690435870 690435736 7.230000e-15 93.5
29 TraesCS1B01G250100 chr2B 94.326 282 16 0 1 282 408316033 408316314 3.750000e-117 433.0
30 TraesCS1B01G250100 chr2B 93.939 99 4 2 583 681 800719561 800719465 1.520000e-31 148.0
31 TraesCS1B01G250100 chr2B 90.476 63 6 0 2031 2093 535565599 535565661 4.350000e-12 84.2
32 TraesCS1B01G250100 chr5A 94.306 281 16 0 2 282 618261831 618262111 1.350000e-116 431.0
33 TraesCS1B01G250100 chr5A 91.824 159 12 1 4977 5135 86662012 86662169 3.180000e-53 220.0
34 TraesCS1B01G250100 chr5A 91.824 159 10 3 4979 5135 139927975 139927818 1.140000e-52 219.0
35 TraesCS1B01G250100 chr4B 94.326 282 15 1 1 282 185875416 185875136 1.350000e-116 431.0
36 TraesCS1B01G250100 chr6B 86.072 359 41 5 6366 6722 591460530 591460179 1.780000e-100 377.0
37 TraesCS1B01G250100 chr7A 93.631 157 9 1 4980 5135 462978745 462978589 4.080000e-57 233.0
38 TraesCS1B01G250100 chr7A 89.815 108 10 1 572 678 624811431 624811324 3.290000e-28 137.0
39 TraesCS1B01G250100 chr7D 93.421 152 9 1 4985 5135 436961948 436961797 2.460000e-54 224.0
40 TraesCS1B01G250100 chr7D 91.875 160 7 2 4982 5135 42644753 42644594 1.140000e-52 219.0
41 TraesCS1B01G250100 chr3D 88.889 153 13 4 6365 6517 489157695 489157843 1.160000e-42 185.0
42 TraesCS1B01G250100 chr3B 94.681 94 5 0 585 678 550976730 550976637 5.470000e-31 147.0
43 TraesCS1B01G250100 chr3B 80.198 101 14 5 4487 4582 817063773 817063674 3.390000e-08 71.3
44 TraesCS1B01G250100 chr5D 80.392 153 22 7 4495 4642 539145787 539145638 7.180000e-20 110.0
45 TraesCS1B01G250100 chr6A 92.754 69 4 1 2031 2098 463805572 463805504 1.550000e-16 99.0
46 TraesCS1B01G250100 chr2D 77.500 160 28 7 4487 4642 157035415 157035570 9.350000e-14 89.8


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 TraesCS1B01G250100 chr1B 442175482 442182251 6769 True 5984.5 11448 100.00000 1 6770 2 chr1B.!!$R3 6769
1 TraesCS1B01G250100 chr1D 328097592 328103278 5686 True 4622.0 6887 95.68900 677 6326 2 chr1D.!!$R1 5649
2 TraesCS1B01G250100 chr1A 407322981 407329257 6276 True 2396.0 4434 95.78625 738 6769 4 chr1A.!!$R2 6031
3 TraesCS1B01G250100 chr5B 106354498 106355344 846 True 314.5 486 95.81100 1 678 2 chr5B.!!$R1 677
4 TraesCS1B01G250100 chr7B 395639145 395639940 795 True 301.5 453 95.29500 1 679 2 chr7B.!!$R2 678

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
636 807 0.108041 GGAATGTTGGCTTGGGCATG 60.108 55.000 0.00 0.0 38.08 4.06 F
1528 1727 0.761187 ACCATGTGGCGCATCTATCT 59.239 50.000 11.25 0.0 39.32 1.98 F
2476 2713 1.071128 GGCCACAAAGCAATTGCCA 59.929 52.632 26.45 0.0 43.13 4.92 F
2622 2861 1.135803 CGACAGCGTTTTTATGTGGGG 60.136 52.381 0.00 0.0 0.00 4.96 F
4221 4668 1.174712 ACCATCAACACACTGCCTGC 61.175 55.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2527 1.134220 ACTTGAACAACTCCTGCGGAA 60.134 47.619 0.00 0.00 0.00 4.30 R
3103 3344 0.107081 TGGTCCGTGTTCAACCGAAT 59.893 50.000 0.53 0.00 35.76 3.34 R
3378 3664 2.759191 CTGACAGTCAGCTAGTTGCAA 58.241 47.619 17.77 0.00 45.94 4.08 R
4531 4978 3.119779 TGGTCAAAACAACGGTCAAAGAC 60.120 43.478 0.00 0.00 0.00 3.01 R
6216 6670 0.174845 CTTACCGGATCCGCAACAGA 59.825 55.000 29.12 9.34 38.24 3.41 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
65 66 3.399305 ACTCCAATTTCCCTGACCTTCTT 59.601 43.478 0.00 0.00 0.00 2.52
82 83 0.883814 CTTGCGGAGATCCATGCCTC 60.884 60.000 0.00 0.00 35.14 4.70
601 772 2.347731 TCTTGTGTGTGTGTTTGCGTA 58.652 42.857 0.00 0.00 0.00 4.42
613 784 3.495377 GTGTTTGCGTATGTGTGAACCTA 59.505 43.478 0.00 0.00 0.00 3.08
636 807 0.108041 GGAATGTTGGCTTGGGCATG 60.108 55.000 0.00 0.00 38.08 4.06
685 856 7.563888 AAAGCCCTTTTCGGTAATATAAGAC 57.436 36.000 0.00 0.00 0.00 3.01
805 976 8.671384 TTTATGCCACATAAAGTAGATACACC 57.329 34.615 8.34 0.00 0.00 4.16
1356 1555 2.100631 ACTCTCCGAAATTGCCGCG 61.101 57.895 0.00 0.00 0.00 6.46
1382 1581 5.410924 TGTCTCCGACAAGATGTAAATCTG 58.589 41.667 0.00 0.00 39.78 2.90
1394 1593 2.025037 TGTAAATCTGCTGGGCCTTGAT 60.025 45.455 4.53 0.08 0.00 2.57
1395 1594 2.242882 AAATCTGCTGGGCCTTGATT 57.757 45.000 4.53 6.57 0.00 2.57
1404 1603 3.367395 GCTGGGCCTTGATTTAGTTTGTC 60.367 47.826 4.53 0.00 0.00 3.18
1422 1621 2.736721 TGTCTCAGTTCATACGCAAAGC 59.263 45.455 0.00 0.00 0.00 3.51
1448 1647 4.319177 ACTATCAGTTTGGTCTTGACAGC 58.681 43.478 3.08 0.00 0.00 4.40
1528 1727 0.761187 ACCATGTGGCGCATCTATCT 59.239 50.000 11.25 0.00 39.32 1.98
1529 1728 1.970640 ACCATGTGGCGCATCTATCTA 59.029 47.619 11.25 0.00 39.32 1.98
1533 1732 4.502016 CATGTGGCGCATCTATCTAGAAT 58.498 43.478 11.25 0.00 35.19 2.40
1534 1733 4.179926 TGTGGCGCATCTATCTAGAATC 57.820 45.455 10.83 0.00 35.69 2.52
1700 1899 2.224670 TGCCCTTTGGAATACAACGAGT 60.225 45.455 0.00 0.00 39.19 4.18
2156 2355 4.823442 TGAGCATTGTCAACTTTGATCTGT 59.177 37.500 4.94 0.00 39.73 3.41
2200 2399 6.476378 ACATCCTACTTGAAGCATAAACACT 58.524 36.000 0.00 0.00 0.00 3.55
2201 2400 6.595716 ACATCCTACTTGAAGCATAAACACTC 59.404 38.462 0.00 0.00 0.00 3.51
2202 2401 6.360370 TCCTACTTGAAGCATAAACACTCT 57.640 37.500 0.00 0.00 0.00 3.24
2219 2455 8.506168 AAACACTCTGTACAAAAGATCTTTCA 57.494 30.769 20.71 13.03 31.45 2.69
2290 2527 3.637229 CCAATAGTACTGGTGATCTCCGT 59.363 47.826 5.39 11.57 0.00 4.69
2473 2710 1.598601 GTGTTGGCCACAAAGCAATTG 59.401 47.619 3.88 0.00 43.92 2.32
2476 2713 1.071128 GGCCACAAAGCAATTGCCA 59.929 52.632 26.45 0.00 43.13 4.92
2577 2814 9.529325 CATACTGTTAGTGTTTATGCTAAGCTA 57.471 33.333 0.00 0.00 0.00 3.32
2579 2816 8.425577 ACTGTTAGTGTTTATGCTAAGCTATG 57.574 34.615 0.00 0.00 0.00 2.23
2608 2847 3.825308 TCAAAATTTGAGATGCGACAGC 58.175 40.909 4.03 0.00 38.20 4.40
2622 2861 1.135803 CGACAGCGTTTTTATGTGGGG 60.136 52.381 0.00 0.00 0.00 4.96
2626 2865 3.244630 ACAGCGTTTTTATGTGGGGTCTA 60.245 43.478 0.00 0.00 0.00 2.59
2688 2927 5.856455 CCTTAAAAGTAAGTTGGTTCGCATG 59.144 40.000 0.00 0.00 35.82 4.06
2785 3024 5.119588 TGAATTCTACTTTAGAAACGCACCG 59.880 40.000 7.05 0.00 46.81 4.94
3103 3344 4.640201 GGCAAGCTCCATTAATGAACTGTA 59.360 41.667 17.23 0.00 0.00 2.74
3378 3664 4.285003 TGTAGTGTTATTGGCTGTGGTACT 59.715 41.667 0.00 0.00 0.00 2.73
3423 3709 3.815401 GCTTACTGGAGTTTTTCTGAGCA 59.185 43.478 0.00 0.00 0.00 4.26
3571 3858 1.923395 CCCCAGCACTTAGACCCCA 60.923 63.158 0.00 0.00 0.00 4.96
3968 4415 5.219343 TGATCTTTGGCTCGATCATGTAT 57.781 39.130 8.96 0.00 40.62 2.29
4221 4668 1.174712 ACCATCAACACACTGCCTGC 61.175 55.000 0.00 0.00 0.00 4.85
4399 4846 3.565307 TGCTTTCCACCTCTTTTCACAT 58.435 40.909 0.00 0.00 0.00 3.21
4531 4978 8.621286 ACTCAACTACCTTGTATTTTGTTTCTG 58.379 33.333 0.00 0.00 0.00 3.02
4622 5070 9.270640 TCATATTTGAAAAACTTTCCAATGGTG 57.729 29.630 0.00 7.32 0.00 4.17
4628 5076 7.262048 TGAAAAACTTTCCAATGGTGTACTTC 58.738 34.615 0.00 5.01 0.00 3.01
4697 5145 5.860716 ACGGTCAAAGTTAGACTCGAAATAC 59.139 40.000 0.00 0.00 36.29 1.89
4792 5240 9.862149 AGTATTTTTCTTCTTCCTTCTACCAAA 57.138 29.630 0.00 0.00 0.00 3.28
5127 5576 8.312896 TGCAAAACGTCTTATAATAGTGAACA 57.687 30.769 0.00 0.00 0.00 3.18
5147 5596 3.508793 ACAGAGGGAGCACATCATTTTTG 59.491 43.478 0.00 0.00 0.00 2.44
5341 5790 9.531942 GAAATATCATAAATGGTCATGTGCAAA 57.468 29.630 0.00 0.00 0.00 3.68
5392 5842 4.901197 TGTGGTCTAATCAGCCTGTTTA 57.099 40.909 0.00 0.00 0.00 2.01
5604 6055 9.381033 CCATTCTGCATTACAATAATTTTGGAA 57.619 29.630 0.00 1.99 0.00 3.53
6024 6478 4.622740 GTGCTTGTGATTTAATGCCAACTC 59.377 41.667 0.00 0.00 0.00 3.01
6033 6487 7.283127 GTGATTTAATGCCAACTCCTTATCTCA 59.717 37.037 0.00 0.00 0.00 3.27
6069 6523 3.055385 GCAGGTGTAGGACAAGATAACCA 60.055 47.826 0.00 0.00 0.00 3.67
6081 6535 6.349363 GGACAAGATAACCAAATGACTGTTCC 60.349 42.308 0.00 0.00 0.00 3.62
6230 6684 0.389817 TTGTCTCTGTTGCGGATCCG 60.390 55.000 30.03 30.03 43.09 4.18
6274 6730 2.081462 GCTTTAACACGTACTGCCCAT 58.919 47.619 0.00 0.00 0.00 4.00
6348 6804 2.025155 TGCGGTTGGTAAGCTTGAAAA 58.975 42.857 9.86 0.00 0.00 2.29
6350 6806 2.223618 GCGGTTGGTAAGCTTGAAAACA 60.224 45.455 9.86 0.00 0.00 2.83
6389 6845 2.040544 GGCACGTCCTGAACCCATG 61.041 63.158 0.00 0.00 0.00 3.66
6397 6853 1.145531 TCCTGAACCCATGGGCATATG 59.854 52.381 31.73 16.62 39.32 1.78
6423 6879 9.949174 GTATCCACTTTTTGAAAAATGCATTTT 57.051 25.926 27.73 27.73 43.85 1.82
6479 6935 1.640428 ACTCCACGCATACATGTTCG 58.360 50.000 2.30 8.45 0.00 3.95
6483 6939 1.529622 CCACGCATACATGTTCGCAAG 60.530 52.381 2.30 2.55 0.00 4.01
6644 7101 9.995003 TGTTATTTTTCCATGAAACTTTATGCT 57.005 25.926 0.00 0.00 30.83 3.79
6649 7106 3.947196 TCCATGAAACTTTATGCTCGCAT 59.053 39.130 9.57 9.57 40.19 4.73
6664 7121 6.048073 TGCTCGCATATAAAACATGAAGAC 57.952 37.500 0.00 0.00 0.00 3.01
6665 7122 5.584251 TGCTCGCATATAAAACATGAAGACA 59.416 36.000 0.00 0.00 0.00 3.41
6683 7140 5.296813 AGACATATTCGTGCAACCTTTTC 57.703 39.130 0.00 0.00 0.00 2.29
6686 7143 4.082787 ACATATTCGTGCAACCTTTTCCAG 60.083 41.667 0.00 0.00 0.00 3.86
6688 7145 2.270352 TCGTGCAACCTTTTCCAGAT 57.730 45.000 0.00 0.00 0.00 2.90
6690 7147 2.955660 TCGTGCAACCTTTTCCAGATTT 59.044 40.909 0.00 0.00 0.00 2.17
6691 7148 3.383185 TCGTGCAACCTTTTCCAGATTTT 59.617 39.130 0.00 0.00 0.00 1.82
6692 7149 3.735746 CGTGCAACCTTTTCCAGATTTTC 59.264 43.478 0.00 0.00 0.00 2.29
6739 7196 9.005777 GTTTTCTAAAGTGGGTTCATATGTACA 57.994 33.333 13.65 0.00 0.00 2.90
6762 7219 1.017387 GTTCATCGATGCACTTCCCC 58.983 55.000 20.81 0.00 0.00 4.81
6769 7226 1.133025 CGATGCACTTCCCCAAACATC 59.867 52.381 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.811514 GGAGGCATGGATCTCCGCA 61.812 63.158 0.00 0.00 39.95 5.69
601 772 4.922206 ACATTCCACATAGGTTCACACAT 58.078 39.130 0.00 0.00 39.02 3.21
613 784 1.269012 CCCAAGCCAACATTCCACAT 58.731 50.000 0.00 0.00 0.00 3.21
701 872 9.948964 TTAGTTTTAGTTTACAGAGGGAATACC 57.051 33.333 0.00 0.00 40.67 2.73
707 878 8.146479 ACGTTTTAGTTTTAGTTTACAGAGGG 57.854 34.615 0.00 0.00 0.00 4.30
753 924 3.657398 TTCATCACCGTACTCCCTCTA 57.343 47.619 0.00 0.00 0.00 2.43
756 927 5.687166 TTAATTTCATCACCGTACTCCCT 57.313 39.130 0.00 0.00 0.00 4.20
757 928 6.937436 AATTAATTTCATCACCGTACTCCC 57.063 37.500 0.00 0.00 0.00 4.30
835 1006 5.763698 ACTTTGAACCTTAGGTTTCACTAGC 59.236 40.000 18.52 4.04 46.95 3.42
1149 1348 2.303660 AGGTACCTTGGGGATTGGAT 57.696 50.000 9.21 0.00 36.25 3.41
1382 1581 2.562738 ACAAACTAAATCAAGGCCCAGC 59.437 45.455 0.00 0.00 0.00 4.85
1394 1593 5.986741 TGCGTATGAACTGAGACAAACTAAA 59.013 36.000 0.00 0.00 0.00 1.85
1395 1594 5.534407 TGCGTATGAACTGAGACAAACTAA 58.466 37.500 0.00 0.00 0.00 2.24
1404 1603 5.980116 AGTATAGCTTTGCGTATGAACTGAG 59.020 40.000 0.00 0.00 0.00 3.35
1422 1621 7.436673 GCTGTCAAGACCAAACTGATAGTATAG 59.563 40.741 0.00 0.00 0.00 1.31
1448 1647 6.884280 AAACAAATCTAGAACCAGGACAAG 57.116 37.500 0.00 0.00 0.00 3.16
1700 1899 3.619733 GCGGCATCATGACAGGGAATATA 60.620 47.826 0.00 0.00 0.00 0.86
2156 2355 7.669722 AGGATGTTTGCTAAAGAGGAACAATAA 59.330 33.333 0.00 0.00 31.94 1.40
2200 2399 7.726216 TCTCACTGAAAGATCTTTTGTACAGA 58.274 34.615 28.15 23.12 37.43 3.41
2201 2400 7.953158 TCTCACTGAAAGATCTTTTGTACAG 57.047 36.000 21.33 22.47 37.43 2.74
2202 2401 9.996554 TTATCTCACTGAAAGATCTTTTGTACA 57.003 29.630 21.33 13.39 37.43 2.90
2217 2453 9.770097 GATCCATTACAGAAATTATCTCACTGA 57.230 33.333 0.00 0.00 35.73 3.41
2290 2527 1.134220 ACTTGAACAACTCCTGCGGAA 60.134 47.619 0.00 0.00 0.00 4.30
2437 2674 1.730501 ACACAGAGATCATTGCACCG 58.269 50.000 0.00 0.00 0.00 4.94
2473 2710 7.274447 TTTCAAATGAATTTCCAGGATATGGC 58.726 34.615 0.00 0.00 40.39 4.40
2476 2713 8.995577 ACCATTTCAAATGAATTTCCAGGATAT 58.004 29.630 11.98 0.00 33.54 1.63
2577 2814 7.843490 CATCTCAAATTTTGAAATGCTCCAT 57.157 32.000 11.43 0.00 39.58 3.41
2596 2835 3.181520 ACATAAAAACGCTGTCGCATCTC 60.182 43.478 0.00 0.00 39.84 2.75
2602 2841 1.135803 CCCCACATAAAAACGCTGTCG 60.136 52.381 0.00 0.00 42.43 4.35
2604 2843 1.883926 GACCCCACATAAAAACGCTGT 59.116 47.619 0.00 0.00 0.00 4.40
2608 2847 6.168389 ACTAACTAGACCCCACATAAAAACG 58.832 40.000 0.00 0.00 0.00 3.60
2688 2927 7.596494 TCAATGATGAAAGAGGACACATTTTC 58.404 34.615 0.00 0.00 30.99 2.29
2785 3024 4.009370 AGGAAAGAGCTACTGGTTGAAC 57.991 45.455 0.00 0.00 0.00 3.18
2880 3121 7.993183 TCTTTATCTTTTCTATAAGCTGGTGGG 59.007 37.037 0.00 0.00 0.00 4.61
3103 3344 0.107081 TGGTCCGTGTTCAACCGAAT 59.893 50.000 0.53 0.00 35.76 3.34
3342 3583 9.109393 CCAATAACACTACACAATAAGCATACT 57.891 33.333 0.00 0.00 0.00 2.12
3344 3585 7.773224 AGCCAATAACACTACACAATAAGCATA 59.227 33.333 0.00 0.00 0.00 3.14
3345 3586 6.603201 AGCCAATAACACTACACAATAAGCAT 59.397 34.615 0.00 0.00 0.00 3.79
3347 3588 6.128007 ACAGCCAATAACACTACACAATAAGC 60.128 38.462 0.00 0.00 0.00 3.09
3348 3589 7.243487 CACAGCCAATAACACTACACAATAAG 58.757 38.462 0.00 0.00 0.00 1.73
3349 3590 6.150307 CCACAGCCAATAACACTACACAATAA 59.850 38.462 0.00 0.00 0.00 1.40
3350 3591 5.645929 CCACAGCCAATAACACTACACAATA 59.354 40.000 0.00 0.00 0.00 1.90
3351 3592 4.458989 CCACAGCCAATAACACTACACAAT 59.541 41.667 0.00 0.00 0.00 2.71
3352 3593 3.818210 CCACAGCCAATAACACTACACAA 59.182 43.478 0.00 0.00 0.00 3.33
3353 3594 3.181449 ACCACAGCCAATAACACTACACA 60.181 43.478 0.00 0.00 0.00 3.72
3354 3595 3.408634 ACCACAGCCAATAACACTACAC 58.591 45.455 0.00 0.00 0.00 2.90
3355 3596 3.780804 ACCACAGCCAATAACACTACA 57.219 42.857 0.00 0.00 0.00 2.74
3356 3597 4.828829 AGTACCACAGCCAATAACACTAC 58.171 43.478 0.00 0.00 0.00 2.73
3357 3598 5.242434 CAAGTACCACAGCCAATAACACTA 58.758 41.667 0.00 0.00 0.00 2.74
3358 3599 4.072131 CAAGTACCACAGCCAATAACACT 58.928 43.478 0.00 0.00 0.00 3.55
3359 3600 3.365969 GCAAGTACCACAGCCAATAACAC 60.366 47.826 0.00 0.00 0.00 3.32
3360 3601 2.817258 GCAAGTACCACAGCCAATAACA 59.183 45.455 0.00 0.00 0.00 2.41
3361 3602 2.817258 TGCAAGTACCACAGCCAATAAC 59.183 45.455 0.00 0.00 0.00 1.89
3378 3664 2.759191 CTGACAGTCAGCTAGTTGCAA 58.241 47.619 17.77 0.00 45.94 4.08
3423 3709 6.419484 AAAAGCTTTAAACAACAGGCCTAT 57.581 33.333 13.10 0.00 0.00 2.57
3571 3858 5.452341 AATTCTTAACCCGATTCCCTTCT 57.548 39.130 0.00 0.00 0.00 2.85
3659 3946 7.332182 CGTTAGGCAGAAAAGATAACTCTTCTT 59.668 37.037 0.00 0.00 40.93 2.52
4168 4615 8.478877 GGTACTATATTCATAATCCAGACAGGG 58.521 40.741 0.00 0.00 38.24 4.45
4221 4668 5.488341 CAATTAACCCCCGGTCATAGATAG 58.512 45.833 0.00 0.00 33.12 2.08
4399 4846 5.629133 GCAACCTCCTACATGACCTTGATAA 60.629 44.000 0.00 0.00 0.00 1.75
4507 4954 8.514330 ACAGAAACAAAATACAAGGTAGTTGA 57.486 30.769 8.66 0.00 38.60 3.18
4527 4974 4.456222 TCAAAACAACGGTCAAAGACAGAA 59.544 37.500 4.38 0.00 33.68 3.02
4531 4978 3.119779 TGGTCAAAACAACGGTCAAAGAC 60.120 43.478 0.00 0.00 0.00 3.01
4647 5095 7.490725 TCGATTTGGCCATTAAAACATATGTTG 59.509 33.333 21.46 9.46 38.44 3.33
4697 5145 4.637483 ACATATTTGAATCAAGGCCACG 57.363 40.909 5.01 0.00 0.00 4.94
4819 5267 7.365741 ACATGAATCACTCTTTCAATGAACAC 58.634 34.615 0.00 0.00 36.72 3.32
5127 5576 3.771216 ACAAAAATGATGTGCTCCCTCT 58.229 40.909 0.00 0.00 0.00 3.69
5147 5596 3.650139 TCGAAGGAGCAGTTTTCACTAC 58.350 45.455 0.00 0.00 0.00 2.73
5341 5790 5.949354 TCGTATTTCCCTGGACAATCATTTT 59.051 36.000 0.00 0.00 0.00 1.82
5392 5842 7.211573 CACATGGCCAATTGTTATACATTGAT 58.788 34.615 10.96 0.00 0.00 2.57
5604 6055 8.000709 TCTCTGATAATGATAAAACCCTGCATT 58.999 33.333 0.00 0.00 34.05 3.56
5948 6402 5.495926 AATCTCAGTCATGTCCTCTGTTT 57.504 39.130 0.00 0.00 0.00 2.83
5949 6403 5.486526 GAAATCTCAGTCATGTCCTCTGTT 58.513 41.667 0.00 0.00 0.00 3.16
5950 6404 4.081198 GGAAATCTCAGTCATGTCCTCTGT 60.081 45.833 0.00 0.00 0.00 3.41
6024 6478 4.920340 CCGATTCGTCATTCTGAGATAAGG 59.080 45.833 5.20 0.00 0.00 2.69
6033 6487 0.537188 ACCTGCCGATTCGTCATTCT 59.463 50.000 5.20 0.00 0.00 2.40
6127 6581 5.471797 GGTTCTCCAGAAGAAGAGGAAAAAG 59.528 44.000 0.00 0.00 44.66 2.27
6216 6670 0.174845 CTTACCGGATCCGCAACAGA 59.825 55.000 29.12 9.34 38.24 3.41
6230 6684 3.003480 GAGTGCCTGATTCACACTTACC 58.997 50.000 10.30 0.00 44.40 2.85
6274 6730 2.820178 TCTCTCCACACTATCCAAGCA 58.180 47.619 0.00 0.00 0.00 3.91
6348 6804 3.541632 ACTCGTGATGTTTGTTTCCTGT 58.458 40.909 0.00 0.00 0.00 4.00
6350 6806 2.800544 CGACTCGTGATGTTTGTTTCCT 59.199 45.455 0.00 0.00 0.00 3.36
6397 6853 9.949174 AAAATGCATTTTTCAAAAAGTGGATAC 57.051 25.926 27.73 0.84 42.62 2.24
6445 6901 7.835634 TGCGTGGAGTTTTCTTTTAATTTTT 57.164 28.000 0.00 0.00 0.00 1.94
6446 6902 8.974408 GTATGCGTGGAGTTTTCTTTTAATTTT 58.026 29.630 0.00 0.00 0.00 1.82
6447 6903 8.138712 TGTATGCGTGGAGTTTTCTTTTAATTT 58.861 29.630 0.00 0.00 0.00 1.82
6448 6904 7.653647 TGTATGCGTGGAGTTTTCTTTTAATT 58.346 30.769 0.00 0.00 0.00 1.40
6449 6905 7.209471 TGTATGCGTGGAGTTTTCTTTTAAT 57.791 32.000 0.00 0.00 0.00 1.40
6450 6906 6.621316 TGTATGCGTGGAGTTTTCTTTTAA 57.379 33.333 0.00 0.00 0.00 1.52
6456 6912 4.403453 GAACATGTATGCGTGGAGTTTTC 58.597 43.478 7.96 0.00 35.99 2.29
6461 6917 0.301687 GCGAACATGTATGCGTGGAG 59.698 55.000 7.96 0.00 35.99 3.86
6479 6935 4.962122 CCGCACGCACACACTTGC 62.962 66.667 0.00 0.00 39.28 4.01
6491 6947 3.006659 TCACAAAACTTTATGCCGCAC 57.993 42.857 0.00 0.00 0.00 5.34
6492 6948 3.717400 TTCACAAAACTTTATGCCGCA 57.283 38.095 0.00 0.00 0.00 5.69
6554 7011 8.688151 GTCATAGGACACTATCTAGAAACACTT 58.312 37.037 1.92 0.00 43.73 3.16
6620 7077 9.352784 CGAGCATAAAGTTTCATGGAAAAATAA 57.647 29.630 0.00 0.00 33.14 1.40
6621 7078 7.487829 GCGAGCATAAAGTTTCATGGAAAAATA 59.512 33.333 0.00 0.00 33.14 1.40
6627 7084 3.342719 TGCGAGCATAAAGTTTCATGGA 58.657 40.909 0.00 0.00 0.00 3.41
6649 7106 9.103861 TGCACGAATATGTCTTCATGTTTTATA 57.896 29.630 0.00 0.00 35.95 0.98
6664 7121 4.155826 TCTGGAAAAGGTTGCACGAATATG 59.844 41.667 0.00 0.00 31.02 1.78
6665 7122 4.331968 TCTGGAAAAGGTTGCACGAATAT 58.668 39.130 0.00 0.00 31.02 1.28
6711 7168 8.650143 ACATATGAACCCACTTTAGAAAACAT 57.350 30.769 10.38 0.00 0.00 2.71
6718 7175 5.522460 CCGTGTACATATGAACCCACTTTAG 59.478 44.000 10.38 0.00 0.00 1.85
6719 7176 5.421277 CCGTGTACATATGAACCCACTTTA 58.579 41.667 10.38 0.00 0.00 1.85
6726 7183 3.864243 TGAACCCGTGTACATATGAACC 58.136 45.455 10.38 0.00 0.00 3.62
6727 7184 4.208460 CGATGAACCCGTGTACATATGAAC 59.792 45.833 10.38 3.97 0.00 3.18
6734 7191 1.737696 GCATCGATGAACCCGTGTACA 60.738 52.381 29.20 0.00 0.00 2.90
6735 7192 0.928229 GCATCGATGAACCCGTGTAC 59.072 55.000 29.20 3.09 0.00 2.90
6739 7196 0.036388 AAGTGCATCGATGAACCCGT 60.036 50.000 29.28 14.72 37.01 5.28


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

AutoCloner maintained by Alex Coulton.