Multiple sequence alignment - TraesCS7A01G291800

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 TraesCS7A01G291800 chr7A 100.000 5981 0 0 1 5981 360083969 360077989 0.000000e+00 11045.0
1 TraesCS7A01G291800 chr7B 96.496 4480 112 20 856 5326 346678502 346674059 0.000000e+00 7361.0
2 TraesCS7A01G291800 chr7B 81.800 489 70 14 5494 5968 259788679 259788196 5.620000e-105 392.0
3 TraesCS7A01G291800 chr7B 93.277 119 8 0 5375 5493 346674065 346673947 6.160000e-40 176.0
4 TraesCS7A01G291800 chr7D 96.407 4481 100 21 869 5326 337559772 337555330 0.000000e+00 7326.0
5 TraesCS7A01G291800 chr7D 93.770 610 33 4 5375 5980 337555336 337554728 0.000000e+00 911.0
6 TraesCS7A01G291800 chr7D 81.748 389 63 8 5494 5877 286667700 286667315 9.670000e-83 318.0
7 TraesCS7A01G291800 chr7D 89.888 89 7 2 1666 1753 1963816 1963903 4.900000e-21 113.0
8 TraesCS7A01G291800 chr7D 82.353 102 16 2 1650 1750 454075493 454075593 2.970000e-13 87.9
9 TraesCS7A01G291800 chr7D 100.000 30 0 0 2887 2916 337557653 337557624 8.370000e-04 56.5
10 TraesCS7A01G291800 chr3B 90.773 867 68 8 1 866 75979928 75980783 0.000000e+00 1147.0
11 TraesCS7A01G291800 chr3B 80.287 487 62 23 5493 5954 323682642 323682165 2.670000e-88 337.0
12 TraesCS7A01G291800 chr3B 85.437 103 15 0 1650 1752 457631397 457631295 2.280000e-19 108.0
13 TraesCS7A01G291800 chr5D 92.683 492 28 7 5493 5980 225528812 225529299 0.000000e+00 702.0
14 TraesCS7A01G291800 chr5D 91.700 494 34 6 5491 5980 225492988 225493478 0.000000e+00 678.0
15 TraesCS7A01G291800 chr5D 83.299 491 57 16 5493 5968 157440584 157440104 4.280000e-116 429.0
16 TraesCS7A01G291800 chr6D 91.304 483 32 7 388 866 467537672 467538148 0.000000e+00 651.0
17 TraesCS7A01G291800 chr6D 94.375 160 9 0 4 163 467537380 467537539 4.630000e-61 246.0
18 TraesCS7A01G291800 chr6D 100.000 29 0 0 179 207 467537537 467537565 3.000000e-03 54.7
19 TraesCS7A01G291800 chr4D 87.781 311 28 8 5674 5978 180345990 180345684 7.370000e-94 355.0
20 TraesCS7A01G291800 chr4D 89.873 237 12 6 607 842 342698209 342698434 1.630000e-75 294.0
21 TraesCS7A01G291800 chr3D 80.392 459 71 18 5494 5942 244227827 244228276 1.240000e-86 331.0
22 TraesCS7A01G291800 chr4A 79.596 446 70 18 5494 5925 277382136 277382574 3.500000e-77 300.0
23 TraesCS7A01G291800 chr4B 89.744 234 17 5 607 840 424721035 424721261 5.860000e-75 292.0
24 TraesCS7A01G291800 chr4B 85.577 104 15 0 1650 1753 621511686 621511583 6.340000e-20 110.0
25 TraesCS7A01G291800 chr4B 86.517 89 10 2 1666 1753 411629663 411629576 4.930000e-16 97.1
26 TraesCS7A01G291800 chr2B 82.895 228 27 8 5750 5965 349761088 349760861 1.700000e-45 195.0
27 TraesCS7A01G291800 chr2B 88.043 92 7 1 1648 1739 56897190 56897277 8.200000e-19 106.0
28 TraesCS7A01G291800 chr2B 93.056 72 5 0 612 683 97952553 97952482 8.200000e-19 106.0
29 TraesCS7A01G291800 chr5A 85.556 90 11 2 1665 1753 577485291 577485379 6.380000e-15 93.5


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 TraesCS7A01G291800 chr7A 360077989 360083969 5980 True 11045.000000 11045 100.000000 1 5981 1 chr7A.!!$R1 5980
1 TraesCS7A01G291800 chr7B 346673947 346678502 4555 True 3768.500000 7361 94.886500 856 5493 2 chr7B.!!$R2 4637
2 TraesCS7A01G291800 chr7D 337554728 337559772 5044 True 2764.500000 7326 96.725667 869 5980 3 chr7D.!!$R2 5111
3 TraesCS7A01G291800 chr3B 75979928 75980783 855 False 1147.000000 1147 90.773000 1 866 1 chr3B.!!$F1 865
4 TraesCS7A01G291800 chr6D 467537380 467538148 768 False 317.233333 651 95.226333 4 866 3 chr6D.!!$F1 862


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
244 325 0.251354 GCTGAGAAGCTCCACATCCA 59.749 55.000 0.00 0.00 0.00 3.41 F
589 672 0.528249 CCAACTTGTGCAAGCGCTTT 60.528 50.000 22.51 0.03 41.99 3.51 F
1392 1478 1.079197 TGCGTCGCACTCCATCAAT 60.079 52.632 17.58 0.00 31.71 2.57 F
2029 2115 2.285368 TCCCCTCGCAATGGACCT 60.285 61.111 0.00 0.00 0.00 3.85 F
2879 2968 4.202010 GCAGCAACACGGAAACCAATATAT 60.202 41.667 0.00 0.00 0.00 0.86 F
3364 3477 4.260985 TCTGCCAATACATGTGTACCTTG 58.739 43.478 9.11 4.55 32.72 3.61 F
4324 4439 1.950216 TGATCTCTCCGATGGACTTCG 59.050 52.381 0.00 1.14 38.83 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1826 0.030807 TCTCATGCTCCCTCCATCCA 60.031 55.000 0.0 0.0 0.00 3.41 R
2152 2238 2.093973 AGGTGCATAGAAACAGGACTCG 60.094 50.000 0.0 0.0 0.00 4.18 R
3304 3416 1.696884 GCTTTGGGGGAACAAAATCCA 59.303 47.619 0.0 0.0 41.55 3.41 R
3990 4105 2.161855 CAATTGCTGCCAGGTAAGTGA 58.838 47.619 0.0 0.0 30.83 3.41 R
4313 4428 0.103026 TGCCAGATCGAAGTCCATCG 59.897 55.000 0.0 0.0 44.04 3.84 R
4347 4462 2.279173 AGGCAAAGGTCCAGTATTCCT 58.721 47.619 0.0 0.0 0.00 3.36 R
5452 5567 0.813610 CTTGCGTGTGACCCAGTTGA 60.814 55.000 0.0 0.0 0.00 3.18 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
20 21 2.047742 GCCTAAGGATGAGGATGGGGT 61.048 57.143 0.00 0.00 40.24 4.95
45 46 9.243637 GTGCACATTTTCTTAAGATGTAAACAA 57.756 29.630 13.17 0.00 33.03 2.83
57 58 6.377327 AGATGTAAACAAGTCAAACCACTG 57.623 37.500 0.00 0.00 0.00 3.66
92 93 4.379918 GCAGTTGGAGCAAACTAGAATTCC 60.380 45.833 0.65 0.00 38.34 3.01
118 119 1.191489 TGATGAGGTGGGTGCGAAGA 61.191 55.000 0.00 0.00 0.00 2.87
139 140 5.273208 AGAAGCTAGTCACCAGAATCCTAA 58.727 41.667 0.00 0.00 0.00 2.69
235 316 2.264166 GTGAGCCGCTGAGAAGCT 59.736 61.111 0.00 0.00 40.24 3.74
237 318 2.202864 GAGCCGCTGAGAAGCTCC 60.203 66.667 11.70 0.00 45.83 4.70
238 319 2.999648 AGCCGCTGAGAAGCTCCA 61.000 61.111 0.00 0.00 28.40 3.86
242 323 0.809241 CCGCTGAGAAGCTCCACATC 60.809 60.000 0.00 0.00 0.00 3.06
243 324 0.809241 CGCTGAGAAGCTCCACATCC 60.809 60.000 0.00 0.00 0.00 3.51
244 325 0.251354 GCTGAGAAGCTCCACATCCA 59.749 55.000 0.00 0.00 0.00 3.41
271 352 3.107402 AGAGGATTAGGAGTGCAGTGA 57.893 47.619 0.00 0.00 0.00 3.41
293 374 2.034124 AGATGCAAAGCTTGTTGGTGT 58.966 42.857 0.00 0.00 0.00 4.16
312 393 7.372451 TGGTGTGAGGAAAAATTCTATAACG 57.628 36.000 0.00 0.00 0.00 3.18
317 398 7.132863 GTGAGGAAAAATTCTATAACGATGCC 58.867 38.462 0.00 0.00 0.00 4.40
332 413 1.834263 GATGCCAGAGAGTAGTTGGGT 59.166 52.381 0.00 0.00 32.53 4.51
351 432 3.674997 GGTACCTTCAGAACAGAATGCA 58.325 45.455 4.06 0.00 42.53 3.96
362 443 9.453572 TTCAGAACAGAATGCACTAAAGATTAT 57.546 29.630 0.00 0.00 42.53 1.28
366 447 9.875675 GAACAGAATGCACTAAAGATTATCATC 57.124 33.333 0.00 0.00 42.53 2.92
386 467 6.996509 TCATCGATGGAAGTATGAATGATGA 58.003 36.000 24.61 0.00 37.83 2.92
398 481 4.824479 TGAATGATGACCTAGCAACAGA 57.176 40.909 0.00 0.00 0.00 3.41
438 521 1.160137 GTGACAGTCAAGGACATGCC 58.840 55.000 4.32 0.00 34.60 4.40
573 656 2.228582 CGTTGAAACAGATGCATCCCAA 59.771 45.455 23.06 15.29 0.00 4.12
589 672 0.528249 CCAACTTGTGCAAGCGCTTT 60.528 50.000 22.51 0.03 41.99 3.51
594 677 1.661498 TTGTGCAAGCGCTTTGGTCA 61.661 50.000 22.51 14.22 39.64 4.02
620 703 6.745116 ACGACCAAGATATGACGATAAATGA 58.255 36.000 0.00 0.00 34.51 2.57
690 774 2.994186 TCCGTATTACTTTCTGCCCC 57.006 50.000 0.00 0.00 0.00 5.80
774 858 4.314522 TCCCAGCTTTATGGTCAAATGA 57.685 40.909 0.00 0.00 38.81 2.57
800 884 4.440880 CCCTGATTTTGTGCAAAACTTGA 58.559 39.130 11.64 0.00 42.32 3.02
823 907 2.359602 AGCGATGCTGCTGTGCTT 60.360 55.556 0.00 0.00 45.28 3.91
840 924 6.818142 GCTGTGCTTTTTGGTTAATGGAATAT 59.182 34.615 0.00 0.00 0.00 1.28
841 925 7.978975 GCTGTGCTTTTTGGTTAATGGAATATA 59.021 33.333 0.00 0.00 0.00 0.86
842 926 9.301153 CTGTGCTTTTTGGTTAATGGAATATAC 57.699 33.333 0.00 0.00 0.00 1.47
843 927 9.030452 TGTGCTTTTTGGTTAATGGAATATACT 57.970 29.630 0.00 0.00 0.00 2.12
844 928 9.516314 GTGCTTTTTGGTTAATGGAATATACTC 57.484 33.333 0.00 0.00 0.00 2.59
845 929 9.474313 TGCTTTTTGGTTAATGGAATATACTCT 57.526 29.630 0.00 0.00 0.00 3.24
916 1000 6.578944 ACAATACCGCATCTACTTGTCATAA 58.421 36.000 0.00 0.00 0.00 1.90
933 1017 4.214119 GTCATAACATCCATCCAATCACCG 59.786 45.833 0.00 0.00 0.00 4.94
1392 1478 1.079197 TGCGTCGCACTCCATCAAT 60.079 52.632 17.58 0.00 31.71 2.57
1643 1729 3.986277 AGTAGTGTCGGTGTTGGTTAAG 58.014 45.455 0.00 0.00 0.00 1.85
1648 1734 3.059393 GTGTCGGTGTTGGTTAAGTTAGC 60.059 47.826 0.00 0.00 0.00 3.09
1720 1806 7.847711 AGTATTTCAGTGCTAGATACATCCT 57.152 36.000 0.00 0.00 0.00 3.24
1740 1826 6.385649 TCCTTTTGAGCGACAAGTAATTTT 57.614 33.333 0.00 0.00 39.77 1.82
2029 2115 2.285368 TCCCCTCGCAATGGACCT 60.285 61.111 0.00 0.00 0.00 3.85
2152 2238 4.916983 AGCTCACATCTCTACAGATCAC 57.083 45.455 0.00 0.00 37.25 3.06
2199 2285 8.898761 TCTACAGAAAACTTGCACAAATCTTAA 58.101 29.630 0.00 0.00 0.00 1.85
2200 2286 9.683069 CTACAGAAAACTTGCACAAATCTTAAT 57.317 29.630 0.00 0.00 0.00 1.40
2233 2321 6.727394 AGTTACAAGAATGTAGGGGCAAATA 58.273 36.000 0.00 0.00 42.72 1.40
2243 2331 4.228666 TGTAGGGGCAAATATGTACCAGTT 59.771 41.667 0.00 0.00 0.00 3.16
2250 2338 6.376018 GGGCAAATATGTACCAGTTACAGAAA 59.624 38.462 0.00 0.00 44.14 2.52
2338 2426 9.499479 AGCTCCTTTGTCAGATATTATGTATTG 57.501 33.333 0.00 0.00 0.00 1.90
2339 2427 9.277783 GCTCCTTTGTCAGATATTATGTATTGT 57.722 33.333 0.00 0.00 0.00 2.71
2391 2479 6.070251 TGCATTATCTCCCTGAAACTAAGACA 60.070 38.462 0.00 0.00 0.00 3.41
2394 2482 7.496346 TTATCTCCCTGAAACTAAGACACAT 57.504 36.000 0.00 0.00 0.00 3.21
2666 2754 7.092079 CAGAAAATTGTTCCTACATGCATGAA 58.908 34.615 32.75 14.86 33.44 2.57
2831 2919 5.033589 TCAAAGTTTTACGAGGGGTGTAA 57.966 39.130 0.00 0.00 0.00 2.41
2879 2968 4.202010 GCAGCAACACGGAAACCAATATAT 60.202 41.667 0.00 0.00 0.00 0.86
3095 3205 5.067273 CCACACTATGTTGGGTTAAGTTGA 58.933 41.667 0.00 0.00 0.00 3.18
3235 3345 8.367156 TCTTTTCTCCTGTGAAATTTTTATGGG 58.633 33.333 0.00 0.00 36.07 4.00
3364 3477 4.260985 TCTGCCAATACATGTGTACCTTG 58.739 43.478 9.11 4.55 32.72 3.61
3422 3535 7.333528 AGCAATTTGAAGTTTCACTAGTTCA 57.666 32.000 0.00 0.00 36.83 3.18
3543 3656 4.631813 GCAGAAGTAACAGGTTCTACCATG 59.368 45.833 0.00 0.00 41.95 3.66
3767 3882 9.425893 GTTTTTAGCTTTGCTGAATTTTCTTTC 57.574 29.630 0.00 0.00 40.10 2.62
3807 3922 5.106515 GGTTTGCACCTTTTCTCTGTCTATC 60.107 44.000 0.00 0.00 40.44 2.08
3990 4105 5.369110 AGAGCTGGAACTAGATCATCCAATT 59.631 40.000 0.00 0.00 42.41 2.32
4313 4428 3.557228 ACATGGCTTCTTGATCTCTCC 57.443 47.619 0.00 0.00 0.00 3.71
4324 4439 1.950216 TGATCTCTCCGATGGACTTCG 59.050 52.381 0.00 1.14 38.83 3.79
4347 4462 3.430862 GCAGTTGGCGCCGAATGA 61.431 61.111 40.62 14.24 0.00 2.57
4350 4465 2.435938 GTTGGCGCCGAATGAGGA 60.436 61.111 20.60 0.00 0.00 3.71
4451 4566 6.013379 TGGTAGAGGATCAGAATATGAGGTC 58.987 44.000 0.00 0.00 42.53 3.85
5173 5288 1.653151 GGTGATGTAGAGCGGGTTTC 58.347 55.000 0.00 0.00 0.00 2.78
5217 5332 9.722184 ATGTACATCCTTTCTCAGATTCATATG 57.278 33.333 1.41 0.00 0.00 1.78
5249 5364 3.912496 TGTCTGTCAATACCATCTGGG 57.088 47.619 0.54 0.00 44.81 4.45
5274 5389 2.856760 TTGCTACTCCCTCTGATCCT 57.143 50.000 0.00 0.00 0.00 3.24
5282 5397 7.176490 GCTACTCCCTCTGATCCTTATTACTA 58.824 42.308 0.00 0.00 0.00 1.82
5283 5398 7.121611 GCTACTCCCTCTGATCCTTATTACTAC 59.878 44.444 0.00 0.00 0.00 2.73
5284 5399 7.169287 ACTCCCTCTGATCCTTATTACTACT 57.831 40.000 0.00 0.00 0.00 2.57
5306 5421 6.634805 ACTTGTGATGACTTCTCATTATCGT 58.365 36.000 0.00 0.00 37.24 3.73
5322 5437 8.335532 TCATTATCGTTGTGAAAAGAAGGATT 57.664 30.769 0.00 0.00 31.14 3.01
5323 5438 9.443323 TCATTATCGTTGTGAAAAGAAGGATTA 57.557 29.630 0.00 0.00 31.14 1.75
5324 5439 9.708222 CATTATCGTTGTGAAAAGAAGGATTAG 57.292 33.333 0.00 0.00 31.14 1.73
5325 5440 8.842358 TTATCGTTGTGAAAAGAAGGATTAGT 57.158 30.769 0.00 0.00 31.14 2.24
5326 5441 7.745620 ATCGTTGTGAAAAGAAGGATTAGTT 57.254 32.000 0.00 0.00 0.00 2.24
5327 5442 7.562454 TCGTTGTGAAAAGAAGGATTAGTTT 57.438 32.000 0.00 0.00 0.00 2.66
5328 5443 8.665643 TCGTTGTGAAAAGAAGGATTAGTTTA 57.334 30.769 0.00 0.00 0.00 2.01
5329 5444 9.280174 TCGTTGTGAAAAGAAGGATTAGTTTAT 57.720 29.630 0.00 0.00 0.00 1.40
5330 5445 9.543018 CGTTGTGAAAAGAAGGATTAGTTTATC 57.457 33.333 0.00 0.00 0.00 1.75
5446 5561 6.040166 ACAGAAATTGTGGATGGATGATTAGC 59.960 38.462 0.00 0.00 38.99 3.09
5469 5584 0.884259 CATCAACTGGGTCACACGCA 60.884 55.000 0.00 0.00 38.80 5.24
5503 5618 4.336993 TGTGTTGAACTGTTGTAACATCCC 59.663 41.667 17.51 9.57 38.41 3.85
5569 5684 5.982465 TTTAAAATTGGCTTGTGTTGCTC 57.018 34.783 0.00 0.00 0.00 4.26
5588 5703 7.276658 TGTTGCTCGTTGTTTGTAAATTTTGAT 59.723 29.630 0.00 0.00 0.00 2.57
5736 5851 3.003793 GCTTCCTGAATATTCCTTTCGGC 59.996 47.826 12.90 6.79 0.00 5.54
5750 5865 4.830600 TCCTTTCGGCCTTATTTTGAACTT 59.169 37.500 0.00 0.00 0.00 2.66
5826 5944 9.919416 TTCCTCAAAGAATGATATTGGTGAATA 57.081 29.630 0.00 0.00 37.44 1.75
5877 5995 9.401058 TCAACATTTAAAACAAATCCAACCAAT 57.599 25.926 0.00 0.00 0.00 3.16
5925 6043 6.601332 ACTCCTTCAATACAAAAGAGTTGGA 58.399 36.000 0.00 0.00 0.00 3.53
5980 6099 7.655732 CCCGGAGTTGAAAAGAATGTTTTTATT 59.344 33.333 0.73 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.072965 GCACCCCATCCTCATCCTTAG 59.927 57.143 0.00 0.00 0.00 2.18
20 21 9.462174 CTTGTTTACATCTTAAGAAAATGTGCA 57.538 29.630 16.87 11.40 35.38 4.57
45 46 0.474184 CCCTCCACAGTGGTTTGACT 59.526 55.000 19.65 0.00 39.03 3.41
57 58 0.890996 CCAACTGCAACTCCCTCCAC 60.891 60.000 0.00 0.00 0.00 4.02
92 93 1.806542 CACCCACCTCATCAAGAAACG 59.193 52.381 0.00 0.00 0.00 3.60
118 119 4.777896 TGTTAGGATTCTGGTGACTAGCTT 59.222 41.667 0.00 0.00 0.00 3.74
139 140 1.490490 TCTTTTGTCCTCTGGCAGTGT 59.510 47.619 15.27 0.00 0.00 3.55
212 293 3.677284 CTCAGCGGCTCACCTGCAT 62.677 63.158 0.00 0.00 37.76 3.96
215 296 1.447489 CTTCTCAGCGGCTCACCTG 60.447 63.158 0.00 0.00 0.00 4.00
238 319 5.429762 TCCTAATCCTCTTCACAATGGATGT 59.570 40.000 0.00 0.00 45.34 3.06
242 323 5.121811 CACTCCTAATCCTCTTCACAATGG 58.878 45.833 0.00 0.00 0.00 3.16
243 324 4.574013 GCACTCCTAATCCTCTTCACAATG 59.426 45.833 0.00 0.00 0.00 2.82
244 325 4.225942 TGCACTCCTAATCCTCTTCACAAT 59.774 41.667 0.00 0.00 0.00 2.71
251 332 3.107402 TCACTGCACTCCTAATCCTCT 57.893 47.619 0.00 0.00 0.00 3.69
257 338 3.244526 TGCATCTTTCACTGCACTCCTAA 60.245 43.478 0.00 0.00 43.11 2.69
271 352 3.118665 ACACCAACAAGCTTTGCATCTTT 60.119 39.130 0.00 0.00 0.00 2.52
281 362 2.435372 TTTCCTCACACCAACAAGCT 57.565 45.000 0.00 0.00 0.00 3.74
293 374 6.826231 TGGCATCGTTATAGAATTTTTCCTCA 59.174 34.615 0.00 0.00 0.00 3.86
312 393 1.834263 ACCCAACTACTCTCTGGCATC 59.166 52.381 0.00 0.00 0.00 3.91
317 398 4.087182 TGAAGGTACCCAACTACTCTCTG 58.913 47.826 8.74 0.00 0.00 3.35
332 413 4.623932 AGTGCATTCTGTTCTGAAGGTA 57.376 40.909 0.00 0.08 31.33 3.08
337 418 9.102757 GATAATCTTTAGTGCATTCTGTTCTGA 57.897 33.333 0.00 0.00 0.00 3.27
341 422 8.554528 CGATGATAATCTTTAGTGCATTCTGTT 58.445 33.333 0.00 0.00 0.00 3.16
362 443 6.870439 GTCATCATTCATACTTCCATCGATGA 59.130 38.462 26.86 10.02 35.59 2.92
366 447 5.545588 AGGTCATCATTCATACTTCCATCG 58.454 41.667 0.00 0.00 0.00 3.84
384 465 2.237143 CCATCCTTCTGTTGCTAGGTCA 59.763 50.000 0.00 0.00 0.00 4.02
386 467 1.561542 CCCATCCTTCTGTTGCTAGGT 59.438 52.381 0.00 0.00 0.00 3.08
398 481 2.820178 GGACAATGAAACCCCATCCTT 58.180 47.619 0.00 0.00 0.00 3.36
468 551 1.555075 GCATGTAGAGGGTCTTGGACA 59.445 52.381 0.00 0.00 33.68 4.02
498 581 1.339929 TGCAAGCTCTCAAGACACGTA 59.660 47.619 0.00 0.00 0.00 3.57
499 582 0.104855 TGCAAGCTCTCAAGACACGT 59.895 50.000 0.00 0.00 0.00 4.49
532 615 3.564644 ACGTGGACTTCTGATATACCTCG 59.435 47.826 0.00 0.00 39.27 4.63
534 617 4.954202 TCAACGTGGACTTCTGATATACCT 59.046 41.667 0.00 0.00 0.00 3.08
573 656 1.066257 CCAAAGCGCTTGCACAAGT 59.934 52.632 25.80 2.25 42.66 3.16
594 677 6.387041 TTTATCGTCATATCTTGGTCGTCT 57.613 37.500 0.00 0.00 0.00 4.18
610 693 9.265901 CTCCTTGAAGATAACATCATTTATCGT 57.734 33.333 0.00 0.00 41.53 3.73
690 774 6.744537 GTCTGCAACTTTATTACATGCTCTTG 59.255 38.462 0.00 0.00 37.86 3.02
743 827 1.002857 AAAGCTGGGAATGGTAGCCT 58.997 50.000 0.00 0.00 38.18 4.58
749 833 3.017048 TGACCATAAAGCTGGGAATGG 57.983 47.619 12.81 12.81 43.73 3.16
767 851 3.839490 ACAAAATCAGGGGCATCATTTGA 59.161 39.130 0.00 0.00 32.29 2.69
774 858 1.350071 TTGCACAAAATCAGGGGCAT 58.650 45.000 0.00 0.00 0.00 4.40
873 957 8.796475 GGTATTGTACTACTTCGTCCCATAATA 58.204 37.037 0.00 0.00 0.00 0.98
880 964 3.181497 TGCGGTATTGTACTACTTCGTCC 60.181 47.826 0.00 0.00 0.00 4.79
885 969 6.956202 AGTAGATGCGGTATTGTACTACTT 57.044 37.500 0.00 0.00 36.67 2.24
894 978 6.578944 TGTTATGACAAGTAGATGCGGTATT 58.421 36.000 0.00 0.00 31.49 1.89
916 1000 2.505407 TCTTCGGTGATTGGATGGATGT 59.495 45.455 0.00 0.00 0.00 3.06
933 1017 2.863809 TCTTGGTTTCTTGGCCTCTTC 58.136 47.619 3.32 0.00 0.00 2.87
1493 1579 4.307432 CTCGATGTTATACGAAGCCCAAT 58.693 43.478 0.00 0.00 38.05 3.16
1643 1729 0.100146 CGGACGGAGGTAGTGCTAAC 59.900 60.000 0.00 0.00 0.00 2.34
1648 1734 0.822164 AATTCCGGACGGAGGTAGTG 59.178 55.000 13.64 0.00 46.06 2.74
1720 1806 6.137794 TCCAAAATTACTTGTCGCTCAAAA 57.862 33.333 0.00 0.00 35.48 2.44
1740 1826 0.030807 TCTCATGCTCCCTCCATCCA 60.031 55.000 0.00 0.00 0.00 3.41
2029 2115 2.931105 TTAGCGTCCTGGCCCCAA 60.931 61.111 0.00 0.00 0.00 4.12
2152 2238 2.093973 AGGTGCATAGAAACAGGACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2199 2285 9.988815 CCTACATTCTTGTAACTCTTATGCTAT 57.011 33.333 0.00 0.00 37.86 2.97
2200 2286 8.421784 CCCTACATTCTTGTAACTCTTATGCTA 58.578 37.037 0.00 0.00 37.86 3.49
2233 2321 7.165485 TGCAACTATTTCTGTAACTGGTACAT 58.835 34.615 5.94 0.00 41.93 2.29
2243 2331 5.009631 AGCCACATTGCAACTATTTCTGTA 58.990 37.500 0.00 0.00 0.00 2.74
2250 2338 5.300286 GGATTTAGAGCCACATTGCAACTAT 59.700 40.000 0.00 0.00 0.00 2.12
2335 2423 9.492730 AAAAGGAATGGACATAATAGGAACAAT 57.507 29.630 0.00 0.00 0.00 2.71
2337 2425 8.748412 CAAAAAGGAATGGACATAATAGGAACA 58.252 33.333 0.00 0.00 0.00 3.18
2338 2426 8.966868 TCAAAAAGGAATGGACATAATAGGAAC 58.033 33.333 0.00 0.00 0.00 3.62
2339 2427 9.540538 TTCAAAAAGGAATGGACATAATAGGAA 57.459 29.630 0.00 0.00 0.00 3.36
2340 2428 9.713684 ATTCAAAAAGGAATGGACATAATAGGA 57.286 29.630 0.00 0.00 36.20 2.94
2341 2429 9.754382 CATTCAAAAAGGAATGGACATAATAGG 57.246 33.333 7.78 0.00 46.58 2.57
2391 2479 4.456911 CACAGCAAGAACAATAGACCATGT 59.543 41.667 0.00 0.00 0.00 3.21
2394 2482 3.411446 CCACAGCAAGAACAATAGACCA 58.589 45.455 0.00 0.00 0.00 4.02
2831 2919 4.498009 GCAGTGTGTGAGTATTTGCTTTGT 60.498 41.667 0.00 0.00 0.00 2.83
2951 3040 8.999431 ACAATAATCAGTAACGACAAATGAAGT 58.001 29.630 0.00 0.00 0.00 3.01
2952 3041 9.825972 AACAATAATCAGTAACGACAAATGAAG 57.174 29.630 0.00 0.00 0.00 3.02
2962 3051 7.381139 AGCAAAAACCAACAATAATCAGTAACG 59.619 33.333 0.00 0.00 0.00 3.18
3095 3205 6.719370 TCAACCTACTAAACAAGGCAATCAAT 59.281 34.615 0.00 0.00 0.00 2.57
3235 3345 2.221169 TGAGCAGAAACATCCACACAC 58.779 47.619 0.00 0.00 0.00 3.82
3304 3416 1.696884 GCTTTGGGGGAACAAAATCCA 59.303 47.619 0.00 0.00 41.55 3.41
3364 3477 8.808092 AGGTATCACTTATCTAGCATTTCTACC 58.192 37.037 0.00 0.00 0.00 3.18
3445 3558 5.778750 ACCACCGTTATATATAAGGCTCACT 59.221 40.000 16.39 0.04 0.00 3.41
3458 3571 2.500910 ACCGATGGAAACCACCGTTATA 59.499 45.455 3.85 0.00 39.24 0.98
3569 3684 3.123790 TCACGTTTAGTTGTGTGTGTGTG 59.876 43.478 0.00 0.00 37.38 3.82
3571 3686 4.530094 ATCACGTTTAGTTGTGTGTGTG 57.470 40.909 0.00 0.00 37.38 3.82
3573 3688 5.233476 ACTGTATCACGTTTAGTTGTGTGTG 59.767 40.000 0.00 0.00 37.38 3.82
3767 3882 4.278170 TGCAAACCTCAAACATAAGTCCAG 59.722 41.667 0.00 0.00 0.00 3.86
3807 3922 4.678509 ATGCAACCGTTGTTATGTACAG 57.321 40.909 12.77 0.00 38.19 2.74
3860 3975 8.894409 TCGCAATAAATCAGAACAAACATTAG 57.106 30.769 0.00 0.00 0.00 1.73
3990 4105 2.161855 CAATTGCTGCCAGGTAAGTGA 58.838 47.619 0.00 0.00 30.83 3.41
4313 4428 0.103026 TGCCAGATCGAAGTCCATCG 59.897 55.000 0.00 0.00 44.04 3.84
4347 4462 2.279173 AGGCAAAGGTCCAGTATTCCT 58.721 47.619 0.00 0.00 0.00 3.36
4350 4465 3.690460 CTGAAGGCAAAGGTCCAGTATT 58.310 45.455 0.00 0.00 0.00 1.89
4451 4566 3.340814 AACAGCCAGACATCACTAAGG 57.659 47.619 0.00 0.00 0.00 2.69
5217 5332 8.564574 TGGTATTGACAGACATTCTTTGTTAAC 58.435 33.333 0.00 0.00 39.18 2.01
5249 5364 4.744795 TCAGAGGGAGTAGCAATCTTTC 57.255 45.455 0.00 0.00 0.00 2.62
5282 5397 6.634805 ACGATAATGAGAAGTCATCACAAGT 58.365 36.000 0.00 0.00 43.04 3.16
5283 5398 7.063898 ACAACGATAATGAGAAGTCATCACAAG 59.936 37.037 0.00 0.00 43.04 3.16
5284 5399 6.873605 ACAACGATAATGAGAAGTCATCACAA 59.126 34.615 0.00 0.00 43.04 3.33
5304 5419 9.543018 GATAAACTAATCCTTCTTTTCACAACG 57.457 33.333 0.00 0.00 0.00 4.10
5361 5476 9.002600 GGTGCATACTAATCATCAATTATGTCA 57.997 33.333 0.00 0.00 36.89 3.58
5362 5477 9.002600 TGGTGCATACTAATCATCAATTATGTC 57.997 33.333 0.00 0.00 36.89 3.06
5363 5478 8.922931 TGGTGCATACTAATCATCAATTATGT 57.077 30.769 0.00 0.00 36.89 2.29
5364 5479 9.999009 GATGGTGCATACTAATCATCAATTATG 57.001 33.333 0.00 0.00 36.88 1.90
5365 5480 9.970553 AGATGGTGCATACTAATCATCAATTAT 57.029 29.630 0.00 0.00 34.98 1.28
5366 5481 9.223099 CAGATGGTGCATACTAATCATCAATTA 57.777 33.333 0.00 0.00 34.98 1.40
5367 5482 7.176165 CCAGATGGTGCATACTAATCATCAATT 59.824 37.037 0.00 0.00 34.98 2.32
5368 5483 6.657966 CCAGATGGTGCATACTAATCATCAAT 59.342 38.462 0.00 0.00 34.98 2.57
5369 5484 5.999600 CCAGATGGTGCATACTAATCATCAA 59.000 40.000 0.00 0.00 34.98 2.57
5370 5485 5.513614 CCCAGATGGTGCATACTAATCATCA 60.514 44.000 0.00 0.00 34.98 3.07
5371 5486 4.940046 CCCAGATGGTGCATACTAATCATC 59.060 45.833 0.00 0.00 33.34 2.92
5372 5487 4.263639 CCCCAGATGGTGCATACTAATCAT 60.264 45.833 0.00 0.00 0.00 2.45
5373 5488 3.072915 CCCCAGATGGTGCATACTAATCA 59.927 47.826 0.00 0.00 0.00 2.57
5374 5489 3.679389 CCCCAGATGGTGCATACTAATC 58.321 50.000 0.00 0.00 0.00 1.75
5375 5490 2.224867 GCCCCAGATGGTGCATACTAAT 60.225 50.000 1.08 0.00 32.38 1.73
5376 5491 1.142870 GCCCCAGATGGTGCATACTAA 59.857 52.381 1.08 0.00 32.38 2.24
5417 5532 4.111255 TCCATCCACAATTTCTGTCCAA 57.889 40.909 0.00 0.00 35.47 3.53
5446 5561 1.200716 GTGTGACCCAGTTGATGCATG 59.799 52.381 2.46 0.00 0.00 4.06
5452 5567 0.813610 CTTGCGTGTGACCCAGTTGA 60.814 55.000 0.00 0.00 0.00 3.18
5455 5570 2.111043 CCTTGCGTGTGACCCAGT 59.889 61.111 0.00 0.00 0.00 4.00
5469 5584 3.067180 CAGTTCAACACAACATGCTCCTT 59.933 43.478 0.00 0.00 0.00 3.36
5545 5660 6.292811 CGAGCAACACAAGCCAATTTTAAATT 60.293 34.615 0.00 0.00 0.00 1.82
5625 5740 5.757099 AAGTCCTTTTATTCCCTCTCGAA 57.243 39.130 0.00 0.00 0.00 3.71
5627 5742 4.876679 GGAAAGTCCTTTTATTCCCTCTCG 59.123 45.833 0.00 0.00 36.21 4.04
5701 5816 6.872585 ATTCAGGAAGCCATTTTTATTCCA 57.127 33.333 5.68 0.00 43.04 3.53
5880 5998 8.826765 AGGAGTCATATTACCTTCTCTCAAAAA 58.173 33.333 0.00 0.00 0.00 1.94
5881 5999 8.380742 AGGAGTCATATTACCTTCTCTCAAAA 57.619 34.615 0.00 0.00 0.00 2.44
5882 6000 7.979786 AGGAGTCATATTACCTTCTCTCAAA 57.020 36.000 0.00 0.00 0.00 2.69
5905 6023 9.918630 ATCATTTCCAACTCTTTTGTATTGAAG 57.081 29.630 0.00 0.00 0.00 3.02
5955 6073 8.587952 AATAAAAACATTCTTTTCAACTCCGG 57.412 30.769 0.00 0.00 31.15 5.14



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

AutoCloner maintained by Alex Coulton.