Multiple sequence alignment - TraesCS2D01G480100

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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 TraesCS2D01G480100 chr2D 100.000 4880 0 0 1 4880 580969677 580974556 0.000000e+00 9012.0
1 TraesCS2D01G480100 chr2D 85.256 3052 304 63 689 3688 584234505 584237462 0.000000e+00 3009.0
2 TraesCS2D01G480100 chr2D 83.848 1845 222 34 1978 3782 545727998 545726190 0.000000e+00 1687.0
3 TraesCS2D01G480100 chr2D 87.513 929 108 5 783 1710 545729124 545728203 0.000000e+00 1066.0
4 TraesCS2D01G480100 chr2D 78.001 1641 259 54 1977 3563 582503110 582501518 0.000000e+00 937.0
5 TraesCS2D01G480100 chr2D 77.273 1364 240 28 2230 3552 435926333 435927667 0.000000e+00 737.0
6 TraesCS2D01G480100 chr2D 86.700 203 21 3 514 716 545729522 545729326 2.290000e-53 220.0
7 TraesCS2D01G480100 chr2D 88.462 182 20 1 514 695 584234272 584234452 8.220000e-53 219.0
8 TraesCS2D01G480100 chr2D 87.705 122 8 6 692 806 545729291 545729170 8.520000e-28 135.0
9 TraesCS2D01G480100 chr2D 96.825 63 2 0 2160 2222 580971794 580971856 6.680000e-19 106.0
10 TraesCS2D01G480100 chr2D 96.825 63 2 0 2118 2180 580971836 580971898 6.680000e-19 106.0
11 TraesCS2D01G480100 chr2D 89.873 79 8 0 2165 2243 545727844 545727766 8.640000e-18 102.0
12 TraesCS2D01G480100 chr2D 95.312 64 3 0 2177 2240 584235928 584235991 8.640000e-18 102.0
13 TraesCS2D01G480100 chr2D 98.000 50 1 0 3814 3863 580973445 580973494 2.420000e-13 87.9
14 TraesCS2D01G480100 chr2D 98.000 50 1 0 3769 3818 580973490 580973539 2.420000e-13 87.9
15 TraesCS2D01G480100 chr2D 97.872 47 0 1 556 601 582546481 582546435 4.050000e-11 80.5
16 TraesCS2D01G480100 chr2D 85.246 61 3 1 2183 2243 582502928 582502874 1.900000e-04 58.4
17 TraesCS2D01G480100 chr2B 85.419 3052 308 50 689 3688 703349750 703352716 0.000000e+00 3044.0
18 TraesCS2D01G480100 chr2B 96.581 1784 30 15 2124 3898 700206949 700208710 0.000000e+00 2928.0
19 TraesCS2D01G480100 chr2B 96.005 1727 32 10 540 2264 700205353 700207044 0.000000e+00 2772.0
20 TraesCS2D01G480100 chr2B 93.878 637 16 6 3930 4556 700208867 700209490 0.000000e+00 939.0
21 TraesCS2D01G480100 chr2B 77.547 1639 259 50 1977 3563 701502342 701500761 0.000000e+00 887.0
22 TraesCS2D01G480100 chr2B 77.346 1364 238 32 2230 3552 515049300 515047967 0.000000e+00 741.0
23 TraesCS2D01G480100 chr2B 94.375 320 17 1 4561 4880 700210755 700211073 1.580000e-134 490.0
24 TraesCS2D01G480100 chr2B 94.118 306 6 2 1 294 700204878 700205183 5.760000e-124 455.0
25 TraesCS2D01G480100 chr2B 92.704 233 9 3 286 510 700205123 700205355 3.640000e-86 329.0
26 TraesCS2D01G480100 chr2B 83.239 352 44 10 4541 4880 692717044 692716696 4.740000e-80 309.0
27 TraesCS2D01G480100 chr2B 79.941 339 57 8 1761 2089 515049784 515049447 6.310000e-59 239.0
28 TraesCS2D01G480100 chr2B 88.816 152 16 1 4729 4880 755635311 755635161 8.340000e-43 185.0
29 TraesCS2D01G480100 chr2B 93.827 81 5 0 2160 2240 703351165 703351245 6.630000e-24 122.0
30 TraesCS2D01G480100 chr2B 98.000 50 1 0 3769 3818 700208627 700208676 2.420000e-13 87.9
31 TraesCS2D01G480100 chr2B 92.063 63 2 3 2160 2222 700206904 700206963 8.700000e-13 86.1
32 TraesCS2D01G480100 chr2B 96.000 50 2 0 3814 3863 700208582 700208631 1.130000e-11 82.4
33 TraesCS2D01G480100 chr2B 97.872 47 1 0 3930 3976 700208762 700208808 1.130000e-11 82.4
34 TraesCS2D01G480100 chr2B 91.228 57 4 1 546 601 701506374 701506318 5.240000e-10 76.8
35 TraesCS2D01G480100 chr2B 94.595 37 2 0 2207 2243 701502142 701502106 1.900000e-04 58.4
36 TraesCS2D01G480100 chr2A 83.605 2086 242 44 1750 3787 687313812 687315845 0.000000e+00 1866.0
37 TraesCS2D01G480100 chr2A 87.621 929 105 6 783 1710 687312883 687313802 0.000000e+00 1070.0
38 TraesCS2D01G480100 chr2A 87.200 125 9 7 689 806 687312713 687312837 8.520000e-28 135.0
39 TraesCS2D01G480100 chr2A 90.789 76 7 0 2165 2240 687314185 687314260 8.640000e-18 102.0
40 TraesCS2D01G480100 chr2A 94.118 51 2 1 4276 4326 771809429 771809380 5.240000e-10 76.8
41 TraesCS2D01G480100 chr5B 82.955 176 26 3 4556 4727 565348398 565348223 6.540000e-34 156.0
42 TraesCS2D01G480100 chr1A 92.727 55 2 2 4273 4326 589117617 589117564 1.460000e-10 78.7
43 TraesCS2D01G480100 chr1A 94.118 51 2 1 4276 4326 515792626 515792577 5.240000e-10 76.8


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 TraesCS2D01G480100 chr2D 580969677 580974556 4879 False 1879.96 9012 97.930000 1 4880 5 chr2D.!!$F2 4879
1 TraesCS2D01G480100 chr2D 584234272 584237462 3190 False 1110.00 3009 89.676667 514 3688 3 chr2D.!!$F3 3174
2 TraesCS2D01G480100 chr2D 435926333 435927667 1334 False 737.00 737 77.273000 2230 3552 1 chr2D.!!$F1 1322
3 TraesCS2D01G480100 chr2D 545726190 545729522 3332 True 642.00 1687 87.127800 514 3782 5 chr2D.!!$R2 3268
4 TraesCS2D01G480100 chr2D 582501518 582503110 1592 True 497.70 937 81.623500 1977 3563 2 chr2D.!!$R3 1586
5 TraesCS2D01G480100 chr2B 703349750 703352716 2966 False 1583.00 3044 89.623000 689 3688 2 chr2B.!!$F2 2999
6 TraesCS2D01G480100 chr2B 700204878 700211073 6195 False 825.18 2928 95.159600 1 4880 10 chr2B.!!$F1 4879
7 TraesCS2D01G480100 chr2B 515047967 515049784 1817 True 490.00 741 78.643500 1761 3552 2 chr2B.!!$R4 1791
8 TraesCS2D01G480100 chr2B 701500761 701502342 1581 True 472.70 887 86.071000 1977 3563 2 chr2B.!!$R5 1586
9 TraesCS2D01G480100 chr2A 687312713 687315845 3132 False 793.25 1866 87.303750 689 3787 4 chr2A.!!$F1 3098

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
167 179 2.440539 CTCACGTTGAGGTAGTTGCT 57.559 50.000 7.01 0.00 40.71 3.91 F
376 388 2.485966 AGAGGATGTCCAGGCACTAT 57.514 50.000 1.30 0.00 36.02 2.12 F
402 414 4.755266 TGGAACTAGGCTTTGGATCTAC 57.245 45.455 0.00 0.00 0.00 2.59 F
1334 1486 7.254387 GCTCATGACACTAGAATCTGATTCAAC 60.254 40.741 27.06 13.92 41.71 3.18 F
1957 2115 0.043334 TTGGGAAGAGGAGGAGGAGG 59.957 60.000 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 1486 0.590732 GCGCCTTGAATGAGATTGCG 60.591 55.000 0.00 0.00 43.05 4.85 R
1389 1541 2.579873 GGTATCTCCATGCATGCAACT 58.420 47.619 26.68 6.15 35.97 3.16 R
1476 1628 2.999355 CACCTCTAGAGTTGCTTGCTTC 59.001 50.000 18.42 0.00 0.00 3.86 R
3298 3642 2.191128 ATTGGAGGCTGAAGTGTCAC 57.809 50.000 0.00 0.00 0.00 3.67 R
3899 4281 1.128188 ACCTTCACTCACAGACCCCC 61.128 60.000 0.00 0.00 0.00 5.40 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
154 166 3.637229 TGTTTTTCTCTCTCTCCTCACGT 59.363 43.478 0.00 0.00 0.00 4.49
156 168 3.924918 TTTCTCTCTCTCCTCACGTTG 57.075 47.619 0.00 0.00 0.00 4.10
167 179 2.440539 CTCACGTTGAGGTAGTTGCT 57.559 50.000 7.01 0.00 40.71 3.91
191 203 7.202102 GCTATTTCCTCTTAAGGTCCCTCATTA 60.202 40.741 1.85 0.00 43.82 1.90
290 302 4.658435 TGTAGCTTATATTGCCCCTCTTGA 59.342 41.667 0.00 0.00 0.00 3.02
291 303 5.310594 TGTAGCTTATATTGCCCCTCTTGAT 59.689 40.000 0.00 0.00 0.00 2.57
293 305 6.454223 AGCTTATATTGCCCCTCTTGATTA 57.546 37.500 0.00 0.00 0.00 1.75
295 307 7.473593 AGCTTATATTGCCCCTCTTGATTAAT 58.526 34.615 0.00 0.00 0.00 1.40
296 308 7.613411 AGCTTATATTGCCCCTCTTGATTAATC 59.387 37.037 8.60 8.60 0.00 1.75
297 309 7.394359 GCTTATATTGCCCCTCTTGATTAATCA 59.606 37.037 14.23 14.23 34.44 2.57
298 310 9.471702 CTTATATTGCCCCTCTTGATTAATCAT 57.528 33.333 18.61 2.88 36.56 2.45
301 313 5.912149 TGCCCCTCTTGATTAATCATAGT 57.088 39.130 18.61 0.00 36.56 2.12
302 314 6.266131 TGCCCCTCTTGATTAATCATAGTT 57.734 37.500 18.61 0.00 36.56 2.24
303 315 6.672593 TGCCCCTCTTGATTAATCATAGTTT 58.327 36.000 18.61 0.00 36.56 2.66
304 316 7.811282 TGCCCCTCTTGATTAATCATAGTTTA 58.189 34.615 18.61 2.25 36.56 2.01
305 317 8.278639 TGCCCCTCTTGATTAATCATAGTTTAA 58.721 33.333 18.61 1.55 36.56 1.52
306 318 8.787852 GCCCCTCTTGATTAATCATAGTTTAAG 58.212 37.037 18.61 11.11 36.56 1.85
307 319 9.289782 CCCCTCTTGATTAATCATAGTTTAAGG 57.710 37.037 18.61 17.06 36.56 2.69
320 332 8.934023 TCATAGTTTAAGGATTTCTTTGGTGT 57.066 30.769 0.00 0.00 36.93 4.16
323 335 7.215719 AGTTTAAGGATTTCTTTGGTGTAGC 57.784 36.000 0.00 0.00 36.93 3.58
324 336 7.004691 AGTTTAAGGATTTCTTTGGTGTAGCT 58.995 34.615 0.00 0.00 36.93 3.32
325 337 7.505923 AGTTTAAGGATTTCTTTGGTGTAGCTT 59.494 33.333 0.00 0.00 36.93 3.74
326 338 8.789762 GTTTAAGGATTTCTTTGGTGTAGCTTA 58.210 33.333 0.00 0.00 36.93 3.09
327 339 9.528489 TTTAAGGATTTCTTTGGTGTAGCTTAT 57.472 29.630 0.00 0.00 36.93 1.73
330 342 9.700831 AAGGATTTCTTTGGTGTAGCTTATATT 57.299 29.630 0.00 0.00 29.99 1.28
331 343 9.125026 AGGATTTCTTTGGTGTAGCTTATATTG 57.875 33.333 0.00 0.00 0.00 1.90
332 344 7.862873 GGATTTCTTTGGTGTAGCTTATATTGC 59.137 37.037 0.00 0.00 0.00 3.56
333 345 6.693315 TTCTTTGGTGTAGCTTATATTGCC 57.307 37.500 0.00 0.00 0.00 4.52
334 346 5.130350 TCTTTGGTGTAGCTTATATTGCCC 58.870 41.667 0.00 0.00 0.00 5.36
335 347 3.502123 TGGTGTAGCTTATATTGCCCC 57.498 47.619 0.00 0.00 0.00 5.80
336 348 3.053077 TGGTGTAGCTTATATTGCCCCT 58.947 45.455 0.00 0.00 0.00 4.79
337 349 3.072476 TGGTGTAGCTTATATTGCCCCTC 59.928 47.826 0.00 0.00 0.00 4.30
376 388 2.485966 AGAGGATGTCCAGGCACTAT 57.514 50.000 1.30 0.00 36.02 2.12
402 414 4.755266 TGGAACTAGGCTTTGGATCTAC 57.245 45.455 0.00 0.00 0.00 2.59
821 968 9.000486 GTATTTTAGTTGTAACTTCAAGGCTCT 58.000 33.333 2.20 0.00 40.37 4.09
1334 1486 7.254387 GCTCATGACACTAGAATCTGATTCAAC 60.254 40.741 27.06 13.92 41.71 3.18
1476 1628 2.751806 GGCAAGTTCATCTTCTTCCCTG 59.248 50.000 0.00 0.00 33.63 4.45
1596 1748 5.534207 TCAATGCATTGAAGAACCAAGTT 57.466 34.783 34.23 0.00 43.26 2.66
1956 2114 2.188818 ATTGGGAAGAGGAGGAGGAG 57.811 55.000 0.00 0.00 0.00 3.69
1957 2115 0.043334 TTGGGAAGAGGAGGAGGAGG 59.957 60.000 0.00 0.00 0.00 4.30
1958 2116 0.855855 TGGGAAGAGGAGGAGGAGGA 60.856 60.000 0.00 0.00 0.00 3.71
1959 2117 0.105709 GGGAAGAGGAGGAGGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
1960 2118 0.105709 GGAAGAGGAGGAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
1961 2119 0.930726 GAAGAGGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
2069 2260 4.566004 TCATTTGTTCCACTTCTCCTACG 58.434 43.478 0.00 0.00 0.00 3.51
2162 2389 1.811965 CATTTCCATGACTGCGGAACA 59.188 47.619 0.00 0.00 40.98 3.18
2163 2390 1.974265 TTTCCATGACTGCGGAACAA 58.026 45.000 0.00 0.00 40.98 2.83
2164 2391 1.522668 TTCCATGACTGCGGAACAAG 58.477 50.000 0.00 0.00 36.36 3.16
2658 2966 7.231317 TGTTTTCTTGCAAGAAGTTATGGAGAT 59.769 33.333 33.76 0.00 45.01 2.75
2751 3065 1.977129 GCTTCAGATCTGGCTAGGGAT 59.023 52.381 22.42 0.00 0.00 3.85
2754 3068 4.415596 CTTCAGATCTGGCTAGGGATACT 58.584 47.826 22.42 0.00 0.00 2.12
3220 3564 5.069318 TGTGTGATATTTGCCAAGTCTTGA 58.931 37.500 14.42 0.00 0.00 3.02
3283 3627 6.369615 TGATCATATTATGGATGTTCTGTGCG 59.630 38.462 3.89 0.00 0.00 5.34
3298 3642 2.926200 CTGTGCGAAGGTATGACAGAAG 59.074 50.000 0.00 0.00 36.89 2.85
3350 3694 1.627329 TGGACAGATTGCTCTTGCTCT 59.373 47.619 0.00 0.00 40.48 4.09
3351 3695 2.039480 TGGACAGATTGCTCTTGCTCTT 59.961 45.455 0.00 0.00 40.48 2.85
3352 3696 2.419324 GGACAGATTGCTCTTGCTCTTG 59.581 50.000 0.00 0.00 40.48 3.02
3353 3697 1.811359 ACAGATTGCTCTTGCTCTTGC 59.189 47.619 0.00 0.00 40.48 4.01
3354 3698 2.085320 CAGATTGCTCTTGCTCTTGCT 58.915 47.619 0.00 0.00 40.48 3.91
3355 3699 2.096174 CAGATTGCTCTTGCTCTTGCTC 59.904 50.000 0.00 0.00 40.48 4.26
3421 3765 5.621193 AGCTTCTAGTTGTGGAAAAGCTTA 58.379 37.500 0.00 0.00 45.14 3.09
3427 3777 4.137543 AGTTGTGGAAAAGCTTACTCAGG 58.862 43.478 0.00 0.00 0.00 3.86
3591 3941 4.528596 CAGGAGAGGAAGAGAAGGTAACAA 59.471 45.833 0.00 0.00 41.41 2.83
3647 4004 7.959689 ACTCATATACTCATTGACTGATTGC 57.040 36.000 0.00 0.00 32.10 3.56
3659 4017 7.332430 TCATTGACTGATTGCCAATTGATTTTC 59.668 33.333 7.12 0.00 0.00 2.29
3801 4183 4.647853 AGTATTTATGGTCGAGTGCAGGTA 59.352 41.667 0.00 0.00 0.00 3.08
3893 4275 2.573462 TGAGGTAGCAGAAGGAAAGCAT 59.427 45.455 0.00 0.00 0.00 3.79
3897 4279 0.324091 AGCAGAAGGAAAGCATGGGG 60.324 55.000 0.00 0.00 0.00 4.96
3921 4397 2.370849 GGGGTCTGTGAGTGAAGGTAAA 59.629 50.000 0.00 0.00 0.00 2.01
3922 4398 3.400255 GGGTCTGTGAGTGAAGGTAAAC 58.600 50.000 0.00 0.00 0.00 2.01
3923 4399 3.181458 GGGTCTGTGAGTGAAGGTAAACA 60.181 47.826 0.00 0.00 0.00 2.83
3924 4400 4.058817 GGTCTGTGAGTGAAGGTAAACAG 58.941 47.826 0.00 0.00 37.07 3.16
3926 4402 5.357257 GTCTGTGAGTGAAGGTAAACAGAA 58.643 41.667 4.99 0.00 43.93 3.02
3928 4404 4.703897 TGTGAGTGAAGGTAAACAGAAGG 58.296 43.478 0.00 0.00 0.00 3.46
3946 4452 5.122396 CAGAAGGGACAACTAATTCGGAAAG 59.878 44.000 0.00 0.00 0.00 2.62
3957 4463 5.938710 ACTAATTCGGAAAGGAAGGAAACTC 59.061 40.000 0.00 0.00 42.68 3.01
4062 4568 9.936329 AATTAGAATTATTATGGTGGAGTTGGT 57.064 29.630 0.00 0.00 0.00 3.67
4139 4655 0.620556 GCCTCAATCCCTGGTCTGAA 59.379 55.000 0.00 0.00 0.00 3.02
4170 4686 2.034812 GGACGAGGGTGATTGCTACTAG 59.965 54.545 0.00 0.00 0.00 2.57
4171 4687 2.688958 GACGAGGGTGATTGCTACTAGT 59.311 50.000 0.00 0.00 0.00 2.57
4220 4736 3.726517 ACCAGCGCATGCACGAAC 61.727 61.111 19.57 0.88 46.23 3.95
4221 4737 4.799473 CCAGCGCATGCACGAACG 62.799 66.667 19.57 0.51 46.23 3.95
4251 4767 1.956170 CACGAAACAGGAGCACGCT 60.956 57.895 0.00 0.00 0.00 5.07
4254 4770 3.016474 GAAACAGGAGCACGCTCGC 62.016 63.158 12.65 6.24 43.59 5.03
4435 4951 1.367665 GAAACTGCACACACGTCGC 60.368 57.895 0.00 0.00 0.00 5.19
4540 5056 2.324330 TGTGCATCTCCGGCAAACG 61.324 57.895 0.00 0.00 43.91 3.60
4576 6352 1.542328 CCCATTAATCCGCCGTGATGA 60.542 52.381 0.00 0.00 0.00 2.92
4603 6379 0.524816 ATGCTTGTACGGCTACGACG 60.525 55.000 11.05 0.00 44.60 5.12
4642 6418 1.528542 TCCCATCCTCGACCTAGCG 60.529 63.158 0.00 0.00 0.00 4.26
4666 6442 0.168128 GCGTATTGTGCCTGGTTCAC 59.832 55.000 0.00 0.00 35.14 3.18
4811 6587 3.536917 TCCTCGCTACGCCCATGG 61.537 66.667 4.14 4.14 0.00 3.66
4844 6620 0.889186 TTCCACCGCTCTCTTTTGGC 60.889 55.000 0.00 0.00 0.00 4.52
4848 6624 0.690762 ACCGCTCTCTTTTGGCCTAA 59.309 50.000 3.32 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 166 6.374417 AAGAGGAAATAGCAACTACCTCAA 57.626 37.500 17.03 0.00 44.11 3.02
156 168 6.987404 CCTTAAGAGGAAATAGCAACTACCTC 59.013 42.308 3.36 0.00 46.74 3.85
167 179 8.814448 ATAATGAGGGACCTTAAGAGGAAATA 57.186 34.615 3.36 0.00 46.74 1.40
191 203 6.127730 GGGCATGTAAGCTACACAAAACTAAT 60.128 38.462 5.27 0.00 42.23 1.73
295 307 8.934023 ACACCAAAGAAATCCTTAAACTATGA 57.066 30.769 0.00 0.00 34.00 2.15
297 309 8.957466 GCTACACCAAAGAAATCCTTAAACTAT 58.043 33.333 0.00 0.00 34.00 2.12
298 310 8.161425 AGCTACACCAAAGAAATCCTTAAACTA 58.839 33.333 0.00 0.00 34.00 2.24
299 311 7.004691 AGCTACACCAAAGAAATCCTTAAACT 58.995 34.615 0.00 0.00 34.00 2.66
300 312 7.215719 AGCTACACCAAAGAAATCCTTAAAC 57.784 36.000 0.00 0.00 34.00 2.01
301 313 7.833285 AAGCTACACCAAAGAAATCCTTAAA 57.167 32.000 0.00 0.00 34.00 1.52
304 316 9.700831 AATATAAGCTACACCAAAGAAATCCTT 57.299 29.630 0.00 0.00 36.47 3.36
305 317 9.125026 CAATATAAGCTACACCAAAGAAATCCT 57.875 33.333 0.00 0.00 0.00 3.24
306 318 7.862873 GCAATATAAGCTACACCAAAGAAATCC 59.137 37.037 0.00 0.00 0.00 3.01
307 319 7.862873 GGCAATATAAGCTACACCAAAGAAATC 59.137 37.037 0.00 0.00 0.00 2.17
308 320 7.201911 GGGCAATATAAGCTACACCAAAGAAAT 60.202 37.037 0.00 0.00 0.00 2.17
309 321 6.096282 GGGCAATATAAGCTACACCAAAGAAA 59.904 38.462 0.00 0.00 0.00 2.52
310 322 5.592688 GGGCAATATAAGCTACACCAAAGAA 59.407 40.000 0.00 0.00 0.00 2.52
311 323 5.130350 GGGCAATATAAGCTACACCAAAGA 58.870 41.667 0.00 0.00 0.00 2.52
312 324 4.278419 GGGGCAATATAAGCTACACCAAAG 59.722 45.833 0.00 0.00 0.00 2.77
313 325 4.079443 AGGGGCAATATAAGCTACACCAAA 60.079 41.667 0.00 0.00 0.00 3.28
314 326 3.461831 AGGGGCAATATAAGCTACACCAA 59.538 43.478 0.00 0.00 0.00 3.67
315 327 3.053077 AGGGGCAATATAAGCTACACCA 58.947 45.455 0.00 0.00 0.00 4.17
316 328 3.328050 AGAGGGGCAATATAAGCTACACC 59.672 47.826 0.00 0.00 0.00 4.16
317 329 4.625607 AGAGGGGCAATATAAGCTACAC 57.374 45.455 0.00 0.00 0.00 2.90
318 330 5.844516 ACTAAGAGGGGCAATATAAGCTACA 59.155 40.000 0.00 0.00 0.00 2.74
319 331 6.166982 CACTAAGAGGGGCAATATAAGCTAC 58.833 44.000 0.00 0.00 0.00 3.58
320 332 5.844516 ACACTAAGAGGGGCAATATAAGCTA 59.155 40.000 0.00 0.00 0.00 3.32
321 333 4.660771 ACACTAAGAGGGGCAATATAAGCT 59.339 41.667 0.76 0.00 0.00 3.74
322 334 4.974399 ACACTAAGAGGGGCAATATAAGC 58.026 43.478 0.00 0.00 0.00 3.09
323 335 7.054124 TCAAACACTAAGAGGGGCAATATAAG 58.946 38.462 0.00 0.00 0.00 1.73
324 336 6.964464 TCAAACACTAAGAGGGGCAATATAA 58.036 36.000 0.00 0.00 0.00 0.98
325 337 6.569127 TCAAACACTAAGAGGGGCAATATA 57.431 37.500 0.00 0.00 0.00 0.86
326 338 5.450818 TCAAACACTAAGAGGGGCAATAT 57.549 39.130 0.00 0.00 0.00 1.28
327 339 4.919774 TCAAACACTAAGAGGGGCAATA 57.080 40.909 0.00 0.00 0.00 1.90
328 340 3.806949 TCAAACACTAAGAGGGGCAAT 57.193 42.857 0.00 0.00 0.00 3.56
329 341 3.561313 GGATCAAACACTAAGAGGGGCAA 60.561 47.826 0.00 0.00 0.00 4.52
330 342 2.026262 GGATCAAACACTAAGAGGGGCA 60.026 50.000 0.00 0.00 0.00 5.36
331 343 2.239907 AGGATCAAACACTAAGAGGGGC 59.760 50.000 0.00 0.00 0.00 5.80
332 344 4.717280 ACTAGGATCAAACACTAAGAGGGG 59.283 45.833 0.00 0.00 0.00 4.79
333 345 5.941555 ACTAGGATCAAACACTAAGAGGG 57.058 43.478 0.00 0.00 0.00 4.30
334 346 8.294954 TCTAACTAGGATCAAACACTAAGAGG 57.705 38.462 0.00 0.00 0.00 3.69
335 347 8.410141 CCTCTAACTAGGATCAAACACTAAGAG 58.590 40.741 0.00 0.00 39.15 2.85
336 348 8.114102 TCCTCTAACTAGGATCAAACACTAAGA 58.886 37.037 0.00 0.00 40.86 2.10
337 349 8.294954 TCCTCTAACTAGGATCAAACACTAAG 57.705 38.462 0.00 0.00 40.86 2.18
365 377 1.965414 TCCAAAGGATAGTGCCTGGA 58.035 50.000 0.00 0.00 38.58 3.86
376 388 2.714250 TCCAAAGCCTAGTTCCAAAGGA 59.286 45.455 0.00 0.00 34.58 3.36
402 414 4.522789 ACAAAGTACCAAATGGGCTAGTTG 59.477 41.667 3.91 3.91 42.05 3.16
536 548 7.706179 CACAAAAGGCAATAATACCACCATAAG 59.294 37.037 0.00 0.00 0.00 1.73
538 550 6.406400 GCACAAAAGGCAATAATACCACCATA 60.406 38.462 0.00 0.00 0.00 2.74
808 955 4.401925 ACATTAGCAAGAGCCTTGAAGTT 58.598 39.130 16.28 4.09 43.56 2.66
1334 1486 0.590732 GCGCCTTGAATGAGATTGCG 60.591 55.000 0.00 0.00 43.05 4.85
1386 1538 3.851458 ATCTCCATGCATGCAACTCTA 57.149 42.857 26.68 11.10 0.00 2.43
1389 1541 2.579873 GGTATCTCCATGCATGCAACT 58.420 47.619 26.68 6.15 35.97 3.16
1476 1628 2.999355 CACCTCTAGAGTTGCTTGCTTC 59.001 50.000 18.42 0.00 0.00 3.86
1593 1745 6.295575 CCAGATGGACTTCAGAACTTAGAACT 60.296 42.308 0.00 0.00 37.39 3.01
1596 1748 4.081420 GCCAGATGGACTTCAGAACTTAGA 60.081 45.833 2.18 0.00 37.39 2.10
1956 2114 4.775253 TCTTCTTCTTCTCCTTCTTCCTCC 59.225 45.833 0.00 0.00 0.00 4.30
1957 2115 5.993748 TCTTCTTCTTCTCCTTCTTCCTC 57.006 43.478 0.00 0.00 0.00 3.71
1958 2116 6.081356 TCTTCTTCTTCTTCTCCTTCTTCCT 58.919 40.000 0.00 0.00 0.00 3.36
1959 2117 6.353404 TCTTCTTCTTCTTCTCCTTCTTCC 57.647 41.667 0.00 0.00 0.00 3.46
1960 2118 7.666623 TCTTCTTCTTCTTCTTCTCCTTCTTC 58.333 38.462 0.00 0.00 0.00 2.87
1961 2119 7.610580 TCTTCTTCTTCTTCTTCTCCTTCTT 57.389 36.000 0.00 0.00 0.00 2.52
2069 2260 6.465084 TCTCCCTCTTCTTTTAAGTAAGTGC 58.535 40.000 0.00 0.00 0.00 4.40
2162 2389 4.030216 GTCTCCATCTCCCTCTTCTTCTT 58.970 47.826 0.00 0.00 0.00 2.52
2163 2390 3.012274 TGTCTCCATCTCCCTCTTCTTCT 59.988 47.826 0.00 0.00 0.00 2.85
2164 2391 3.370104 TGTCTCCATCTCCCTCTTCTTC 58.630 50.000 0.00 0.00 0.00 2.87
2658 2966 5.581126 AGTTTGACTTTGACTTTGCATCA 57.419 34.783 0.00 0.00 0.00 3.07
2751 3065 5.366768 ACATGCAAGAAGCCTATAAGGAGTA 59.633 40.000 0.00 0.00 44.83 2.59
2754 3068 4.444876 GGACATGCAAGAAGCCTATAAGGA 60.445 45.833 0.00 0.00 44.83 3.36
2994 3323 8.564574 CATTTAGCAGACCACTTAAGTGTAAAA 58.435 33.333 29.05 18.41 44.21 1.52
3283 3627 5.140747 AGTGTCACTTCTGTCATACCTTC 57.859 43.478 0.00 0.00 0.00 3.46
3298 3642 2.191128 ATTGGAGGCTGAAGTGTCAC 57.809 50.000 0.00 0.00 0.00 3.67
3309 3653 4.868067 CAATGCTTGATAGAATTGGAGGC 58.132 43.478 0.00 0.00 41.84 4.70
3350 3694 5.132502 TCTCAAATTTCTCACCAAGAGCAA 58.867 37.500 0.00 0.00 44.35 3.91
3351 3695 4.717877 TCTCAAATTTCTCACCAAGAGCA 58.282 39.130 0.00 0.00 44.35 4.26
3352 3696 5.695851 TTCTCAAATTTCTCACCAAGAGC 57.304 39.130 0.00 0.00 44.35 4.09
3353 3697 8.239998 GGTATTTCTCAAATTTCTCACCAAGAG 58.760 37.037 0.00 0.00 37.72 2.85
3354 3698 7.944554 AGGTATTTCTCAAATTTCTCACCAAGA 59.055 33.333 0.00 0.00 30.42 3.02
3355 3699 8.025445 CAGGTATTTCTCAAATTTCTCACCAAG 58.975 37.037 0.00 0.00 30.42 3.61
3421 3765 2.630580 GTTCCTCTGACTTGACCTGAGT 59.369 50.000 0.00 0.00 0.00 3.41
3427 3777 3.259374 TCATCCTGTTCCTCTGACTTGAC 59.741 47.826 0.00 0.00 0.00 3.18
3621 3975 8.920665 GCAATCAGTCAATGAGTATATGAGTAC 58.079 37.037 0.00 0.00 42.53 2.73
3647 4004 9.428097 CCCTAGAAGAAAAAGAAAATCAATTGG 57.572 33.333 5.42 0.00 0.00 3.16
3659 4017 4.580868 GTCCCTGTCCCTAGAAGAAAAAG 58.419 47.826 0.00 0.00 0.00 2.27
3801 4183 2.225467 GCTTTCTGCTGTCCTTCTGTT 58.775 47.619 0.00 0.00 38.95 3.16
3899 4281 1.128188 ACCTTCACTCACAGACCCCC 61.128 60.000 0.00 0.00 0.00 5.40
3912 4388 4.165372 AGTTGTCCCTTCTGTTTACCTTCA 59.835 41.667 0.00 0.00 0.00 3.02
3921 4397 3.581332 TCCGAATTAGTTGTCCCTTCTGT 59.419 43.478 0.00 0.00 0.00 3.41
3922 4398 4.202245 TCCGAATTAGTTGTCCCTTCTG 57.798 45.455 0.00 0.00 0.00 3.02
3923 4399 4.903045 TTCCGAATTAGTTGTCCCTTCT 57.097 40.909 0.00 0.00 0.00 2.85
3924 4400 4.395231 CCTTTCCGAATTAGTTGTCCCTTC 59.605 45.833 0.00 0.00 0.00 3.46
3926 4402 3.585732 TCCTTTCCGAATTAGTTGTCCCT 59.414 43.478 0.00 0.00 0.00 4.20
3928 4404 4.395231 CCTTCCTTTCCGAATTAGTTGTCC 59.605 45.833 0.00 0.00 0.00 4.02
3946 4452 6.159293 CCAAAATAAAGCAGAGTTTCCTTCC 58.841 40.000 0.00 0.00 0.00 3.46
3957 4463 7.064490 ACAGTTTTCACAACCAAAATAAAGCAG 59.936 33.333 0.00 0.00 0.00 4.24
4123 4639 7.451731 AATAATACTTCAGACCAGGGATTGA 57.548 36.000 0.00 0.00 0.00 2.57
4126 4642 6.389869 TCCAAATAATACTTCAGACCAGGGAT 59.610 38.462 0.00 0.00 0.00 3.85
4132 4648 5.753921 CCTCGTCCAAATAATACTTCAGACC 59.246 44.000 0.00 0.00 0.00 3.85
4139 4655 5.888982 ATCACCCTCGTCCAAATAATACT 57.111 39.130 0.00 0.00 0.00 2.12
4170 4686 4.142534 TGCCGGCGTGATTCTATATACTAC 60.143 45.833 23.90 0.00 0.00 2.73
4171 4687 4.011698 TGCCGGCGTGATTCTATATACTA 58.988 43.478 23.90 0.00 0.00 1.82
4225 4741 2.551270 CTGTTTCGTGCGAGTGGC 59.449 61.111 0.00 0.00 43.96 5.01
4226 4742 1.284982 CTCCTGTTTCGTGCGAGTGG 61.285 60.000 0.00 0.00 0.00 4.00
4227 4743 1.891060 GCTCCTGTTTCGTGCGAGTG 61.891 60.000 0.00 0.00 0.00 3.51
4228 4744 1.664965 GCTCCTGTTTCGTGCGAGT 60.665 57.895 0.00 0.00 0.00 4.18
4229 4745 1.664649 TGCTCCTGTTTCGTGCGAG 60.665 57.895 0.00 0.00 0.00 5.03
4230 4746 1.954146 GTGCTCCTGTTTCGTGCGA 60.954 57.895 0.00 0.00 0.00 5.10
4307 4823 2.282462 GGGGTCCCTGTGCAGTTG 60.282 66.667 8.15 0.00 0.00 3.16
4473 4989 3.285215 GCCATCTGATGCCGGCAG 61.285 66.667 35.36 21.54 44.25 4.85
4556 5072 0.874390 CATCACGGCGGATTAATGGG 59.126 55.000 13.24 0.00 0.00 4.00
4557 5073 1.877637 TCATCACGGCGGATTAATGG 58.122 50.000 13.24 0.00 0.00 3.16
4558 5074 2.160219 CCATCATCACGGCGGATTAATG 59.840 50.000 13.24 14.97 0.00 1.90
4559 5075 2.038426 TCCATCATCACGGCGGATTAAT 59.962 45.455 13.24 4.78 0.00 1.40
4576 6352 1.743772 GCCGTACAAGCATCAGTCCAT 60.744 52.381 0.13 0.00 0.00 3.41
4624 6400 1.528542 CGCTAGGTCGAGGATGGGA 60.529 63.158 0.00 0.00 0.00 4.37
4642 6418 3.186047 AGGCACAATACGCGCGAC 61.186 61.111 39.36 15.23 0.00 5.19
4823 6599 1.953686 CCAAAAGAGAGCGGTGGAAAA 59.046 47.619 0.00 0.00 0.00 2.29
4824 6600 1.604604 CCAAAAGAGAGCGGTGGAAA 58.395 50.000 0.00 0.00 0.00 3.13
4825 6601 0.889186 GCCAAAAGAGAGCGGTGGAA 60.889 55.000 0.00 0.00 0.00 3.53
4826 6602 1.302511 GCCAAAAGAGAGCGGTGGA 60.303 57.895 0.00 0.00 0.00 4.02
4828 6604 0.036388 TAGGCCAAAAGAGAGCGGTG 60.036 55.000 5.01 0.00 0.00 4.94
4829 6605 0.690762 TTAGGCCAAAAGAGAGCGGT 59.309 50.000 5.01 0.00 0.00 5.68
4831 6607 2.100605 AGTTAGGCCAAAAGAGAGCG 57.899 50.000 5.01 0.00 0.00 5.03
4832 6608 3.057946 CACAAGTTAGGCCAAAAGAGAGC 60.058 47.826 5.01 0.00 0.00 4.09
4833 6609 3.503748 CCACAAGTTAGGCCAAAAGAGAG 59.496 47.826 5.01 0.00 0.00 3.20
4834 6610 3.486383 CCACAAGTTAGGCCAAAAGAGA 58.514 45.455 5.01 0.00 0.00 3.10
4835 6611 2.558359 CCCACAAGTTAGGCCAAAAGAG 59.442 50.000 5.01 0.00 0.00 2.85
4836 6612 2.175931 TCCCACAAGTTAGGCCAAAAGA 59.824 45.455 5.01 0.00 0.00 2.52
4837 6613 2.296190 GTCCCACAAGTTAGGCCAAAAG 59.704 50.000 5.01 0.00 0.00 2.27
4838 6614 2.312390 GTCCCACAAGTTAGGCCAAAA 58.688 47.619 5.01 0.00 0.00 2.44
4844 6620 0.250124 TGCACGTCCCACAAGTTAGG 60.250 55.000 0.00 0.00 0.00 2.69
4848 6624 2.591715 GCTGCACGTCCCACAAGT 60.592 61.111 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.