Multiple sequence alignment - TraesCS5A01G444200

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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 TraesCS5A01G444200 chr5A 100.000 5247 0 0 1 5247 624217916 624212670 0.000000e+00 9690.0
1 TraesCS5A01G444200 chr5B 94.525 4712 195 26 1 4681 621267277 621262598 0.000000e+00 7214.0
2 TraesCS5A01G444200 chr5B 76.970 495 47 38 4793 5247 621262533 621262066 2.460000e-53 220.0
3 TraesCS5A01G444200 chr5B 84.733 131 10 7 4682 4806 265435469 265435343 7.140000e-24 122.0
4 TraesCS5A01G444200 chr5B 81.295 139 11 8 4677 4806 312761812 312761944 1.200000e-16 99.0
5 TraesCS5A01G444200 chr5D 94.973 2248 81 15 299 2531 499875808 499873578 0.000000e+00 3496.0
6 TraesCS5A01G444200 chr5D 96.323 1251 40 5 2574 3823 499873577 499872332 0.000000e+00 2050.0
7 TraesCS5A01G444200 chr5D 87.164 1488 105 35 3801 5244 499872322 499870877 0.000000e+00 1611.0
8 TraesCS5A01G444200 chr5D 90.980 255 18 2 1 251 499876073 499875820 6.510000e-89 339.0
9 TraesCS5A01G444200 chr5D 82.308 130 9 7 4683 4801 18193872 18193746 3.340000e-17 100.0
10 TraesCS5A01G444200 chr5D 81.343 134 11 11 4677 4800 294640229 294640358 4.320000e-16 97.1
11 TraesCS5A01G444200 chr6D 84.496 129 8 6 4680 4802 221219671 221219549 3.320000e-22 117.0
12 TraesCS5A01G444200 chr6B 83.459 133 10 7 4680 4806 365700752 365700878 4.290000e-21 113.0
13 TraesCS5A01G444200 chr1B 82.946 129 16 4 4677 4800 240487906 240488033 1.540000e-20 111.0
14 TraesCS5A01G444200 chr1D 82.353 136 9 9 4680 4808 35756865 35756992 2.580000e-18 104.0
15 TraesCS5A01G444200 chr7B 83.333 126 3 9 4683 4801 475307981 475308095 3.340000e-17 100.0
16 TraesCS5A01G444200 chr7B 80.808 99 17 2 1969 2066 602894589 602894686 5.630000e-10 76.8
17 TraesCS5A01G444200 chr2D 95.918 49 2 0 1969 2017 32187423 32187375 4.360000e-11 80.5
18 TraesCS5A01G444200 chr2A 95.918 49 2 0 1969 2017 34327542 34327494 4.360000e-11 80.5
19 TraesCS5A01G444200 chr2B 93.878 49 3 0 1969 2017 52871308 52871260 2.030000e-09 75.0


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 TraesCS5A01G444200 chr5A 624212670 624217916 5246 True 9690 9690 100.0000 1 5247 1 chr5A.!!$R1 5246
1 TraesCS5A01G444200 chr5B 621262066 621267277 5211 True 3717 7214 85.7475 1 5247 2 chr5B.!!$R2 5246
2 TraesCS5A01G444200 chr5D 499870877 499876073 5196 True 1874 3496 92.3600 1 5244 4 chr5D.!!$R2 5243


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
390 395 0.461961 AGAGGCATAAGTCTGGACGC 59.538 55.0 0.00 0.0 36.20 5.19 F
1927 1952 0.102120 CGGTTGAGGTTTTGCTTGCA 59.898 50.0 0.00 0.0 0.00 4.08 F
2359 2385 1.168714 GGTGACACCCAAGAAGATGC 58.831 55.0 14.16 0.0 30.04 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 2385 0.965363 AATGTAAGGCCAGGTTGCGG 60.965 55.0 5.01 0.0 0.00 5.69 R
3716 3753 0.035534 TAAGGCGCTGGCTCATTTCA 60.036 50.0 7.64 0.0 37.50 2.69 R
4332 4403 1.514003 TAACTTGACCGCGAAATGCA 58.486 45.0 8.23 0.0 46.97 3.96 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
37 38 6.603940 TTTGTTTTTCAGGAGGGGATTATG 57.396 37.500 0.00 0.00 0.00 1.90
49 50 1.355210 GATTATGTGGGCGCCGTTG 59.645 57.895 22.54 0.00 0.00 4.10
131 132 2.247311 ACGATTCATGCGTGCTTTTC 57.753 45.000 0.00 0.00 40.94 2.29
140 141 2.380660 TGCGTGCTTTTCGTGATTTTC 58.619 42.857 0.00 0.00 0.00 2.29
142 143 2.786578 GCGTGCTTTTCGTGATTTTCAA 59.213 40.909 0.00 0.00 0.00 2.69
201 202 2.482490 CGACCTAGGGTTTCGTATTGGG 60.482 54.545 14.81 0.00 35.25 4.12
226 231 3.126831 GACAGATTCAACATAGCCCTCG 58.873 50.000 0.00 0.00 0.00 4.63
270 275 4.281941 GGTTTCAGGAGAAGGAATGCTTTT 59.718 41.667 0.00 0.00 34.71 2.27
280 285 3.359950 AGGAATGCTTTTAGGAGCCAAG 58.640 45.455 0.00 0.00 42.01 3.61
290 295 2.563427 GAGCCAAGCGCAGTTTCC 59.437 61.111 11.47 0.00 41.38 3.13
297 302 3.308530 CCAAGCGCAGTTTCCTTTTTAG 58.691 45.455 11.47 0.00 0.00 1.85
299 304 2.583143 AGCGCAGTTTCCTTTTTAGGT 58.417 42.857 11.47 0.00 0.00 3.08
354 359 4.949856 AGCTTTGAGAACTTCTTGTTTCCA 59.050 37.500 0.00 0.00 39.30 3.53
383 388 2.119495 TCCCTTCCAGAGGCATAAGTC 58.881 52.381 0.00 0.00 44.85 3.01
390 395 0.461961 AGAGGCATAAGTCTGGACGC 59.538 55.000 0.00 0.00 36.20 5.19
434 439 9.361281 GCTCTAGCAAGCTTGAATCATTCTAGC 62.361 44.444 30.39 22.02 46.81 3.42
446 451 4.063998 TCATTCTAGCGTGCATGAGAAT 57.936 40.909 10.93 12.99 38.81 2.40
484 489 1.672356 CCTCAACTTCCACCGGCAG 60.672 63.158 0.00 0.00 0.00 4.85
501 506 5.995897 ACCGGCAGATTTTAGTTGTATATCC 59.004 40.000 0.00 0.00 0.00 2.59
779 787 6.881065 TCTTATTAGATGCTTGGCCACATATC 59.119 38.462 3.88 9.63 0.00 1.63
783 791 5.052693 AGATGCTTGGCCACATATCTTTA 57.947 39.130 3.88 0.00 0.00 1.85
825 839 8.352201 TCCTTTTGTTGAGAACATTAAGACATG 58.648 33.333 10.86 0.00 41.79 3.21
871 887 5.411977 AGAGCAACTCAATTCAGATGTTCAG 59.588 40.000 6.28 0.00 31.38 3.02
895 911 3.849911 TGAAGAGTTATGAGAAGTGGCG 58.150 45.455 0.00 0.00 0.00 5.69
899 915 2.673368 GAGTTATGAGAAGTGGCGTTGG 59.327 50.000 0.00 0.00 0.00 3.77
1245 1270 6.985653 TCCCTCTCATTACAATTCCTAGAG 57.014 41.667 0.00 0.00 0.00 2.43
1506 1531 6.966534 AACCAAGATTCACTGAAGTTGATT 57.033 33.333 14.34 4.96 0.00 2.57
1733 1758 3.950397 AGAAGGTATGTTGGCGATTTCA 58.050 40.909 0.00 0.00 0.00 2.69
1753 1778 4.686972 TCACTATGCTCTATTGCACTGTC 58.313 43.478 0.00 0.00 46.33 3.51
1867 1892 3.202906 TCATTGCTATGGAACGTTAGCC 58.797 45.455 16.08 8.48 40.49 3.93
1927 1952 0.102120 CGGTTGAGGTTTTGCTTGCA 59.898 50.000 0.00 0.00 0.00 4.08
1963 1988 5.902613 TCATTGGCTAGAAAAATGGACTG 57.097 39.130 0.00 0.00 33.14 3.51
2102 2128 4.095483 GGTGATGCTTGGAAGAGTGTAATG 59.905 45.833 0.00 0.00 0.00 1.90
2201 2227 7.392953 TCTTTTATGAACCTGAACATATGCACA 59.607 33.333 1.58 2.53 0.00 4.57
2359 2385 1.168714 GGTGACACCCAAGAAGATGC 58.831 55.000 14.16 0.00 30.04 3.91
2552 2578 7.363268 GGCTGAAAGATGACTGGAAAATTACAT 60.363 37.037 0.00 0.00 34.07 2.29
2560 2586 6.980593 TGACTGGAAAATTACATTGTTCTGG 58.019 36.000 0.00 0.00 0.00 3.86
2603 2629 8.690203 TTTCTGGAAGATCTTACAATTTGTGA 57.310 30.769 20.85 10.85 46.36 3.58
2771 2797 2.370189 AGCTGGCAGAACTAAGACAACT 59.630 45.455 20.86 0.00 0.00 3.16
3119 3147 3.055602 ACGGGTATCCTTTGTTCTGTACC 60.056 47.826 0.00 0.00 0.00 3.34
3122 3150 3.930848 GGTATCCTTTGTTCTGTACCACG 59.069 47.826 0.00 0.00 33.49 4.94
3363 3393 5.172205 GTTCAAGCCTAGGTTAGACTCTTG 58.828 45.833 11.31 12.86 33.22 3.02
3383 3413 4.487714 TGTGAATTCGAGCCCTAGATTT 57.512 40.909 0.04 0.00 0.00 2.17
3691 3728 5.329035 ACATTTAATGGATGTGGTGCTTC 57.671 39.130 9.88 0.00 36.43 3.86
3728 3765 8.309656 TCTGTATATATCACTGAAATGAGCCAG 58.690 37.037 0.00 0.00 36.53 4.85
3729 3766 6.875726 TGTATATATCACTGAAATGAGCCAGC 59.124 38.462 0.00 0.00 33.90 4.85
3735 3772 0.035534 TGAAATGAGCCAGCGCCTTA 60.036 50.000 2.29 0.00 34.57 2.69
3791 3829 3.620488 ACACATGTTGCCCCTAATACAG 58.380 45.455 0.00 0.00 0.00 2.74
3842 3912 8.520351 AGGTGTAATTTGCTTCATAAAGTTACC 58.480 33.333 0.00 0.00 34.79 2.85
3844 3914 9.341899 GTGTAATTTGCTTCATAAAGTTACCTG 57.658 33.333 0.00 0.00 34.79 4.00
3871 3941 8.823220 ATAAGGCTTTCCATTTGTGTTATAGT 57.177 30.769 4.45 0.00 33.74 2.12
3908 3978 6.426980 TGCATAGTTTTATGACAAGCAGAG 57.573 37.500 0.00 0.00 39.22 3.35
3928 3998 6.678900 GCAGAGCATTTAACTAACTTCCCATG 60.679 42.308 0.00 0.00 0.00 3.66
3976 4047 5.295787 GCAAGAAATATAACACACCCGATGA 59.704 40.000 0.00 0.00 0.00 2.92
3980 4051 6.538742 AGAAATATAACACACCCGATGAACTG 59.461 38.462 0.00 0.00 0.00 3.16
4016 4087 4.651994 CTCAGTCACGGATTTACATTTGC 58.348 43.478 0.00 0.00 0.00 3.68
4021 4092 3.120130 TCACGGATTTACATTTGCGGTTC 60.120 43.478 0.00 0.00 0.00 3.62
4180 4251 1.162698 GGAACCCTAAAGACGCCAAC 58.837 55.000 0.00 0.00 0.00 3.77
4203 4274 2.347490 GCAGTGCTCCCCGAAGAA 59.653 61.111 8.18 0.00 0.00 2.52
4332 4403 3.387050 ACCCTAACTCAACGTTGTCTCTT 59.613 43.478 26.47 15.34 37.05 2.85
4333 4404 3.741344 CCCTAACTCAACGTTGTCTCTTG 59.259 47.826 26.47 12.91 37.05 3.02
4334 4405 3.184581 CCTAACTCAACGTTGTCTCTTGC 59.815 47.826 26.47 0.00 37.05 4.01
4335 4406 2.309528 ACTCAACGTTGTCTCTTGCA 57.690 45.000 26.47 5.08 0.00 4.08
4345 4424 0.095417 GTCTCTTGCATTTCGCGGTC 59.905 55.000 6.13 0.00 46.97 4.79
4351 4430 1.514003 TGCATTTCGCGGTCAAGTTA 58.486 45.000 6.13 0.00 46.97 2.24
4408 4490 0.320374 TTTGATGCCCTCGACGAACT 59.680 50.000 0.00 0.00 0.00 3.01
4409 4491 0.389817 TTGATGCCCTCGACGAACTG 60.390 55.000 0.00 0.00 0.00 3.16
4440 4522 2.762327 CTGAACTTATTGCATTGCCCCT 59.238 45.455 6.12 0.00 0.00 4.79
4476 4558 2.197324 GGGTCTGGGTGGTTTGCA 59.803 61.111 0.00 0.00 0.00 4.08
4548 4630 9.964303 TCATGTTTGTATTATTATTGTCATGGC 57.036 29.630 0.00 0.00 32.65 4.40
4567 4649 4.260170 TGGCTTGAGTTTTGCAAATTTGT 58.740 34.783 19.03 0.00 0.00 2.83
4568 4650 4.094590 TGGCTTGAGTTTTGCAAATTTGTG 59.905 37.500 19.03 3.76 0.00 3.33
4614 4696 2.177451 TGGCCACCATGATAATGGATGT 59.823 45.455 16.78 0.00 44.39 3.06
4635 4717 5.500234 TGTGCCAGCTTTACATCTAGAAAT 58.500 37.500 0.00 0.00 0.00 2.17
4685 4767 2.177016 GCCACCCCTGGGAAATAATACT 59.823 50.000 16.20 0.00 38.13 2.12
4714 4804 8.378172 TCCGTCCTAATATAAGAGCATTTTTG 57.622 34.615 0.00 0.00 0.00 2.44
4757 4847 8.397951 AATGCTCTTATATTATGGGATGGAGA 57.602 34.615 0.00 0.00 0.00 3.71
4759 4849 8.397951 TGCTCTTATATTATGGGATGGAGATT 57.602 34.615 0.00 0.00 0.00 2.40
4760 4850 8.270030 TGCTCTTATATTATGGGATGGAGATTG 58.730 37.037 0.00 0.00 0.00 2.67
4796 4887 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4913 5019 7.348201 CAACGTGAAGGATCTCAATTATTAGC 58.652 38.462 0.00 0.00 0.00 3.09
4916 5022 6.925718 CGTGAAGGATCTCAATTATTAGCAGA 59.074 38.462 0.00 0.00 0.00 4.26
4917 5023 7.601886 CGTGAAGGATCTCAATTATTAGCAGAT 59.398 37.037 0.00 0.00 0.00 2.90
4922 5041 9.732130 AGGATCTCAATTATTAGCAGATAAACC 57.268 33.333 0.00 0.00 0.00 3.27
4947 5066 5.538463 ACTTTTCCAAGCTCCATTTCCTGG 61.538 45.833 0.00 0.00 38.88 4.45
4948 5067 1.075601 TCCAAGCTCCATTTCCTGGT 58.924 50.000 0.00 0.00 46.08 4.00
4958 5077 0.991920 ATTTCCTGGTCCGGTGTCAT 59.008 50.000 0.00 0.00 0.00 3.06
4959 5078 0.323629 TTTCCTGGTCCGGTGTCATC 59.676 55.000 0.00 0.00 0.00 2.92
4960 5079 0.834261 TTCCTGGTCCGGTGTCATCA 60.834 55.000 0.00 0.00 0.00 3.07
4977 5096 8.542953 GGTGTCATCAGAAATGAAAAGAAAAAC 58.457 33.333 0.00 0.00 0.00 2.43
5020 5147 6.243811 TGGGACACAACGACATATTTAAAC 57.756 37.500 0.00 0.00 0.00 2.01
5050 5180 1.440618 TTGAGAAAGCCACCACCCTA 58.559 50.000 0.00 0.00 0.00 3.53
5067 5198 8.342634 CACCACCCTATTATGTTTATTTCGAAG 58.657 37.037 0.00 0.00 0.00 3.79
5150 5295 3.659786 TCTCGTGTACATTTCCAACCTG 58.340 45.455 0.00 0.00 0.00 4.00
5151 5296 2.147958 TCGTGTACATTTCCAACCTGC 58.852 47.619 0.00 0.00 0.00 4.85
5153 5298 2.235016 GTGTACATTTCCAACCTGCCA 58.765 47.619 0.00 0.00 0.00 4.92
5154 5299 2.825532 GTGTACATTTCCAACCTGCCAT 59.174 45.455 0.00 0.00 0.00 4.40
5158 5303 1.894466 CATTTCCAACCTGCCATGACA 59.106 47.619 0.00 0.00 0.00 3.58
5159 5304 1.619654 TTTCCAACCTGCCATGACAG 58.380 50.000 1.37 1.37 37.42 3.51
5165 5310 3.895025 CTGCCATGACAGGTTCCG 58.105 61.111 0.22 0.00 33.85 4.30
5166 5311 1.746615 CTGCCATGACAGGTTCCGG 60.747 63.158 0.22 0.00 33.85 5.14
5167 5312 2.438434 GCCATGACAGGTTCCGGG 60.438 66.667 0.00 0.00 0.00 5.73
5168 5313 2.272146 CCATGACAGGTTCCGGGG 59.728 66.667 0.00 0.00 0.00 5.73
5169 5314 2.272146 CATGACAGGTTCCGGGGG 59.728 66.667 0.00 0.00 0.00 5.40
5170 5315 2.204090 ATGACAGGTTCCGGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
5171 5316 1.081462 ATGACAGGTTCCGGGGGTA 59.919 57.895 0.00 0.00 0.00 3.69
5175 5320 2.365237 AGGTTCCGGGGGTAGAGC 60.365 66.667 0.00 0.00 0.00 4.09
5195 5340 2.060383 CATCCCTCTCGCTGTCCCA 61.060 63.158 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 6.681777 AGAATCCCTTGAAAATCACGAAAAG 58.318 36.000 0.00 0.00 0.00 2.27
131 132 7.147976 AGAAAAAGAATCCCTTGAAAATCACG 58.852 34.615 0.00 0.00 34.79 4.35
140 141 5.279156 CCAGACCAAGAAAAAGAATCCCTTG 60.279 44.000 0.00 0.00 34.79 3.61
142 143 4.411013 CCAGACCAAGAAAAAGAATCCCT 58.589 43.478 0.00 0.00 0.00 4.20
201 202 3.471680 GGCTATGTTGAATCTGTCTCCC 58.528 50.000 0.00 0.00 0.00 4.30
226 231 2.731976 CTGAGTTCAGTGTAAGGCGTTC 59.268 50.000 0.00 0.00 39.09 3.95
251 256 4.536090 TCCTAAAAGCATTCCTTCTCCTGA 59.464 41.667 0.00 0.00 31.99 3.86
257 262 3.356290 TGGCTCCTAAAAGCATTCCTTC 58.644 45.455 0.00 0.00 44.35 3.46
270 275 0.673644 GAAACTGCGCTTGGCTCCTA 60.674 55.000 9.73 0.00 44.05 2.94
280 285 3.364889 AACCTAAAAAGGAAACTGCGC 57.635 42.857 0.00 0.00 42.68 6.09
290 295 6.220930 GGCTCCTAACCAAAAACCTAAAAAG 58.779 40.000 0.00 0.00 0.00 2.27
297 302 1.893137 CTGGGCTCCTAACCAAAAACC 59.107 52.381 0.00 0.00 36.09 3.27
299 304 1.146982 AGCTGGGCTCCTAACCAAAAA 59.853 47.619 0.00 0.00 36.09 1.94
383 388 1.000843 TGGAATATCCATCGCGTCCAG 59.999 52.381 5.77 0.00 42.67 3.86
434 439 3.495193 CACCAGAAAATTCTCATGCACG 58.505 45.455 0.00 0.00 34.74 5.34
446 451 0.537143 AGCGCACATCCACCAGAAAA 60.537 50.000 11.47 0.00 0.00 2.29
484 489 7.801716 TGTGCCAGGATATACAACTAAAATC 57.198 36.000 0.00 0.00 0.00 2.17
501 506 5.649782 AAAATTCCTGTAAGATGTGCCAG 57.350 39.130 0.00 0.00 34.07 4.85
541 548 3.763360 CACATGGAAAGGCTGGTGAATAA 59.237 43.478 0.00 0.00 0.00 1.40
542 549 3.010027 TCACATGGAAAGGCTGGTGAATA 59.990 43.478 0.00 0.00 32.85 1.75
543 550 2.173519 CACATGGAAAGGCTGGTGAAT 58.826 47.619 0.00 0.00 0.00 2.57
544 551 1.144708 TCACATGGAAAGGCTGGTGAA 59.855 47.619 0.00 0.00 32.85 3.18
553 560 8.954350 ACTATCTCAAAATCTTCACATGGAAAG 58.046 33.333 0.00 0.00 34.44 2.62
648 655 2.734723 CTGCATATCGACCGGCCG 60.735 66.667 21.04 21.04 0.00 6.13
783 791 9.918630 CAACAAAAGGAAAAGATCTGTGATAAT 57.081 29.630 0.00 0.00 0.00 1.28
806 814 7.301054 CCAGTTCATGTCTTAATGTTCTCAAC 58.699 38.462 0.00 0.00 0.00 3.18
854 870 7.868775 TCTTCAAACTGAACATCTGAATTGAG 58.131 34.615 0.00 0.00 32.21 3.02
857 873 7.814264 ACTCTTCAAACTGAACATCTGAATT 57.186 32.000 0.00 0.00 32.21 2.17
871 887 5.389935 CGCCACTTCTCATAACTCTTCAAAC 60.390 44.000 0.00 0.00 0.00 2.93
1199 1224 6.328934 GGAATAAATGGATAAACATTGGGGGT 59.671 38.462 0.00 0.00 40.71 4.95
1506 1531 4.940046 GGAAGAGCAGACATTTCTTGATCA 59.060 41.667 0.00 0.00 31.67 2.92
1659 1684 4.501071 CTTGCCCAGATTTTTCTCCATTG 58.499 43.478 0.00 0.00 0.00 2.82
1805 1830 7.888250 AGGGCCAAAAATCAAATTAAAAACA 57.112 28.000 6.18 0.00 0.00 2.83
1867 1892 8.549548 CAATCTTGCTTCTGTATGATCTAGTTG 58.450 37.037 0.00 0.00 0.00 3.16
1927 1952 1.140052 CCAATGATGGCCAATGCATGT 59.860 47.619 10.96 0.00 40.58 3.21
1959 1984 3.737972 CCAACTTTTTGGCAACTCCAGTC 60.738 47.826 0.00 0.00 46.09 3.51
2359 2385 0.965363 AATGTAAGGCCAGGTTGCGG 60.965 55.000 5.01 0.00 0.00 5.69
2501 2527 3.934579 GAGCCTTGGTATGCAAAAATTGG 59.065 43.478 0.00 0.00 0.00 3.16
2552 2578 5.746245 CGTAAGAAACAAATTGCCAGAACAA 59.254 36.000 0.00 0.00 43.02 2.83
2560 2586 6.474102 TCCAGAAAACGTAAGAAACAAATTGC 59.526 34.615 0.00 0.00 43.62 3.56
2603 2629 5.636903 AGATACAGCTTGTGGGTTCATAT 57.363 39.130 0.00 0.00 0.00 1.78
2771 2797 2.584835 ATGTAGGAGCAAAGGCAACA 57.415 45.000 0.00 0.00 44.61 3.33
3082 3110 5.293569 GGATACCCGTGTTAAATCAAGACAG 59.706 44.000 0.00 0.00 30.81 3.51
3119 3147 4.147479 GGAAAATCCGTTTGTTTAAGCGTG 59.853 41.667 0.00 0.00 38.62 5.34
3122 3150 4.149922 GCTGGAAAATCCGTTTGTTTAAGC 59.850 41.667 0.00 0.00 40.17 3.09
3241 3269 2.306805 AGGAGATGCAAATCCTCACACA 59.693 45.455 15.52 0.00 42.44 3.72
3242 3270 2.996631 AGGAGATGCAAATCCTCACAC 58.003 47.619 15.52 0.00 42.44 3.82
3363 3393 4.698575 AGAAATCTAGGGCTCGAATTCAC 58.301 43.478 6.22 0.00 0.00 3.18
3383 3413 1.623311 TGGCAGTAGCAAGCTGTTAGA 59.377 47.619 4.53 0.00 44.61 2.10
3632 3662 6.513806 TGAAACATGTATAAGCAACTGCAT 57.486 33.333 0.00 0.00 45.16 3.96
3667 3704 6.127479 GGAAGCACCACATCCATTAAATGTAA 60.127 38.462 0.00 0.00 35.62 2.41
3716 3753 0.035534 TAAGGCGCTGGCTCATTTCA 60.036 50.000 7.64 0.00 37.50 2.69
3728 3765 7.323656 CAGCACATTAACTAATTATTAAGGCGC 59.676 37.037 0.00 0.00 33.70 6.53
3729 3766 8.342634 ACAGCACATTAACTAATTATTAAGGCG 58.657 33.333 9.77 4.97 28.69 5.52
3791 3829 6.395426 TGATATCATTCAATGGGTTGCTTC 57.605 37.500 0.00 0.00 35.26 3.86
3842 3912 6.515272 ACACAAATGGAAAGCCTTATACAG 57.485 37.500 0.00 0.00 34.31 2.74
3871 3941 9.836864 ATAAAACTATGCATCAACATCTACTCA 57.163 29.630 0.19 0.00 0.00 3.41
3908 3978 9.435688 AAAAATCATGGGAAGTTAGTTAAATGC 57.564 29.630 0.00 0.00 0.00 3.56
3976 4047 7.171678 GTGACTGAGCATAGTTTAAAGTCAGTT 59.828 37.037 12.87 1.31 42.40 3.16
3980 4051 5.062308 CCGTGACTGAGCATAGTTTAAAGTC 59.938 44.000 0.00 0.00 34.52 3.01
4016 4087 1.867233 CACCTTCACAGAACAGAACCG 59.133 52.381 0.00 0.00 0.00 4.44
4021 4092 1.517242 GAGGCACCTTCACAGAACAG 58.483 55.000 0.00 0.00 0.00 3.16
4121 4192 4.819761 GTGAGATGCGGCGCTGGA 62.820 66.667 33.26 17.29 0.00 3.86
4203 4274 2.358247 CTTTGGCGCCTACACCGT 60.358 61.111 29.70 0.00 0.00 4.83
4293 4364 2.147958 GGGTTTGTACAGCGACATTCA 58.852 47.619 0.00 0.00 0.00 2.57
4332 4403 1.514003 TAACTTGACCGCGAAATGCA 58.486 45.000 8.23 0.00 46.97 3.96
4333 4404 2.604969 TTAACTTGACCGCGAAATGC 57.395 45.000 8.23 0.00 41.47 3.56
4334 4405 4.717991 TGAATTAACTTGACCGCGAAATG 58.282 39.130 8.23 0.00 0.00 2.32
4335 4406 5.106317 ACATGAATTAACTTGACCGCGAAAT 60.106 36.000 8.23 0.00 0.00 2.17
4345 4424 8.055279 ACATCCACCTTACATGAATTAACTTG 57.945 34.615 0.00 0.00 0.00 3.16
4351 4430 5.819991 ACAGACATCCACCTTACATGAATT 58.180 37.500 0.00 0.00 0.00 2.17
4408 4490 5.706833 TGCAATAAGTTCAGCTCTCAAATCA 59.293 36.000 0.00 0.00 0.00 2.57
4409 4491 6.187125 TGCAATAAGTTCAGCTCTCAAATC 57.813 37.500 0.00 0.00 0.00 2.17
4440 4522 1.250328 CAGGCAAGCAAACATCCAGA 58.750 50.000 0.00 0.00 0.00 3.86
4538 4620 3.069872 TGCAAAACTCAAGCCATGACAAT 59.930 39.130 0.00 0.00 33.47 2.71
4542 4624 3.815856 TTTGCAAAACTCAAGCCATGA 57.184 38.095 10.02 0.00 36.38 3.07
4548 4630 4.265371 CGCACAAATTTGCAAAACTCAAG 58.735 39.130 17.19 6.27 43.15 3.02
4576 4658 2.781595 CCACGTCTGGAACCCGAAGG 62.782 65.000 0.00 0.00 44.94 3.46
4614 4696 7.508687 TCATATTTCTAGATGTAAAGCTGGCA 58.491 34.615 0.00 0.00 0.00 4.92
4635 4717 4.451891 TGGGGATGCTTATGCTTTCATA 57.548 40.909 1.96 0.00 40.48 2.15
4685 4767 4.202641 TGCTCTTATATTAGGACGGAGGGA 60.203 45.833 0.00 0.00 0.00 4.20
4732 4822 8.397951 TCTCCATCCCATAATATAAGAGCATT 57.602 34.615 0.00 0.00 0.00 3.56
4733 4823 8.578593 ATCTCCATCCCATAATATAAGAGCAT 57.421 34.615 0.00 0.00 0.00 3.79
4734 4824 8.270030 CAATCTCCATCCCATAATATAAGAGCA 58.730 37.037 0.00 0.00 0.00 4.26
4735 4825 8.270744 ACAATCTCCATCCCATAATATAAGAGC 58.729 37.037 0.00 0.00 0.00 4.09
4766 4856 8.768397 TCCGTCCCATAATATAAGAGCATTATT 58.232 33.333 0.20 0.00 0.00 1.40
4767 4857 8.319057 TCCGTCCCATAATATAAGAGCATTAT 57.681 34.615 0.00 0.00 0.00 1.28
4768 4858 7.147724 CCTCCGTCCCATAATATAAGAGCATTA 60.148 40.741 0.00 0.00 0.00 1.90
4824 4915 2.259917 TGTGAATGCTCCTTCTCTCCA 58.740 47.619 0.00 0.00 0.00 3.86
4825 4916 3.557228 ATGTGAATGCTCCTTCTCTCC 57.443 47.619 0.00 0.00 0.00 3.71
4913 5019 4.455877 AGCTTGGAAAAGTCGGTTTATCTG 59.544 41.667 0.00 0.00 0.00 2.90
4916 5022 3.756963 GGAGCTTGGAAAAGTCGGTTTAT 59.243 43.478 0.00 0.00 0.00 1.40
4917 5023 3.143728 GGAGCTTGGAAAAGTCGGTTTA 58.856 45.455 0.00 0.00 0.00 2.01
4922 5041 3.366374 GGAAATGGAGCTTGGAAAAGTCG 60.366 47.826 0.00 0.00 0.00 4.18
4947 5066 2.972625 TCATTTCTGATGACACCGGAC 58.027 47.619 9.46 0.00 0.00 4.79
4948 5067 3.694043 TTCATTTCTGATGACACCGGA 57.306 42.857 9.46 0.00 0.00 5.14
4958 5077 9.369904 CCTTTCTGTTTTTCTTTTCATTTCTGA 57.630 29.630 0.00 0.00 0.00 3.27
4959 5078 9.369904 TCCTTTCTGTTTTTCTTTTCATTTCTG 57.630 29.630 0.00 0.00 0.00 3.02
4960 5079 9.942850 TTCCTTTCTGTTTTTCTTTTCATTTCT 57.057 25.926 0.00 0.00 0.00 2.52
4977 5096 6.010219 TCCCATCTAAACCTTTTCCTTTCTG 58.990 40.000 0.00 0.00 0.00 3.02
5020 5147 5.335191 GGTGGCTTTCTCAATTAGTTGTCAG 60.335 44.000 0.00 0.00 36.69 3.51
5067 5198 7.133513 GTGAATGCTGATGATGATCTTTTCTC 58.866 38.462 0.00 0.00 0.00 2.87
5150 5295 2.438434 CCCGGAACCTGTCATGGC 60.438 66.667 0.73 0.00 0.00 4.40
5151 5296 2.272146 CCCCGGAACCTGTCATGG 59.728 66.667 0.73 0.00 0.00 3.66
5153 5298 0.981277 CTACCCCCGGAACCTGTCAT 60.981 60.000 0.73 0.00 0.00 3.06
5154 5299 1.611261 CTACCCCCGGAACCTGTCA 60.611 63.158 0.73 0.00 0.00 3.58
5158 5303 2.365237 GCTCTACCCCCGGAACCT 60.365 66.667 0.73 0.00 0.00 3.50
5159 5304 2.365237 AGCTCTACCCCCGGAACC 60.365 66.667 0.73 0.00 0.00 3.62
5161 5306 0.759436 GATGAGCTCTACCCCCGGAA 60.759 60.000 16.19 0.00 0.00 4.30
5162 5307 1.152525 GATGAGCTCTACCCCCGGA 60.153 63.158 16.19 0.00 0.00 5.14
5163 5308 2.210711 GGATGAGCTCTACCCCCGG 61.211 68.421 16.19 0.00 0.00 5.73
5164 5309 2.210711 GGGATGAGCTCTACCCCCG 61.211 68.421 27.09 0.00 36.65 5.73
5165 5310 0.834261 GAGGGATGAGCTCTACCCCC 60.834 65.000 30.79 25.10 42.97 5.40
5166 5311 0.189822 AGAGGGATGAGCTCTACCCC 59.810 60.000 30.79 26.95 42.97 4.95
5167 5312 1.627864 GAGAGGGATGAGCTCTACCC 58.372 60.000 28.85 28.85 42.36 3.69
5168 5313 1.243902 CGAGAGGGATGAGCTCTACC 58.756 60.000 16.19 16.86 0.00 3.18
5169 5314 0.596082 GCGAGAGGGATGAGCTCTAC 59.404 60.000 16.19 8.63 0.00 2.59
5170 5315 0.476338 AGCGAGAGGGATGAGCTCTA 59.524 55.000 16.19 1.49 31.94 2.43
5171 5316 1.108727 CAGCGAGAGGGATGAGCTCT 61.109 60.000 16.19 0.00 35.82 4.09
5175 5320 1.739049 GGACAGCGAGAGGGATGAG 59.261 63.158 0.00 0.00 0.00 2.90
5195 5340 9.261180 CTACGTGTATCAATAATTCCAGTCAAT 57.739 33.333 0.00 0.00 0.00 2.57
5216 5370 3.626930 AGGCTGAGAGAGATTTCTACGT 58.373 45.455 0.00 0.00 32.53 3.57



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

AutoCloner maintained by Alex Coulton.