Multiple sequence alignment - TraesCS6D01G115300

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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 TraesCS6D01G115300 chr6D 100.000 5150 0 0 1 5150 81927164 81922015 0.000000e+00 9511.0
1 TraesCS6D01G115300 chr6D 85.395 3492 462 33 893 4358 82237751 82234282 0.000000e+00 3579.0
2 TraesCS6D01G115300 chr6D 83.287 3267 504 38 886 4131 81759811 81756566 0.000000e+00 2970.0
3 TraesCS6D01G115300 chr6D 82.936 3317 536 28 1056 4359 81773806 81770507 0.000000e+00 2963.0
4 TraesCS6D01G115300 chr6D 82.336 3374 548 29 912 4265 82139214 82135869 0.000000e+00 2885.0
5 TraesCS6D01G115300 chr6D 81.393 3547 581 63 893 4403 82204078 82200575 0.000000e+00 2820.0
6 TraesCS6D01G115300 chr6D 89.955 667 47 12 4491 5150 81917118 81916465 0.000000e+00 843.0
7 TraesCS6D01G115300 chr6D 78.485 330 44 17 4491 4803 82200575 82200256 1.890000e-44 191.0
8 TraesCS6D01G115300 chr6D 89.167 120 13 0 5015 5134 82205830 82205711 3.210000e-32 150.0
9 TraesCS6D01G115300 chr6D 79.039 229 27 13 647 868 82210467 82210253 2.500000e-28 137.0
10 TraesCS6D01G115300 chr6D 82.209 163 18 8 635 797 82139860 82139709 4.180000e-26 130.0
11 TraesCS6D01G115300 chr6D 86.667 75 8 2 5065 5138 82233661 82233588 1.190000e-11 82.4
12 TraesCS6D01G115300 chr6B 96.494 3765 116 5 528 4278 156655305 156651543 0.000000e+00 6207.0
13 TraesCS6D01G115300 chr6B 85.587 3483 457 35 893 4352 157489397 157485937 0.000000e+00 3609.0
14 TraesCS6D01G115300 chr6B 83.528 3254 497 33 894 4131 156529010 156525780 0.000000e+00 3003.0
15 TraesCS6D01G115300 chr6B 82.239 3395 561 31 989 4351 156550956 156547572 0.000000e+00 2891.0
16 TraesCS6D01G115300 chr6B 90.514 875 39 18 4274 5124 156651442 156650588 0.000000e+00 1116.0
17 TraesCS6D01G115300 chr6B 93.261 371 24 1 95 465 156659813 156659444 3.510000e-151 545.0
18 TraesCS6D01G115300 chr6B 80.645 279 31 15 4535 4803 157104006 157103741 1.460000e-45 195.0
19 TraesCS6D01G115300 chr6B 94.444 90 5 0 7 96 156659931 156659842 6.950000e-29 139.0
20 TraesCS6D01G115300 chr6B 80.982 163 20 6 635 797 157028133 157027982 9.060000e-23 119.0
21 TraesCS6D01G115300 chr6B 96.825 63 2 0 458 520 156655402 156655340 7.050000e-19 106.0
22 TraesCS6D01G115300 chr6A 93.206 3827 238 18 581 4399 98316364 98312552 0.000000e+00 5607.0
23 TraesCS6D01G115300 chr6A 82.719 3339 533 36 989 4305 98309983 98306667 0.000000e+00 2929.0
24 TraesCS6D01G115300 chr6A 92.326 430 31 2 93 520 98316900 98316471 1.230000e-170 610.0
25 TraesCS6D01G115300 chr6A 87.845 362 25 3 4767 5124 98312299 98311953 1.730000e-109 407.0
26 TraesCS6D01G115300 chr6A 74.410 551 97 26 4601 5134 98913667 98913144 4.070000e-46 196.0
27 TraesCS6D01G115300 chr6A 77.670 309 58 8 4832 5138 99012506 99012207 1.470000e-40 178.0
28 TraesCS6D01G115300 chr6A 77.922 231 30 15 644 867 98917893 98917677 1.950000e-24 124.0
29 TraesCS6D01G115300 chr2B 86.873 259 33 1 4491 4748 49185501 49185243 6.520000e-74 289.0
30 TraesCS6D01G115300 chr2B 91.765 85 6 1 4408 4492 674302641 674302558 3.260000e-22 117.0
31 TraesCS6D01G115300 chr2B 77.311 119 14 7 4400 4506 752488065 752488182 2.000000e-04 58.4
32 TraesCS6D01G115300 chr3A 90.426 94 6 3 4406 4499 40354777 40354867 2.520000e-23 121.0
33 TraesCS6D01G115300 chr4D 88.776 98 10 1 4401 4498 450203796 450203700 9.060000e-23 119.0
34 TraesCS6D01G115300 chr7A 88.660 97 8 3 4405 4500 654797034 654796940 1.170000e-21 115.0
35 TraesCS6D01G115300 chr5B 88.660 97 7 4 4405 4499 706306878 706306972 1.170000e-21 115.0
36 TraesCS6D01G115300 chr3D 89.362 94 7 3 4406 4499 29696089 29696179 1.170000e-21 115.0
37 TraesCS6D01G115300 chr1B 88.000 100 8 4 4402 4500 493871876 493871972 1.170000e-21 115.0
38 TraesCS6D01G115300 chr4A 87.755 98 11 1 4401 4498 16469318 16469414 4.210000e-21 113.0
39 TraesCS6D01G115300 chr2A 79.612 103 17 4 4406 4507 160778901 160779000 2.570000e-08 71.3


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 TraesCS6D01G115300 chr6D 81922015 81927164 5149 True 9511.000000 9511 100.0000 1 5150 1 chr6D.!!$R4 5149
1 TraesCS6D01G115300 chr6D 81756566 81759811 3245 True 2970.000000 2970 83.2870 886 4131 1 chr6D.!!$R1 3245
2 TraesCS6D01G115300 chr6D 81770507 81773806 3299 True 2963.000000 2963 82.9360 1056 4359 1 chr6D.!!$R2 3303
3 TraesCS6D01G115300 chr6D 82233588 82237751 4163 True 1830.700000 3579 86.0310 893 5138 2 chr6D.!!$R8 4245
4 TraesCS6D01G115300 chr6D 82135869 82139860 3991 True 1507.500000 2885 82.2725 635 4265 2 chr6D.!!$R6 3630
5 TraesCS6D01G115300 chr6D 82200256 82205830 5574 True 1053.666667 2820 83.0150 893 5134 3 chr6D.!!$R7 4241
6 TraesCS6D01G115300 chr6D 81916465 81917118 653 True 843.000000 843 89.9550 4491 5150 1 chr6D.!!$R3 659
7 TraesCS6D01G115300 chr6B 157485937 157489397 3460 True 3609.000000 3609 85.5870 893 4352 1 chr6B.!!$R5 3459
8 TraesCS6D01G115300 chr6B 156525780 156529010 3230 True 3003.000000 3003 83.5280 894 4131 1 chr6B.!!$R1 3237
9 TraesCS6D01G115300 chr6B 156547572 156550956 3384 True 2891.000000 2891 82.2390 989 4351 1 chr6B.!!$R2 3362
10 TraesCS6D01G115300 chr6B 156650588 156655402 4814 True 2476.333333 6207 94.6110 458 5124 3 chr6B.!!$R6 4666
11 TraesCS6D01G115300 chr6A 98306667 98316900 10233 True 2388.250000 5607 89.0240 93 5124 4 chr6A.!!$R4 5031

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
961 1823 0.036732 TCCAGTCAGGGCACAACATC 59.963 55.0 0.00 0.0 38.24 3.06 F
1075 1937 0.313043 CCTTGCTCTTGTGCTGTTGG 59.687 55.0 0.00 0.0 0.00 3.77 F
1531 2405 0.820891 CGCATGGAAGGGAATGGAGG 60.821 60.0 0.00 0.0 0.00 4.30 F
2823 3703 0.838122 ACCTGCTGGTGCTAGACCTT 60.838 55.0 15.36 0.0 46.51 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2992 0.391661 ATAACCGCAGTGCAGTCAGG 60.392 55.000 16.83 10.19 0.00 3.86 R
2969 3849 1.608590 AGCCACACAACTTTGGATTCG 59.391 47.619 0.00 0.00 34.46 3.34 R
3574 4454 7.329471 GTCAAAATATGAGCTAGCATCGTCATA 59.671 37.037 20.45 20.45 39.19 2.15 R
4854 11936 0.690192 TTTGCCGAGTGAATCCTCCA 59.310 50.000 0.00 0.00 0.00 3.86 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
46 47 8.460831 AACAACTTGAACTAAAAACATGACAC 57.539 30.769 0.00 0.00 0.00 3.67
47 48 7.826690 ACAACTTGAACTAAAAACATGACACT 58.173 30.769 0.00 0.00 0.00 3.55
48 49 8.303876 ACAACTTGAACTAAAAACATGACACTT 58.696 29.630 0.00 0.00 0.00 3.16
49 50 9.781834 CAACTTGAACTAAAAACATGACACTTA 57.218 29.630 0.00 0.00 0.00 2.24
59 60 7.645058 AAAACATGACACTTATTATGGAGGG 57.355 36.000 0.00 0.00 0.00 4.30
60 61 6.575244 AACATGACACTTATTATGGAGGGA 57.425 37.500 0.00 0.00 0.00 4.20
61 62 6.179906 ACATGACACTTATTATGGAGGGAG 57.820 41.667 0.00 0.00 0.00 4.30
62 63 5.667626 ACATGACACTTATTATGGAGGGAGT 59.332 40.000 0.00 0.00 0.00 3.85
64 65 6.978674 TGACACTTATTATGGAGGGAGTAG 57.021 41.667 0.00 0.00 0.00 2.57
65 66 6.441222 TGACACTTATTATGGAGGGAGTAGT 58.559 40.000 0.00 0.00 0.00 2.73
66 67 6.901300 TGACACTTATTATGGAGGGAGTAGTT 59.099 38.462 0.00 0.00 0.00 2.24
67 68 7.402071 TGACACTTATTATGGAGGGAGTAGTTT 59.598 37.037 0.00 0.00 0.00 2.66
68 69 8.159229 ACACTTATTATGGAGGGAGTAGTTTT 57.841 34.615 0.00 0.00 0.00 2.43
69 70 8.265764 ACACTTATTATGGAGGGAGTAGTTTTC 58.734 37.037 0.00 0.00 0.00 2.29
70 71 8.265055 CACTTATTATGGAGGGAGTAGTTTTCA 58.735 37.037 0.00 0.00 0.00 2.69
71 72 8.487028 ACTTATTATGGAGGGAGTAGTTTTCAG 58.513 37.037 0.00 0.00 0.00 3.02
72 73 3.636153 ATGGAGGGAGTAGTTTTCAGC 57.364 47.619 0.00 0.00 0.00 4.26
74 75 3.786553 TGGAGGGAGTAGTTTTCAGCTA 58.213 45.455 0.00 0.00 0.00 3.32
75 76 4.164981 TGGAGGGAGTAGTTTTCAGCTAA 58.835 43.478 0.00 0.00 0.00 3.09
77 78 4.020485 GGAGGGAGTAGTTTTCAGCTAACA 60.020 45.833 0.93 0.00 0.00 2.41
78 79 5.512576 GGAGGGAGTAGTTTTCAGCTAACAA 60.513 44.000 0.93 0.00 0.00 2.83
79 80 5.552178 AGGGAGTAGTTTTCAGCTAACAAG 58.448 41.667 0.93 0.00 0.00 3.16
81 82 6.013293 AGGGAGTAGTTTTCAGCTAACAAGAT 60.013 38.462 0.93 0.00 0.00 2.40
82 83 6.092807 GGGAGTAGTTTTCAGCTAACAAGATG 59.907 42.308 0.93 0.00 0.00 2.90
83 84 6.874134 GGAGTAGTTTTCAGCTAACAAGATGA 59.126 38.462 0.93 0.00 31.89 2.92
86 87 7.816995 AGTAGTTTTCAGCTAACAAGATGAGAG 59.183 37.037 0.93 0.00 35.54 3.20
87 88 6.763355 AGTTTTCAGCTAACAAGATGAGAGA 58.237 36.000 0.93 0.00 35.54 3.10
88 89 6.873076 AGTTTTCAGCTAACAAGATGAGAGAG 59.127 38.462 0.93 0.00 35.54 3.20
89 90 4.383850 TCAGCTAACAAGATGAGAGAGC 57.616 45.455 0.00 0.00 30.17 4.09
91 92 4.114073 CAGCTAACAAGATGAGAGAGCAG 58.886 47.826 0.00 0.00 0.00 4.24
94 95 1.570803 ACAAGATGAGAGAGCAGGCT 58.429 50.000 0.00 0.00 0.00 4.58
95 96 1.207570 ACAAGATGAGAGAGCAGGCTG 59.792 52.381 10.94 10.94 0.00 4.85
96 97 1.207570 CAAGATGAGAGAGCAGGCTGT 59.792 52.381 17.16 2.59 0.00 4.40
109 110 2.196749 CAGGCTGTAGCTACATCAACG 58.803 52.381 26.22 15.31 41.70 4.10
112 113 2.607187 GCTGTAGCTACATCAACGTGT 58.393 47.619 26.22 0.00 38.21 4.49
142 143 4.643387 GTGTGGCCGGCCTCTTGT 62.643 66.667 43.34 0.00 36.94 3.16
147 148 2.594592 GCCGGCCTCTTGTGTTGT 60.595 61.111 18.11 0.00 0.00 3.32
159 160 3.128589 TCTTGTGTTGTGTTCTTGCCTTC 59.871 43.478 0.00 0.00 0.00 3.46
218 219 4.153117 GCACTGTACCTGATAATAGCATGC 59.847 45.833 10.51 10.51 0.00 4.06
272 274 4.873827 GCGATTCCATAAACACTAACAGGA 59.126 41.667 0.00 0.00 0.00 3.86
289 291 0.716108 GGACATCAAGAACGACGCAG 59.284 55.000 0.00 0.00 0.00 5.18
372 374 3.508845 TTTCTCAAACAGAAGAGGGGG 57.491 47.619 0.00 0.00 42.37 5.40
377 379 2.305927 TCAAACAGAAGAGGGGGATCAC 59.694 50.000 0.00 0.00 0.00 3.06
381 383 4.014273 ACAGAAGAGGGGGATCACTAAT 57.986 45.455 0.00 0.00 0.00 1.73
384 386 3.970640 AGAAGAGGGGGATCACTAATCAC 59.029 47.826 0.00 0.00 37.03 3.06
387 389 2.104963 GAGGGGGATCACTAATCACACC 59.895 54.545 0.00 0.00 42.78 4.16
388 390 2.127708 GGGGGATCACTAATCACACCT 58.872 52.381 0.00 0.00 39.80 4.00
396 398 8.543774 GGGATCACTAATCACACCTATAATGAT 58.456 37.037 0.00 0.00 37.76 2.45
441 443 4.638304 AGAAGCAATAACAACGGTACAGT 58.362 39.130 0.00 0.00 0.00 3.55
494 496 6.624423 AGCAATGTGATTCTTAACACCAATC 58.376 36.000 0.00 0.00 36.35 2.67
523 525 7.892241 TCAGCTATAATTAATACTCCTACGGGT 59.108 37.037 0.00 0.00 0.00 5.28
524 526 9.182214 CAGCTATAATTAATACTCCTACGGGTA 57.818 37.037 0.00 0.00 0.00 3.69
525 527 9.183368 AGCTATAATTAATACTCCTACGGGTAC 57.817 37.037 0.00 0.00 0.00 3.34
535 564 1.684983 CCTACGGGTACGGTGATGAAT 59.315 52.381 0.00 0.00 46.48 2.57
549 582 0.106569 ATGAATCAGCCCGCCATTGA 60.107 50.000 0.00 0.00 0.00 2.57
567 600 0.523966 GACAGAGCTCACACGCTACT 59.476 55.000 17.77 0.00 41.08 2.57
598 650 6.590357 ACTTTGAATTCAGACGATAAACACG 58.410 36.000 8.41 0.00 0.00 4.49
608 660 3.307674 ACGATAAACACGAAGCGTTACA 58.692 40.909 0.00 0.00 38.32 2.41
620 672 0.036765 GCGTTACAGTCCATGGTCCA 60.037 55.000 12.58 0.00 0.00 4.02
628 680 1.915489 AGTCCATGGTCCACAATAGCA 59.085 47.619 12.58 0.00 0.00 3.49
630 682 2.423538 GTCCATGGTCCACAATAGCAAC 59.576 50.000 12.58 0.00 0.00 4.17
679 732 1.410517 ACAGCAGACGTATCCATCAGG 59.589 52.381 0.00 0.00 0.00 3.86
710 763 3.788227 TTGCATGACAAGAGGGTAAGT 57.212 42.857 0.00 0.00 33.24 2.24
787 840 1.721093 AACCATCCACCCCGTCCAAA 61.721 55.000 0.00 0.00 0.00 3.28
823 876 1.072965 ACTTCTTCTTGCCCTCCACTG 59.927 52.381 0.00 0.00 0.00 3.66
933 1795 4.816385 TCTTTCATGATTAGACCGCCATTC 59.184 41.667 0.00 0.00 0.00 2.67
961 1823 0.036732 TCCAGTCAGGGCACAACATC 59.963 55.000 0.00 0.00 38.24 3.06
987 1849 1.281867 TGGTTCCCATGCTAGTTCCAG 59.718 52.381 0.00 0.00 0.00 3.86
1024 1886 3.808618 GCAGACACTCCATTTCTCCAACT 60.809 47.826 0.00 0.00 0.00 3.16
1075 1937 0.313043 CCTTGCTCTTGTGCTGTTGG 59.687 55.000 0.00 0.00 0.00 3.77
1141 2012 1.273552 CCTCCCTTCTCCAGTTCCTCT 60.274 57.143 0.00 0.00 0.00 3.69
1370 2244 1.985159 TCTGCCACTGGAACTGGTATT 59.015 47.619 0.00 0.00 0.00 1.89
1453 2327 3.114616 CAGCTTCGACCACTGCCG 61.115 66.667 0.00 0.00 0.00 5.69
1455 2329 4.373116 GCTTCGACCACTGCCGGA 62.373 66.667 5.05 0.00 0.00 5.14
1513 2387 1.078426 GGACAGTTCCCATCCACCG 60.078 63.158 0.00 0.00 35.57 4.94
1531 2405 0.820891 CGCATGGAAGGGAATGGAGG 60.821 60.000 0.00 0.00 0.00 4.30
1614 2488 2.061790 GCACCTCCCCATCCATCTCC 62.062 65.000 0.00 0.00 0.00 3.71
1742 2616 6.183361 GGAACTATCCCAGATGAACTCTTCAT 60.183 42.308 0.00 0.00 45.34 2.57
1791 2665 6.632909 TCTTTCTAACAATCATTTGCATGGG 58.367 36.000 0.00 0.00 36.22 4.00
2118 2992 4.889832 AAGCATATACTCTTGCAGCAAC 57.110 40.909 2.83 0.00 41.35 4.17
2823 3703 0.838122 ACCTGCTGGTGCTAGACCTT 60.838 55.000 15.36 0.00 46.51 3.50
2969 3849 7.029563 ACATTTCCGAATTCTAGTTTTGATGC 58.970 34.615 3.52 0.00 0.00 3.91
3250 4130 5.636903 AGTAGTGATAAGGATGCCACAAT 57.363 39.130 0.00 0.00 32.35 2.71
3574 4454 5.698104 TGGATGATTGGCTTCATAACAGAT 58.302 37.500 3.93 0.00 36.48 2.90
3819 4699 2.420967 GGTCGGCACTATGGGTTACATT 60.421 50.000 0.00 0.00 41.03 2.71
3990 10845 0.809241 CTGAGGGCAAGCAGATCGAC 60.809 60.000 0.00 0.00 34.06 4.20
4035 10890 6.735556 AGGAACAGGGTATGAAGATCAAATT 58.264 36.000 0.00 0.00 0.00 1.82
4297 11277 0.601558 TTGTACGAGCCTCACAGGTC 59.398 55.000 0.00 0.00 37.80 3.85
4424 11404 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
4711 11777 5.615984 GCGTCAAACAAATGGAACGAGAATA 60.616 40.000 0.00 0.00 0.00 1.75
4725 11791 7.386025 TGGAACGAGAATATGAGAATGCAATAG 59.614 37.037 0.00 0.00 0.00 1.73
4809 11889 6.950619 AGAACAAGAGAGGAATGGCTAAAAAT 59.049 34.615 0.00 0.00 0.00 1.82
4825 11906 2.754946 AAATCACCTGCCTTGCATTG 57.245 45.000 0.00 0.00 38.13 2.82
4826 11907 0.248289 AATCACCTGCCTTGCATTGC 59.752 50.000 0.46 0.46 38.13 3.56
4871 11955 1.900351 CTGGAGGATTCACTCGGCA 59.100 57.895 0.00 0.00 38.39 5.69
4908 11993 3.143515 ATCGCAGCTCGCTCCTCA 61.144 61.111 6.58 0.00 39.08 3.86
4934 12028 5.607477 CGTATAGAAATAGGCCTGGAAACA 58.393 41.667 17.99 0.00 39.59 2.83
4972 12066 2.667470 ACAAGCCCGATCTAGCTTCTA 58.333 47.619 14.23 0.00 46.11 2.10
5044 12138 4.719369 GCCGAACGACCTGAGCGT 62.719 66.667 0.00 0.00 44.94 5.07
5103 12206 0.759346 GCATTGAGTCGGAGGGGTAT 59.241 55.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.921670 GTGTCATGTTTTTAGTTCAAGTTGTTT 58.078 29.630 2.11 0.00 0.00 2.83
21 22 8.303876 AGTGTCATGTTTTTAGTTCAAGTTGTT 58.696 29.630 2.11 0.00 0.00 2.83
22 23 7.826690 AGTGTCATGTTTTTAGTTCAAGTTGT 58.173 30.769 2.11 0.00 0.00 3.32
34 35 7.893302 TCCCTCCATAATAAGTGTCATGTTTTT 59.107 33.333 0.00 0.00 0.00 1.94
35 36 7.410174 TCCCTCCATAATAAGTGTCATGTTTT 58.590 34.615 0.00 0.00 0.00 2.43
36 37 6.969043 TCCCTCCATAATAAGTGTCATGTTT 58.031 36.000 0.00 0.00 0.00 2.83
37 38 6.158695 ACTCCCTCCATAATAAGTGTCATGTT 59.841 38.462 0.00 0.00 0.00 2.71
38 39 5.667626 ACTCCCTCCATAATAAGTGTCATGT 59.332 40.000 0.00 0.00 0.00 3.21
40 41 7.076446 ACTACTCCCTCCATAATAAGTGTCAT 58.924 38.462 0.00 0.00 0.00 3.06
41 42 6.441222 ACTACTCCCTCCATAATAAGTGTCA 58.559 40.000 0.00 0.00 0.00 3.58
43 44 7.750947 AAACTACTCCCTCCATAATAAGTGT 57.249 36.000 0.00 0.00 0.00 3.55
45 46 8.388656 TGAAAACTACTCCCTCCATAATAAGT 57.611 34.615 0.00 0.00 0.00 2.24
46 47 7.442666 GCTGAAAACTACTCCCTCCATAATAAG 59.557 40.741 0.00 0.00 0.00 1.73
47 48 7.127339 AGCTGAAAACTACTCCCTCCATAATAA 59.873 37.037 0.00 0.00 0.00 1.40
48 49 6.615726 AGCTGAAAACTACTCCCTCCATAATA 59.384 38.462 0.00 0.00 0.00 0.98
49 50 5.430089 AGCTGAAAACTACTCCCTCCATAAT 59.570 40.000 0.00 0.00 0.00 1.28
50 51 4.783227 AGCTGAAAACTACTCCCTCCATAA 59.217 41.667 0.00 0.00 0.00 1.90
51 52 4.362677 AGCTGAAAACTACTCCCTCCATA 58.637 43.478 0.00 0.00 0.00 2.74
52 53 3.185455 AGCTGAAAACTACTCCCTCCAT 58.815 45.455 0.00 0.00 0.00 3.41
53 54 2.621070 AGCTGAAAACTACTCCCTCCA 58.379 47.619 0.00 0.00 0.00 3.86
54 55 4.020485 TGTTAGCTGAAAACTACTCCCTCC 60.020 45.833 0.00 0.00 0.00 4.30
56 57 5.307196 TCTTGTTAGCTGAAAACTACTCCCT 59.693 40.000 0.00 0.00 0.00 4.20
58 59 6.874134 TCATCTTGTTAGCTGAAAACTACTCC 59.126 38.462 0.00 0.00 0.00 3.85
59 60 7.815068 TCTCATCTTGTTAGCTGAAAACTACTC 59.185 37.037 0.00 0.00 0.00 2.59
60 61 7.671302 TCTCATCTTGTTAGCTGAAAACTACT 58.329 34.615 0.00 0.00 0.00 2.57
61 62 7.815068 TCTCTCATCTTGTTAGCTGAAAACTAC 59.185 37.037 0.00 0.00 0.00 2.73
62 63 7.896811 TCTCTCATCTTGTTAGCTGAAAACTA 58.103 34.615 0.00 0.00 0.00 2.24
64 65 6.402011 GCTCTCTCATCTTGTTAGCTGAAAAC 60.402 42.308 0.00 0.00 0.00 2.43
65 66 5.641209 GCTCTCTCATCTTGTTAGCTGAAAA 59.359 40.000 0.00 0.00 0.00 2.29
66 67 5.174395 GCTCTCTCATCTTGTTAGCTGAAA 58.826 41.667 0.00 0.00 0.00 2.69
67 68 4.221482 TGCTCTCTCATCTTGTTAGCTGAA 59.779 41.667 0.00 0.00 0.00 3.02
68 69 3.766051 TGCTCTCTCATCTTGTTAGCTGA 59.234 43.478 0.00 0.00 0.00 4.26
69 70 4.114073 CTGCTCTCTCATCTTGTTAGCTG 58.886 47.826 0.00 0.00 0.00 4.24
70 71 3.132646 CCTGCTCTCTCATCTTGTTAGCT 59.867 47.826 0.00 0.00 0.00 3.32
71 72 3.456280 CCTGCTCTCTCATCTTGTTAGC 58.544 50.000 0.00 0.00 0.00 3.09
72 73 3.132646 AGCCTGCTCTCTCATCTTGTTAG 59.867 47.826 0.00 0.00 0.00 2.34
74 75 1.907936 AGCCTGCTCTCTCATCTTGTT 59.092 47.619 0.00 0.00 0.00 2.83
75 76 1.207570 CAGCCTGCTCTCTCATCTTGT 59.792 52.381 0.00 0.00 0.00 3.16
77 78 1.570803 ACAGCCTGCTCTCTCATCTT 58.429 50.000 0.00 0.00 0.00 2.40
78 79 2.309613 CTACAGCCTGCTCTCTCATCT 58.690 52.381 0.00 0.00 0.00 2.90
79 80 1.269726 GCTACAGCCTGCTCTCTCATC 60.270 57.143 0.00 0.00 34.31 2.92
81 82 0.324183 AGCTACAGCCTGCTCTCTCA 60.324 55.000 0.00 0.00 43.38 3.27
82 83 1.336755 GTAGCTACAGCCTGCTCTCTC 59.663 57.143 19.15 0.00 43.38 3.20
83 84 1.341482 TGTAGCTACAGCCTGCTCTCT 60.341 52.381 22.67 0.00 43.38 3.10
86 87 1.410517 TGATGTAGCTACAGCCTGCTC 59.589 52.381 32.85 22.91 41.60 4.26
87 88 1.489481 TGATGTAGCTACAGCCTGCT 58.511 50.000 32.85 16.21 41.60 4.24
88 89 1.936547 GTTGATGTAGCTACAGCCTGC 59.063 52.381 32.85 21.00 41.60 4.85
89 90 2.196749 CGTTGATGTAGCTACAGCCTG 58.803 52.381 32.85 20.96 41.60 4.85
91 92 1.927174 CACGTTGATGTAGCTACAGCC 59.073 52.381 32.85 24.65 41.60 4.85
94 95 4.245845 TCAACACGTTGATGTAGCTACA 57.754 40.909 27.91 27.91 43.90 2.74
138 139 3.129287 AGAAGGCAAGAACACAACACAAG 59.871 43.478 0.00 0.00 0.00 3.16
142 143 2.945008 CAGAGAAGGCAAGAACACAACA 59.055 45.455 0.00 0.00 0.00 3.33
147 148 1.271054 GGAGCAGAGAAGGCAAGAACA 60.271 52.381 0.00 0.00 0.00 3.18
201 202 2.606108 CGCGCATGCTATTATCAGGTA 58.394 47.619 17.13 0.00 39.65 3.08
218 219 4.320928 TTTTTCTGCGGTGGCGCG 62.321 61.111 0.00 0.00 44.10 6.86
248 250 4.876107 CCTGTTAGTGTTTATGGAATCGCT 59.124 41.667 0.00 0.00 0.00 4.93
250 252 5.872617 TGTCCTGTTAGTGTTTATGGAATCG 59.127 40.000 0.00 0.00 0.00 3.34
272 274 1.617755 CGCTGCGTCGTTCTTGATGT 61.618 55.000 14.93 0.00 0.00 3.06
300 302 1.992170 TTAAGGCTCTCGCGAACTTC 58.008 50.000 11.33 0.28 36.88 3.01
314 316 4.058817 CCAGCCGCTCTACTTAATTAAGG 58.941 47.826 25.25 11.51 37.62 2.69
360 362 3.491766 TTAGTGATCCCCCTCTTCTGT 57.508 47.619 0.00 0.00 0.00 3.41
363 365 3.711704 TGTGATTAGTGATCCCCCTCTTC 59.288 47.826 0.00 0.00 33.60 2.87
371 373 9.593134 GATCATTATAGGTGTGATTAGTGATCC 57.407 37.037 0.00 0.00 34.81 3.36
381 383 9.933723 CTGTATCATTGATCATTATAGGTGTGA 57.066 33.333 1.55 0.00 0.00 3.58
384 386 8.663025 GCACTGTATCATTGATCATTATAGGTG 58.337 37.037 1.55 8.15 0.00 4.00
387 389 8.388853 GCTGCACTGTATCATTGATCATTATAG 58.611 37.037 1.55 0.00 0.00 1.31
388 390 7.879160 TGCTGCACTGTATCATTGATCATTATA 59.121 33.333 1.55 0.00 0.00 0.98
396 398 4.146745 AGATGCTGCACTGTATCATTGA 57.853 40.909 3.57 0.00 32.64 2.57
405 407 2.353323 TGCTTCTTAGATGCTGCACTG 58.647 47.619 18.58 0.00 34.46 3.66
520 522 1.583054 GCTGATTCATCACCGTACCC 58.417 55.000 0.00 0.00 32.50 3.69
521 523 1.583054 GGCTGATTCATCACCGTACC 58.417 55.000 0.00 0.00 32.50 3.34
523 525 0.104120 CGGGCTGATTCATCACCGTA 59.896 55.000 12.81 0.00 39.91 4.02
524 526 1.153369 CGGGCTGATTCATCACCGT 60.153 57.895 12.81 0.00 39.91 4.83
525 527 2.537560 GCGGGCTGATTCATCACCG 61.538 63.158 15.37 15.37 44.51 4.94
535 564 2.046023 CTGTCAATGGCGGGCTGA 60.046 61.111 0.00 0.00 0.00 4.26
549 582 0.523966 GAGTAGCGTGTGAGCTCTGT 59.476 55.000 16.19 0.00 45.67 3.41
567 600 7.962964 ATCGTCTGAATTCAAAGTAAACTGA 57.037 32.000 9.88 0.00 0.00 3.41
594 646 0.386476 TGGACTGTAACGCTTCGTGT 59.614 50.000 0.00 0.00 39.99 4.49
598 650 2.000447 GACCATGGACTGTAACGCTTC 59.000 52.381 21.47 0.00 0.00 3.86
608 660 1.915489 TGCTATTGTGGACCATGGACT 59.085 47.619 21.47 0.00 0.00 3.85
620 672 4.734652 CCACCGGGTTGCTATTGT 57.265 55.556 6.32 0.00 0.00 2.71
638 690 1.314730 GTTTTTCCGTTCTCCTGGCA 58.685 50.000 0.00 0.00 0.00 4.92
702 755 4.897509 AGGCGTTTACTTTACTTACCCT 57.102 40.909 0.00 0.00 0.00 4.34
710 763 7.879160 TCCTCTTGATTTTAGGCGTTTACTTTA 59.121 33.333 0.00 0.00 0.00 1.85
787 840 2.358898 AGAAGTGCGATGTTGTTGCTTT 59.641 40.909 0.00 0.00 38.13 3.51
823 876 1.898574 CAGTGTGTGGACAAGGCCC 60.899 63.158 0.00 0.00 32.49 5.80
933 1795 1.171308 CCCTGACTGGACAAAGCATG 58.829 55.000 0.00 0.00 38.35 4.06
987 1849 2.230992 TGTCTGCATGGTTTATTGGTGC 59.769 45.455 0.00 0.00 36.39 5.01
1024 1886 3.003394 CAATATCTTGCTGTGTCCCCA 57.997 47.619 0.00 0.00 0.00 4.96
1075 1937 1.133407 CGTAGGAGAGACCAAGCAGAC 59.867 57.143 0.00 0.00 42.04 3.51
1141 2012 1.301401 CGTCTTGTGAAAGCCCGGA 60.301 57.895 0.73 0.00 0.00 5.14
1190 2061 2.036098 CCCACTGGCAGCAATCCA 59.964 61.111 15.89 0.00 0.00 3.41
1370 2244 0.321919 GACAAGGATGCTGCTGGACA 60.322 55.000 0.00 0.00 0.00 4.02
1447 2321 2.743718 CTTGAGTGGTCCGGCAGT 59.256 61.111 0.00 0.00 0.00 4.40
1453 2327 2.367567 TGTTGAGTACCTTGAGTGGTCC 59.632 50.000 0.00 0.00 41.22 4.46
1455 2329 3.904339 AGATGTTGAGTACCTTGAGTGGT 59.096 43.478 0.00 0.00 43.66 4.16
1513 2387 0.552848 TCCTCCATTCCCTTCCATGC 59.447 55.000 0.00 0.00 0.00 4.06
1531 2405 1.930100 CATTGAGCGCGACCAGATC 59.070 57.895 12.10 0.00 0.00 2.75
1579 2453 4.563580 GGAGGTGCTACAGAAATGAGTTGA 60.564 45.833 0.00 0.00 0.00 3.18
1614 2488 4.936396 GTTGAAAGACAAATCAAGCACG 57.064 40.909 0.00 0.00 40.36 5.34
1742 2616 4.250464 CAGGTATTCCAACGAAGTAGCAA 58.750 43.478 0.00 0.00 45.00 3.91
1791 2665 5.824904 ATATGTGTGCATCTTCAAGAACC 57.175 39.130 0.00 0.00 36.58 3.62
1953 2827 6.710597 ATCAGATTTATGCAATTGCTCACT 57.289 33.333 29.37 16.61 42.66 3.41
2118 2992 0.391661 ATAACCGCAGTGCAGTCAGG 60.392 55.000 16.83 10.19 0.00 3.86
2823 3703 4.037446 GCACCTGTAAGATTGTTGTTGGAA 59.963 41.667 0.00 0.00 34.07 3.53
2969 3849 1.608590 AGCCACACAACTTTGGATTCG 59.391 47.619 0.00 0.00 34.46 3.34
3574 4454 7.329471 GTCAAAATATGAGCTAGCATCGTCATA 59.671 37.037 20.45 20.45 39.19 2.15
3819 4699 0.988145 CTTGCCCATACTCAGGGGGA 60.988 60.000 2.60 0.00 46.53 4.81
4035 10890 1.593196 CGGTTTCAAGCACCTTCAGA 58.407 50.000 0.00 0.00 31.32 3.27
4266 11140 4.271776 AGGCTCGTACAAAGTACAAAACAC 59.728 41.667 7.93 0.00 0.00 3.32
4297 11277 3.836949 ACATGTAAAGCTGAAAATGGCG 58.163 40.909 0.00 0.00 0.00 5.69
4482 11462 7.444487 GTGAACCATAAAACATATACTCCCTCC 59.556 40.741 0.00 0.00 0.00 4.30
4554 11555 4.990526 ACCACTTTCAATCTTCCAGTGAT 58.009 39.130 0.00 0.00 37.63 3.06
4711 11777 8.427902 TGATAGTAGTCCTATTGCATTCTCAT 57.572 34.615 0.00 0.00 36.47 2.90
4809 11889 1.531128 TGCAATGCAAGGCAGGTGA 60.531 52.632 5.01 0.00 43.65 4.02
4854 11936 0.690192 TTTGCCGAGTGAATCCTCCA 59.310 50.000 0.00 0.00 0.00 3.86
4871 11955 0.752658 GCAAGGCAGGTGGTTTCTTT 59.247 50.000 0.00 0.00 0.00 2.52
4908 11993 2.567615 CCAGGCCTATTTCTATACGCCT 59.432 50.000 3.98 0.00 44.57 5.52
4912 11997 5.465724 CGTGTTTCCAGGCCTATTTCTATAC 59.534 44.000 3.98 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.