Multiple sequence alignment - TraesCS6B01G367300

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 TraesCS6B01G367300 chr6B 100.000 5455 0 0 1 5455 641294955 641300409 0.000000e+00 10074.0
1 TraesCS6B01G367300 chr6B 85.921 2074 223 40 1517 3567 133122942 133124969 0.000000e+00 2148.0
2 TraesCS6B01G367300 chr6B 82.874 835 111 18 638 1458 133122102 133122918 0.000000e+00 721.0
3 TraesCS6B01G367300 chr6B 81.431 517 50 26 3922 4432 133125843 133126319 1.110000e-101 381.0
4 TraesCS6B01G367300 chr6D 94.775 3866 141 20 1611 5455 426070316 426074141 0.000000e+00 5963.0
5 TraesCS6B01G367300 chr6D 92.831 1646 72 13 1 1612 426068620 426070253 0.000000e+00 2344.0
6 TraesCS6B01G367300 chr6D 86.296 1868 198 32 1717 3567 59623259 59625085 0.000000e+00 1978.0
7 TraesCS6B01G367300 chr6D 82.854 834 113 16 638 1458 59622135 59622951 0.000000e+00 721.0
8 TraesCS6B01G367300 chr6D 89.524 105 2 3 4876 4980 426073218 426073313 2.060000e-24 124.0
9 TraesCS6B01G367300 chr6D 85.981 107 4 6 4530 4627 426073562 426073666 2.690000e-18 104.0
10 TraesCS6B01G367300 chr6D 83.784 74 10 2 5019 5091 276667446 276667518 9.800000e-08 69.4
11 TraesCS6B01G367300 chr6A 95.778 3482 96 22 258 3712 570933143 570936600 0.000000e+00 5568.0
12 TraesCS6B01G367300 chr6A 85.590 2075 227 43 1517 3567 75911477 75913503 0.000000e+00 2109.0
13 TraesCS6B01G367300 chr6A 90.702 1495 87 27 4000 5455 570936975 570938456 0.000000e+00 1943.0
14 TraesCS6B01G367300 chr6A 82.521 841 112 21 638 1463 75910637 75911457 0.000000e+00 706.0
15 TraesCS6B01G367300 chr6A 84.524 168 7 8 3763 3921 570936598 570936755 1.220000e-31 148.0
16 TraesCS6B01G367300 chr6A 93.827 81 3 2 3920 3998 570936796 570936876 2.670000e-23 121.0
17 TraesCS6B01G367300 chr6A 85.849 106 10 3 4527 4627 570937858 570937963 2.080000e-19 108.0
18 TraesCS6B01G367300 chr6A 85.714 105 6 1 4876 4980 570937518 570937613 9.670000e-18 102.0
19 TraesCS6B01G367300 chr7D 86.957 138 18 0 2132 2269 525372035 525372172 7.320000e-34 156.0
20 TraesCS6B01G367300 chr7D 87.805 82 8 1 5264 5343 206611151 206611070 1.620000e-15 95.3
21 TraesCS6B01G367300 chr7D 87.838 74 5 3 5270 5342 549364120 549364050 3.500000e-12 84.2
22 TraesCS6B01G367300 chr7B 86.957 138 18 0 2132 2269 561745032 561745169 7.320000e-34 156.0
23 TraesCS6B01G367300 chr7B 95.556 45 1 1 3683 3727 493525846 493525889 2.730000e-08 71.3
24 TraesCS6B01G367300 chr1D 92.105 76 3 2 5266 5341 441569170 441569098 2.690000e-18 104.0
25 TraesCS6B01G367300 chr1D 97.561 41 0 1 3688 3727 59131210 59131250 9.800000e-08 69.4
26 TraesCS6B01G367300 chr2B 91.026 78 4 2 5266 5343 795073864 795073790 9.670000e-18 102.0
27 TraesCS6B01G367300 chr2A 88.750 80 6 3 5328 5407 762261245 762261321 1.620000e-15 95.3
28 TraesCS6B01G367300 chr2A 91.667 48 2 2 3682 3727 4211709 4211756 1.270000e-06 65.8
29 TraesCS6B01G367300 chr4B 83.529 85 7 7 5328 5410 190196961 190196882 7.580000e-09 73.1
30 TraesCS6B01G367300 chr4B 93.878 49 0 2 5295 5343 190197022 190196977 2.730000e-08 71.3
31 TraesCS6B01G367300 chr3B 100.000 37 0 0 3691 3727 245510736 245510700 9.800000e-08 69.4
32 TraesCS6B01G367300 chr3A 100.000 37 0 0 3691 3727 659015508 659015472 9.800000e-08 69.4
33 TraesCS6B01G367300 chr3A 97.500 40 0 1 3689 3727 8867710 8867749 3.530000e-07 67.6
34 TraesCS6B01G367300 chr2D 100.000 36 0 0 3692 3727 547203609 547203574 3.530000e-07 67.6


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 TraesCS6B01G367300 chr6B 641294955 641300409 5454 False 10074.000000 10074 100.000000 1 5455 1 chr6B.!!$F1 5454
1 TraesCS6B01G367300 chr6B 133122102 133126319 4217 False 1083.333333 2148 83.408667 638 4432 3 chr6B.!!$F2 3794
2 TraesCS6B01G367300 chr6D 426068620 426074141 5521 False 2133.750000 5963 90.777750 1 5455 4 chr6D.!!$F3 5454
3 TraesCS6B01G367300 chr6D 59622135 59625085 2950 False 1349.500000 1978 84.575000 638 3567 2 chr6D.!!$F2 2929
4 TraesCS6B01G367300 chr6A 75910637 75913503 2866 False 1407.500000 2109 84.055500 638 3567 2 chr6A.!!$F1 2929
5 TraesCS6B01G367300 chr6A 570933143 570938456 5313 False 1331.666667 5568 89.399000 258 5455 6 chr6A.!!$F2 5197

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
426 456 0.248907 CCACGACCACGATAGCGATT 60.249 55.000 7.69 0.00 42.66 3.34 F
1287 1332 0.032952 GGTGGAAGAGCACGTGTACA 59.967 55.000 18.38 0.28 0.00 2.90 F
1333 1378 2.575532 GCATGGCTCCTTAATGCACTA 58.424 47.619 0.00 0.00 44.83 2.74 F
2868 3081 3.181491 CCTTGGATTGACACACGTGTTTT 60.181 43.478 20.79 9.12 45.05 2.43 F
3826 4596 0.036875 GGGTGTCTCTTGGGGAGTTG 59.963 60.000 0.00 0.00 42.40 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1307 1352 2.148446 TTAAGGAGCCATGCATTGCT 57.852 45.0 24.12 24.12 41.42 3.91 R
2482 2692 0.734889 CAGTGGCTGCTTTAATCCCG 59.265 55.0 0.00 0.00 0.00 5.14 R
3285 3498 0.894835 CAAAAATGAGGGGGTTCCGG 59.105 55.0 0.00 0.00 41.52 5.14 R
3829 4599 0.254178 ATGCAGTCATCTGGGGTGAC 59.746 55.0 3.03 3.03 44.85 3.67 R
5366 6336 0.112412 AAAGTTGGGCGGGTCAGATT 59.888 50.0 0.00 0.00 0.00 2.40 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
36 37 4.072131 GTGGATTGGAGTTTCTTGTGCTA 58.928 43.478 0.00 0.00 0.00 3.49
38 39 4.202461 TGGATTGGAGTTTCTTGTGCTAGT 60.202 41.667 0.00 0.00 0.00 2.57
69 70 3.086600 GAGCAGAGGTGGGGAGGG 61.087 72.222 0.00 0.00 0.00 4.30
70 71 3.615811 AGCAGAGGTGGGGAGGGA 61.616 66.667 0.00 0.00 0.00 4.20
72 73 2.366167 CAGAGGTGGGGAGGGAGG 60.366 72.222 0.00 0.00 0.00 4.30
73 74 2.540910 AGAGGTGGGGAGGGAGGA 60.541 66.667 0.00 0.00 0.00 3.71
74 75 2.041405 GAGGTGGGGAGGGAGGAG 60.041 72.222 0.00 0.00 0.00 3.69
75 76 4.423209 AGGTGGGGAGGGAGGAGC 62.423 72.222 0.00 0.00 0.00 4.70
76 77 4.741239 GGTGGGGAGGGAGGAGCA 62.741 72.222 0.00 0.00 0.00 4.26
77 78 3.403558 GTGGGGAGGGAGGAGCAC 61.404 72.222 0.00 0.00 0.00 4.40
78 79 3.940480 TGGGGAGGGAGGAGCACA 61.940 66.667 0.00 0.00 0.00 4.57
82 83 2.217038 GGAGGGAGGAGCACACACA 61.217 63.158 0.00 0.00 0.00 3.72
94 95 2.246397 CACACAGCGTTGCTCGTG 59.754 61.111 15.09 15.09 40.60 4.35
103 129 0.587737 CGTTGCTCGTGCGTTTTTGA 60.588 50.000 4.84 0.00 43.34 2.69
121 147 7.696453 CGTTTTTGACTTCTAGATTTGTTGTGT 59.304 33.333 0.00 0.00 0.00 3.72
138 164 0.753848 TGTCCTGTGTGTGGTCGAGA 60.754 55.000 0.00 0.00 0.00 4.04
199 225 5.509670 GCTATGAAAATAAGGCATTGGGGTC 60.510 44.000 0.00 0.00 0.00 4.46
224 250 6.060788 AGTTTTCTGAATCTGCACTTCTTCT 58.939 36.000 5.99 0.00 0.00 2.85
231 257 1.980765 TCTGCACTTCTTCTCCCATGT 59.019 47.619 0.00 0.00 0.00 3.21
232 258 2.373169 TCTGCACTTCTTCTCCCATGTT 59.627 45.455 0.00 0.00 0.00 2.71
235 261 1.466167 CACTTCTTCTCCCATGTTGCG 59.534 52.381 0.00 0.00 0.00 4.85
245 271 1.363443 CATGTTGCGGTTTGGTGCT 59.637 52.632 0.00 0.00 0.00 4.40
246 272 0.249405 CATGTTGCGGTTTGGTGCTT 60.249 50.000 0.00 0.00 0.00 3.91
251 277 3.119193 CGGTTTGGTGCTTGTGCT 58.881 55.556 0.00 0.00 40.48 4.40
253 279 0.665835 CGGTTTGGTGCTTGTGCTTA 59.334 50.000 0.00 0.00 40.48 3.09
254 280 1.334960 CGGTTTGGTGCTTGTGCTTAG 60.335 52.381 0.00 0.00 40.48 2.18
256 282 0.673437 TTTGGTGCTTGTGCTTAGGC 59.327 50.000 0.00 0.00 40.48 3.93
262 288 1.090728 GCTTGTGCTTAGGCTTCCTC 58.909 55.000 0.00 0.00 39.59 3.71
265 291 1.362224 TGTGCTTAGGCTTCCTCCTT 58.638 50.000 0.00 0.00 37.66 3.36
269 295 1.740718 GCTTAGGCTTCCTCCTTGACG 60.741 57.143 0.00 0.00 37.66 4.35
277 303 3.516615 CTTCCTCCTTGACGATCTGAAC 58.483 50.000 0.00 0.00 0.00 3.18
296 322 2.342650 CCGTTTGCCTGTCCATGGG 61.343 63.158 13.02 0.00 0.00 4.00
297 323 2.342650 CGTTTGCCTGTCCATGGGG 61.343 63.158 13.02 6.52 0.00 4.96
298 324 1.228862 GTTTGCCTGTCCATGGGGT 60.229 57.895 13.02 0.00 34.93 4.95
299 325 1.228831 TTTGCCTGTCCATGGGGTG 60.229 57.895 13.02 1.80 34.93 4.61
316 342 1.477558 GGTGGGGCTAGTGATTGGATG 60.478 57.143 0.00 0.00 0.00 3.51
323 352 3.370953 GGCTAGTGATTGGATGGAGTGTT 60.371 47.826 0.00 0.00 0.00 3.32
426 456 0.248907 CCACGACCACGATAGCGATT 60.249 55.000 7.69 0.00 42.66 3.34
550 581 5.408299 TCATAATGTTTTCTCAGGACACACG 59.592 40.000 0.00 0.00 0.00 4.49
752 783 6.816640 GCGAAATGGACCATACTATGCTTATA 59.183 38.462 7.59 0.00 0.00 0.98
754 785 8.656849 CGAAATGGACCATACTATGCTTATAAC 58.343 37.037 7.59 0.00 0.00 1.89
841 872 2.820197 GGTTGAAGGACAGATGTTTCCC 59.180 50.000 0.00 0.00 31.51 3.97
862 893 3.055891 CCAAGGCCCGATTTCAGAAAAAT 60.056 43.478 0.00 0.00 0.00 1.82
920 951 5.758296 TCCGTATTTCTATTCTGATGGTTGC 59.242 40.000 0.00 0.00 0.00 4.17
1094 1138 7.812690 ATTGCTATATTGATGAAGTGAAGCA 57.187 32.000 0.00 0.00 35.79 3.91
1215 1260 1.552337 CTTAAGCTGGAGAGACAGGCA 59.448 52.381 0.00 0.00 38.90 4.75
1222 1267 3.005539 AGAGACAGGCACGGGCAT 61.006 61.111 13.89 0.00 43.71 4.40
1223 1268 2.512515 GAGACAGGCACGGGCATC 60.513 66.667 13.89 5.73 43.71 3.91
1276 1321 4.879545 GTGAAACTAAGTGTTGGTGGAAGA 59.120 41.667 0.00 0.00 39.13 2.87
1287 1332 0.032952 GGTGGAAGAGCACGTGTACA 59.967 55.000 18.38 0.28 0.00 2.90
1307 1352 9.891828 GTGTACATCATTTGTTTATGTTTCTCA 57.108 29.630 0.00 0.00 39.87 3.27
1333 1378 2.575532 GCATGGCTCCTTAATGCACTA 58.424 47.619 0.00 0.00 44.83 2.74
1340 1385 3.748568 GCTCCTTAATGCACTATGGTAGC 59.251 47.826 6.96 10.11 0.00 3.58
1539 1584 7.161404 GGGCCTGTTTAATTTTTCTTTCAGAT 58.839 34.615 0.84 0.00 0.00 2.90
1642 1756 9.990868 AGGTATACCATTTTGGAGAATTAACTT 57.009 29.630 23.87 0.00 40.96 2.66
2097 2302 8.893727 AGTATTTTGATAGAAATGTTTCCTCCG 58.106 33.333 2.04 0.00 37.92 4.63
2280 2485 5.670361 TCCAAGGTAGGAACTTATGCCTAAT 59.330 40.000 0.00 0.00 41.75 1.73
2482 2692 5.586643 GGATTCTGTGAAATACTTCAGACCC 59.413 44.000 0.00 0.00 42.27 4.46
2577 2787 6.956299 ATGCTGAATTTTAATCACAGTTGC 57.044 33.333 0.00 0.00 0.00 4.17
2595 2805 6.128035 ACAGTTGCGAATATATTTGCTGTTGA 60.128 34.615 29.41 12.99 45.35 3.18
2868 3081 3.181491 CCTTGGATTGACACACGTGTTTT 60.181 43.478 20.79 9.12 45.05 2.43
3043 3256 5.176958 GCTAAAGTTACTGCTTCTCGTTTGA 59.823 40.000 0.00 0.00 0.00 2.69
3285 3498 8.030106 GCACCTCTTGTAATACTGTATATCTCC 58.970 40.741 0.00 0.00 0.00 3.71
3440 3657 5.068198 CCATTTGCAGTATTCTTGTAGCCAT 59.932 40.000 0.00 0.00 0.00 4.40
3503 3720 8.791675 TGTCATCAATGCAGAAGTTTTTACATA 58.208 29.630 0.00 0.00 0.00 2.29
3517 3734 9.893305 AAGTTTTTACATATGTGACAAGTAAGC 57.107 29.630 18.81 3.56 0.00 3.09
3667 4049 2.619074 GCCTTGAGATAAACAGGTGCCT 60.619 50.000 0.00 0.00 0.00 4.75
3730 4112 7.499232 CCGAATTAGTTGTCTTAGATTTGGGAT 59.501 37.037 0.00 0.00 0.00 3.85
3779 4192 6.401581 GCAGCAGTTTAAGTAGCTTTGTCTAG 60.402 42.308 0.00 0.00 34.61 2.43
3783 4196 5.634020 AGTTTAAGTAGCTTTGTCTAGCACG 59.366 40.000 0.00 0.00 43.68 5.34
3822 4592 1.538876 CTGGGGTGTCTCTTGGGGA 60.539 63.158 0.00 0.00 0.00 4.81
3823 4593 1.538876 TGGGGTGTCTCTTGGGGAG 60.539 63.158 0.00 0.00 43.12 4.30
3824 4594 1.539124 GGGGTGTCTCTTGGGGAGT 60.539 63.158 0.00 0.00 42.40 3.85
3825 4595 1.134438 GGGGTGTCTCTTGGGGAGTT 61.134 60.000 0.00 0.00 42.40 3.01
3826 4596 0.036875 GGGTGTCTCTTGGGGAGTTG 59.963 60.000 0.00 0.00 42.40 3.16
3827 4597 0.036875 GGTGTCTCTTGGGGAGTTGG 59.963 60.000 0.00 0.00 42.40 3.77
3828 4598 0.036875 GTGTCTCTTGGGGAGTTGGG 59.963 60.000 0.00 0.00 42.40 4.12
3829 4599 1.133809 TGTCTCTTGGGGAGTTGGGG 61.134 60.000 0.00 0.00 42.40 4.96
3897 4674 0.553333 TGATGTCCACCCCAAACACA 59.447 50.000 0.00 0.00 0.00 3.72
4043 4965 5.465390 GCCATTTTCGAAAAACCTTTAGCTT 59.535 36.000 25.77 3.96 0.00 3.74
4306 5248 5.839063 AGGATGGAGACGGTATCATAGAAAA 59.161 40.000 5.02 0.00 0.00 2.29
4434 5376 3.454447 CCACCTACATAATCCCACTGTCA 59.546 47.826 0.00 0.00 0.00 3.58
4438 5380 5.962031 ACCTACATAATCCCACTGTCAAGTA 59.038 40.000 0.00 0.00 33.79 2.24
4479 5427 1.430992 CCCGTCCATAGGGGTACATT 58.569 55.000 0.00 0.00 44.50 2.71
4585 5533 0.173481 TCGATCTTTGCTCCGTGGAG 59.827 55.000 11.67 11.67 44.56 3.86
4586 5534 0.173481 CGATCTTTGCTCCGTGGAGA 59.827 55.000 19.98 2.27 44.53 3.71
4598 5546 1.066573 CCGTGGAGAGAAAGCTGTGAT 60.067 52.381 0.00 0.00 0.00 3.06
4599 5547 2.266554 CGTGGAGAGAAAGCTGTGATC 58.733 52.381 0.00 0.00 0.00 2.92
4681 5629 4.508461 TGAGTTTGATGTTTCATGCCAG 57.492 40.909 0.00 0.00 0.00 4.85
4708 5656 5.810587 TGCATTACTTAGTGCTGCTACTTAC 59.189 40.000 17.43 0.00 39.36 2.34
4741 5689 0.890683 GCAGTCATTTTCCACCTGGG 59.109 55.000 0.00 0.00 35.41 4.45
4782 5730 6.991485 CAAAATGTTGCGAGTTCTAAATGT 57.009 33.333 0.00 0.00 0.00 2.71
4794 5742 3.634568 TCTAAATGTTGTTTGTGGCCG 57.365 42.857 0.00 0.00 0.00 6.13
4833 5781 5.763204 CCACTTACCATTCAACAGTACAAGT 59.237 40.000 0.00 0.00 0.00 3.16
4886 5834 5.598830 TCTGATTAAGACTAGGCCGAGAAAT 59.401 40.000 20.86 12.40 0.00 2.17
4904 5852 6.645415 CGAGAAATGGTAGTGACTGTTTTACT 59.355 38.462 0.00 0.00 0.00 2.24
4968 5916 4.707934 TGGTGACTGTTATACCGAATCTCA 59.292 41.667 0.00 0.00 37.29 3.27
5127 6097 1.304713 ACCACCGGACGACCACTAT 60.305 57.895 9.46 0.00 35.59 2.12
5144 6114 1.672854 TATCGCCACCAGAACGAGGG 61.673 60.000 0.00 0.00 39.48 4.30
5182 6152 2.166459 CACTGCTTCCCTATCGAAGTCA 59.834 50.000 0.00 0.00 41.18 3.41
5197 6167 0.034059 AGTCAGTTGGCTTGACCTCG 59.966 55.000 11.76 0.00 40.22 4.63
5209 6179 3.469008 TTGACCTCGTCAATGACAGTT 57.531 42.857 14.24 0.00 45.88 3.16
5211 6181 2.069273 GACCTCGTCAATGACAGTTGG 58.931 52.381 14.24 10.93 32.09 3.77
5218 6188 3.744660 GTCAATGACAGTTGGGAAGTCT 58.255 45.455 8.74 0.00 33.56 3.24
5231 6201 1.400494 GGAAGTCTTTTGTGCACGTGT 59.600 47.619 18.38 0.00 0.00 4.49
5235 6205 1.003866 GTCTTTTGTGCACGTGTCTCC 60.004 52.381 18.38 0.09 0.00 3.71
5257 6227 0.391263 GGACCAACAACCTAGAGCCG 60.391 60.000 0.00 0.00 0.00 5.52
5264 6234 0.037326 CAACCTAGAGCCGCTGTTGA 60.037 55.000 13.47 0.00 0.00 3.18
5283 6253 0.949105 AAGCTACGTTGTGGCCGAAG 60.949 55.000 0.00 0.00 40.93 3.79
5355 6325 1.759445 GGATCAGCAGCCTAGACTTGA 59.241 52.381 0.00 0.00 0.00 3.02
5366 6336 3.006967 GCCTAGACTTGAGGTCAGTTTCA 59.993 47.826 0.00 0.00 46.72 2.69
5372 6342 5.070981 AGACTTGAGGTCAGTTTCAATCTGA 59.929 40.000 0.00 0.00 46.72 3.27
5440 6410 1.972872 AGGCACAACTGAACTCTTGG 58.027 50.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.609131 AAACTCCAATCCACGGCTGG 60.609 55.000 0.00 0.00 39.23 4.85
14 15 2.887152 AGCACAAGAAACTCCAATCCAC 59.113 45.455 0.00 0.00 0.00 4.02
42 43 2.103143 CTCTGCTCCCGCGTACAG 59.897 66.667 4.92 6.97 39.65 2.74
45 46 3.449227 CACCTCTGCTCCCGCGTA 61.449 66.667 4.92 0.00 39.65 4.42
65 66 1.294780 CTGTGTGTGCTCCTCCCTC 59.705 63.158 0.00 0.00 0.00 4.30
66 67 2.888447 GCTGTGTGTGCTCCTCCCT 61.888 63.158 0.00 0.00 0.00 4.20
69 70 1.595382 AACGCTGTGTGTGCTCCTC 60.595 57.895 0.00 0.00 0.00 3.71
70 71 1.889105 CAACGCTGTGTGTGCTCCT 60.889 57.895 0.00 0.00 0.00 3.69
72 73 2.051882 GCAACGCTGTGTGTGCTC 60.052 61.111 16.01 0.00 34.12 4.26
73 74 2.514592 AGCAACGCTGTGTGTGCT 60.515 55.556 18.55 18.55 37.57 4.40
74 75 2.051882 GAGCAACGCTGTGTGTGC 60.052 61.111 15.71 15.71 39.88 4.57
75 76 2.246397 CGAGCAACGCTGTGTGTG 59.754 61.111 0.00 0.00 39.88 3.82
76 77 2.202878 ACGAGCAACGCTGTGTGT 60.203 55.556 0.00 0.00 46.94 3.72
77 78 2.246397 CACGAGCAACGCTGTGTG 59.754 61.111 0.00 0.00 46.94 3.82
78 79 3.640000 GCACGAGCAACGCTGTGT 61.640 61.111 15.15 0.00 46.94 3.72
82 83 2.317685 AAAAACGCACGAGCAACGCT 62.318 50.000 5.50 0.00 46.94 5.07
94 95 6.691388 ACAACAAATCTAGAAGTCAAAAACGC 59.309 34.615 0.00 0.00 0.00 4.84
103 129 5.760253 CACAGGACACAACAAATCTAGAAGT 59.240 40.000 0.00 0.00 0.00 3.01
121 147 0.467474 ACTCTCGACCACACACAGGA 60.467 55.000 0.00 0.00 0.00 3.86
138 164 2.088423 TCACGCACCTCAAACAAAACT 58.912 42.857 0.00 0.00 0.00 2.66
194 220 2.489722 GCAGATTCAGAAAACTGACCCC 59.510 50.000 18.85 3.88 37.44 4.95
199 225 5.686159 AGAAGTGCAGATTCAGAAAACTG 57.314 39.130 12.75 13.28 38.09 3.16
224 250 1.152652 ACCAAACCGCAACATGGGA 60.153 52.632 0.00 0.00 37.26 4.37
231 257 1.140589 CACAAGCACCAAACCGCAA 59.859 52.632 0.00 0.00 0.00 4.85
232 258 2.804167 CACAAGCACCAAACCGCA 59.196 55.556 0.00 0.00 0.00 5.69
235 261 1.000274 CCTAAGCACAAGCACCAAACC 60.000 52.381 0.00 0.00 45.49 3.27
245 271 1.362224 AGGAGGAAGCCTAAGCACAA 58.638 50.000 0.00 0.00 43.56 3.33
246 272 1.003580 CAAGGAGGAAGCCTAAGCACA 59.996 52.381 0.00 0.00 43.56 4.57
251 277 1.933021 TCGTCAAGGAGGAAGCCTAA 58.067 50.000 0.00 0.00 37.26 2.69
253 279 0.827368 GATCGTCAAGGAGGAAGCCT 59.173 55.000 0.00 0.00 40.93 4.58
254 280 0.827368 AGATCGTCAAGGAGGAAGCC 59.173 55.000 0.00 0.00 30.29 4.35
256 282 3.516615 GTTCAGATCGTCAAGGAGGAAG 58.483 50.000 0.00 0.00 30.29 3.46
262 288 0.246635 ACGGGTTCAGATCGTCAAGG 59.753 55.000 0.00 0.00 30.89 3.61
265 291 1.790755 CAAACGGGTTCAGATCGTCA 58.209 50.000 0.00 0.00 36.01 4.35
269 295 0.804989 CAGGCAAACGGGTTCAGATC 59.195 55.000 0.00 0.00 0.00 2.75
277 303 2.342650 CCATGGACAGGCAAACGGG 61.343 63.158 5.56 0.00 0.00 5.28
296 322 0.846693 ATCCAATCACTAGCCCCACC 59.153 55.000 0.00 0.00 0.00 4.61
297 323 1.477558 CCATCCAATCACTAGCCCCAC 60.478 57.143 0.00 0.00 0.00 4.61
298 324 0.846015 CCATCCAATCACTAGCCCCA 59.154 55.000 0.00 0.00 0.00 4.96
299 325 1.072965 CTCCATCCAATCACTAGCCCC 59.927 57.143 0.00 0.00 0.00 5.80
300 326 1.771255 ACTCCATCCAATCACTAGCCC 59.229 52.381 0.00 0.00 0.00 5.19
316 342 2.808543 CAGCCAAACTACTCAACACTCC 59.191 50.000 0.00 0.00 0.00 3.85
323 352 1.238439 GCAAGCAGCCAAACTACTCA 58.762 50.000 0.00 0.00 37.23 3.41
381 410 9.495754 GAGTTCATACAAAATTCAGATAACAGC 57.504 33.333 0.00 0.00 0.00 4.40
767 798 2.540383 TGGAATACAGACAGAGTGGCT 58.460 47.619 0.00 0.00 34.86 4.75
841 872 3.658757 TTTTTCTGAAATCGGGCCTTG 57.341 42.857 0.84 0.00 0.00 3.61
862 893 9.170734 CATTCTTCAGTTTCCTCATCATTTCTA 57.829 33.333 0.00 0.00 0.00 2.10
944 975 9.151471 TCATTCAGAGAGATTTAGTAAAAACCG 57.849 33.333 0.00 0.00 0.00 4.44
1068 1112 8.996271 TGCTTCACTTCATCAATATAGCAATAG 58.004 33.333 0.00 0.00 33.63 1.73
1215 1260 0.689080 ATCCTGACTGAGATGCCCGT 60.689 55.000 0.00 0.00 0.00 5.28
1222 1267 5.564848 CGTCAAAACTACATCCTGACTGAGA 60.565 44.000 0.00 0.00 35.36 3.27
1223 1268 4.623167 CGTCAAAACTACATCCTGACTGAG 59.377 45.833 0.00 0.00 35.36 3.35
1276 1321 4.829064 AAACAAATGATGTACACGTGCT 57.171 36.364 17.22 5.64 42.99 4.40
1287 1332 9.146984 CATTGCTGAGAAACATAAACAAATGAT 57.853 29.630 0.00 0.00 0.00 2.45
1307 1352 2.148446 TTAAGGAGCCATGCATTGCT 57.852 45.000 24.12 24.12 41.42 3.91
1333 1378 7.116075 TGTCACAAAAGGTAATATGCTACCAT 58.884 34.615 6.41 0.00 43.42 3.55
1539 1584 4.671831 TGATGGAAAAAGTTGCTATGGGA 58.328 39.130 0.00 0.00 0.00 4.37
1768 1967 7.561251 TGGGTCGTAAATAATCAGATGAAAGA 58.439 34.615 0.00 0.00 0.00 2.52
1769 1968 7.786178 TGGGTCGTAAATAATCAGATGAAAG 57.214 36.000 0.00 0.00 0.00 2.62
1803 2002 6.104146 TGTAGTCCAGTTGCTGTTATTGTA 57.896 37.500 0.00 0.00 0.00 2.41
1837 2036 5.144100 TCCTAGGTTGATTTTTCAAGCCAA 58.856 37.500 9.08 3.35 45.92 4.52
2280 2485 9.317936 CTCTCTGTTGTCAGCATAATTTATACA 57.682 33.333 0.00 0.00 41.10 2.29
2482 2692 0.734889 CAGTGGCTGCTTTAATCCCG 59.265 55.000 0.00 0.00 0.00 5.14
2577 2787 7.369803 AGCCTATCAACAGCAAATATATTCG 57.630 36.000 0.00 0.00 0.00 3.34
2588 2798 4.392921 TTCTGACTAGCCTATCAACAGC 57.607 45.455 0.00 0.00 0.00 4.40
2868 3081 4.019321 ACCAGGAGCTAAATGTAAGCAGAA 60.019 41.667 0.00 0.00 42.62 3.02
3043 3256 5.452077 GCCAGTAATCTCCATCGAAGTAAGT 60.452 44.000 0.00 0.00 0.00 2.24
3083 3296 5.355071 TCTTGATGCAGTTGATTGACCATAC 59.645 40.000 0.00 0.00 0.00 2.39
3285 3498 0.894835 CAAAAATGAGGGGGTTCCGG 59.105 55.000 0.00 0.00 41.52 5.14
3440 3657 4.163552 CAGACGACATAAAGCTACGACAA 58.836 43.478 0.00 0.00 0.00 3.18
3503 3720 6.265196 TCAAGAAATTGGCTTACTTGTCACAT 59.735 34.615 0.00 0.00 38.94 3.21
3517 3734 6.153340 AGGTGTCATATGGTTCAAGAAATTGG 59.847 38.462 2.13 0.00 0.00 3.16
3585 3967 3.191162 TGGCACATACAGATGCTTTTGAC 59.809 43.478 0.00 0.00 41.74 3.18
3667 4049 7.822161 ATATAATTTGTCATGCAAGTGCCTA 57.178 32.000 0.00 0.00 41.18 3.93
3779 4192 1.535462 AGGATACAACAGTTTGCGTGC 59.465 47.619 0.00 0.00 36.00 5.34
3783 4196 5.215160 CAGTTCAAGGATACAACAGTTTGC 58.785 41.667 0.00 0.00 36.00 3.68
3828 4598 3.811323 TATGCAGTCATCTGGGGTGACC 61.811 54.545 7.24 0.00 45.47 4.02
3829 4599 0.254178 ATGCAGTCATCTGGGGTGAC 59.746 55.000 3.03 3.03 44.85 3.67
3844 4614 1.905839 TTCCAGGGGAGGATTATGCA 58.094 50.000 0.00 0.00 37.56 3.96
3893 4670 1.222936 GCTAGGCCTGATGCTGTGT 59.777 57.895 17.99 0.00 40.92 3.72
3897 4674 2.450320 CCCAGCTAGGCCTGATGCT 61.450 63.158 17.99 19.01 40.92 3.79
4043 4965 5.000591 TGTTCACAAACACAACTTCAGAGA 58.999 37.500 0.00 0.00 40.45 3.10
4227 5154 8.567285 ACCTAAATGAAGAACATCAAGTTAGG 57.433 34.615 19.46 19.46 45.52 2.69
4306 5248 1.404035 GCCTGGTGTCGAAAAACTTGT 59.596 47.619 0.00 0.00 0.00 3.16
4434 5376 7.848128 AGTAACTACACAGCACCATTATACTT 58.152 34.615 0.00 0.00 0.00 2.24
4438 5380 5.396436 GGGAGTAACTACACAGCACCATTAT 60.396 44.000 0.00 0.00 0.00 1.28
4585 5533 4.441415 CGGTATAACGATCACAGCTTTCTC 59.559 45.833 3.45 0.00 35.47 2.87
4586 5534 4.097437 TCGGTATAACGATCACAGCTTTCT 59.903 41.667 9.25 0.00 38.06 2.52
4598 5546 5.823209 TCAGTTGAGATTCGGTATAACGA 57.177 39.130 9.25 9.25 41.76 3.85
4599 5547 5.803461 TGTTCAGTTGAGATTCGGTATAACG 59.197 40.000 3.05 3.05 0.00 3.18
4681 5629 2.357009 AGCAGCACTAAGTAATGCATGC 59.643 45.455 11.82 11.82 44.59 4.06
4708 5656 0.723981 GACTGCAGAAAGCTAAGCCG 59.276 55.000 23.35 0.00 45.94 5.52
4782 5730 0.749649 AATTCAGCGGCCACAAACAA 59.250 45.000 2.24 0.00 0.00 2.83
4794 5742 3.323751 AAGTGGCATTCCAAATTCAGC 57.676 42.857 0.00 0.00 45.53 4.26
4886 5834 7.276658 TGAATTCAGTAAAACAGTCACTACCA 58.723 34.615 3.38 0.00 0.00 3.25
4904 5852 4.333649 GTGGAGCAAAGATCGATGAATTCA 59.666 41.667 11.26 11.26 0.00 2.57
4968 5916 7.732222 ATCTCCTCTTCTATCTTGTTCAGTT 57.268 36.000 0.00 0.00 0.00 3.16
5127 6097 3.691342 CCCTCGTTCTGGTGGCGA 61.691 66.667 0.00 0.00 0.00 5.54
5144 6114 1.956477 AGTGACAATGGCACTTCAACC 59.044 47.619 17.32 0.00 43.67 3.77
5182 6152 0.468226 TTGACGAGGTCAAGCCAACT 59.532 50.000 7.07 0.00 45.88 3.16
5197 6167 3.744660 AGACTTCCCAACTGTCATTGAC 58.255 45.455 9.93 9.93 33.56 3.18
5209 6179 1.021202 CGTGCACAAAAGACTTCCCA 58.979 50.000 18.64 0.00 0.00 4.37
5211 6181 1.400494 ACACGTGCACAAAAGACTTCC 59.600 47.619 17.22 0.00 0.00 3.46
5218 6188 1.400142 CTTGGAGACACGTGCACAAAA 59.600 47.619 17.22 4.45 42.67 2.44
5231 6201 1.518367 AGGTTGTTGGTCCTTGGAGA 58.482 50.000 0.00 0.00 0.00 3.71
5235 6205 2.427506 GCTCTAGGTTGTTGGTCCTTG 58.572 52.381 0.00 0.00 35.51 3.61
5264 6234 0.949105 CTTCGGCCACAACGTAGCTT 60.949 55.000 2.24 0.00 0.00 3.74
5366 6336 0.112412 AAAGTTGGGCGGGTCAGATT 59.888 50.000 0.00 0.00 0.00 2.40
5372 6342 1.616374 CAAATACAAAGTTGGGCGGGT 59.384 47.619 0.00 0.00 0.00 5.28
5420 6390 2.703536 TCCAAGAGTTCAGTTGTGCCTA 59.296 45.455 0.00 0.00 0.00 3.93
5421 6391 1.490490 TCCAAGAGTTCAGTTGTGCCT 59.510 47.619 0.00 0.00 0.00 4.75
5427 6397 7.064728 GCTTCGTATTAATCCAAGAGTTCAGTT 59.935 37.037 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.