Multiple sequence alignment - TraesCS5D01G157300

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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 TraesCS5D01G157300 chr5D 100.000 4522 0 0 1 4522 245190410 245185889 0.000000e+00 8351
1 TraesCS5D01G157300 chr5B 93.702 3922 147 38 1 3871 278449980 278446108 0.000000e+00 5782
2 TraesCS5D01G157300 chr5B 90.646 449 33 5 4082 4521 278444720 278444272 5.040000e-164 588
3 TraesCS5D01G157300 chr5B 86.364 198 18 6 3874 4063 278446017 278445821 1.650000e-49 207
4 TraesCS5D01G157300 chr5A 94.017 2641 113 18 1908 4520 329225164 329222541 0.000000e+00 3960
5 TraesCS5D01G157300 chr5A 93.859 1726 54 14 1 1685 329226999 329225285 0.000000e+00 2553
6 TraesCS5D01G157300 chr2A 93.878 833 37 6 772 1593 277333293 277334122 0.000000e+00 1243
7 TraesCS5D01G157300 chr2A 90.616 341 14 9 215 546 277332966 277333297 1.930000e-118 436
8 TraesCS5D01G157300 chr3D 91.030 825 33 19 1160 1977 528821303 528822093 0.000000e+00 1075
9 TraesCS5D01G157300 chr3D 90.514 253 7 8 215 459 528820614 528820857 7.300000e-83 318
10 TraesCS5D01G157300 chr3D 92.806 139 7 2 460 595 528821167 528821305 9.920000e-47 198
11 TraesCS5D01G157300 chr7D 91.108 821 31 18 1160 1974 99932192 99932976 0.000000e+00 1074
12 TraesCS5D01G157300 chr7D 91.071 392 15 10 215 595 99931812 99932194 3.120000e-141 512


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 TraesCS5D01G157300 chr5D 245185889 245190410 4521 True 8351.000000 8351 100.000000 1 4522 1 chr5D.!!$R1 4521
1 TraesCS5D01G157300 chr5B 278444272 278449980 5708 True 2192.333333 5782 90.237333 1 4521 3 chr5B.!!$R1 4520
2 TraesCS5D01G157300 chr5A 329222541 329226999 4458 True 3256.500000 3960 93.938000 1 4520 2 chr5A.!!$R1 4519
3 TraesCS5D01G157300 chr2A 277332966 277334122 1156 False 839.500000 1243 92.247000 215 1593 2 chr2A.!!$F1 1378
4 TraesCS5D01G157300 chr3D 528820614 528822093 1479 False 530.333333 1075 91.450000 215 1977 3 chr3D.!!$F1 1762
5 TraesCS5D01G157300 chr7D 99931812 99932976 1164 False 793.000000 1074 91.089500 215 1974 2 chr7D.!!$F1 1759

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
558 891 0.168128 CCGCCTTTCCGTTGCTTAAG 59.832 55.0 0.00 0.00 0.00 1.85 F
1080 1447 0.106669 GGAAGGAGTGCCCCCATTAC 60.107 60.0 0.00 0.00 34.66 1.89 F
1747 2124 0.165295 CATGCTCTGTCAGTGTTGCG 59.835 55.0 0.00 0.00 0.00 4.85 F
1846 2223 0.251354 CTGCTTGGCCTCTAGCTGAA 59.749 55.0 20.55 5.45 40.81 3.02 F
2169 2590 0.392729 CTCTGCCTCTGCTCCCAAAG 60.393 60.0 0.00 0.00 38.71 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2452 0.032912 AATGACTGGATGCCATGCCA 60.033 50.000 0.00 0.0 30.82 4.92 R
2914 3350 0.379669 GCTTTGCATCACCATCCTCG 59.620 55.000 0.00 0.0 0.00 4.63 R
2986 3422 3.319198 TTCGCTCCCACCCACTCC 61.319 66.667 0.00 0.0 0.00 3.85 R
3078 3514 5.293569 GTCAGGTTTAACGGTTGATGGATAG 59.706 44.000 3.07 0.0 0.00 2.08 R
3864 4309 1.032657 TTCCCACCACACACCAAACG 61.033 55.000 0.00 0.0 0.00 3.60 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
365 379 5.163311 ACCGTACCAGTTAAGGTTGTTTAGT 60.163 40.000 0.00 0.00 39.34 2.24
369 383 7.115378 CGTACCAGTTAAGGTTGTTTAGTACTG 59.885 40.741 5.39 0.00 43.08 2.74
385 405 9.582431 GTTTAGTACTGCTACATCAACTGATAA 57.418 33.333 5.39 0.00 32.63 1.75
558 891 0.168128 CCGCCTTTCCGTTGCTTAAG 59.832 55.000 0.00 0.00 0.00 1.85
648 983 0.746063 CTGTGCTAGCTCCTCCTCTG 59.254 60.000 17.23 0.00 0.00 3.35
890 1235 0.536460 AAACACCACCCATCGTCACC 60.536 55.000 0.00 0.00 0.00 4.02
949 1310 4.202441 CCTGCTGCACATTCTTATACCTT 58.798 43.478 0.00 0.00 0.00 3.50
1079 1446 1.286305 GGGAAGGAGTGCCCCCATTA 61.286 60.000 5.04 0.00 38.45 1.90
1080 1447 0.106669 GGAAGGAGTGCCCCCATTAC 60.107 60.000 0.00 0.00 34.66 1.89
1081 1448 0.623723 GAAGGAGTGCCCCCATTACA 59.376 55.000 0.00 0.00 34.66 2.41
1536 1906 3.369157 GGAATGACACCAGGTACCAGTAC 60.369 52.174 15.94 9.09 35.40 2.73
1747 2124 0.165295 CATGCTCTGTCAGTGTTGCG 59.835 55.000 0.00 0.00 0.00 4.85
1794 2171 9.074576 TGGGGAGTAAAAAGAAAGAGTTTTATC 57.925 33.333 0.00 0.00 33.17 1.75
1795 2172 9.298250 GGGGAGTAAAAAGAAAGAGTTTTATCT 57.702 33.333 0.00 0.00 33.17 1.98
1830 2207 5.661056 AAGGGAATTAAAACCTTAGCTGC 57.339 39.130 0.00 0.00 42.53 5.25
1831 2208 4.935578 AGGGAATTAAAACCTTAGCTGCT 58.064 39.130 7.57 7.57 0.00 4.24
1833 2210 5.185828 AGGGAATTAAAACCTTAGCTGCTTG 59.814 40.000 7.79 1.06 0.00 4.01
1834 2211 5.410924 GGAATTAAAACCTTAGCTGCTTGG 58.589 41.667 7.79 13.38 0.00 3.61
1836 2213 0.969149 AAAACCTTAGCTGCTTGGCC 59.031 50.000 7.79 0.00 0.00 5.36
1838 2215 0.322906 AACCTTAGCTGCTTGGCCTC 60.323 55.000 7.79 0.00 0.00 4.70
1839 2216 1.204113 ACCTTAGCTGCTTGGCCTCT 61.204 55.000 7.79 0.00 0.00 3.69
1840 2217 0.833287 CCTTAGCTGCTTGGCCTCTA 59.167 55.000 7.79 0.00 0.00 2.43
1841 2218 1.202627 CCTTAGCTGCTTGGCCTCTAG 60.203 57.143 7.79 0.00 0.00 2.43
1845 2222 1.903294 CTGCTTGGCCTCTAGCTGA 59.097 57.895 20.55 6.00 40.81 4.26
1846 2223 0.251354 CTGCTTGGCCTCTAGCTGAA 59.749 55.000 20.55 5.45 40.81 3.02
1847 2224 0.692476 TGCTTGGCCTCTAGCTGAAA 59.308 50.000 20.55 3.60 41.25 2.69
1848 2225 1.339438 TGCTTGGCCTCTAGCTGAAAG 60.339 52.381 20.55 7.72 41.25 2.62
1874 2251 7.992180 CTTAAACCAAAGGATGCATGATAAC 57.008 36.000 2.46 0.00 0.00 1.89
1882 2269 7.431249 CAAAGGATGCATGATAACTAGCAATT 58.569 34.615 2.46 0.00 40.76 2.32
1888 2275 6.554419 TGCATGATAACTAGCAATTGAACAC 58.446 36.000 10.34 0.00 33.48 3.32
1889 2276 5.973565 GCATGATAACTAGCAATTGAACACC 59.026 40.000 10.34 0.00 0.00 4.16
1891 2278 6.741992 TGATAACTAGCAATTGAACACCTG 57.258 37.500 10.34 0.00 0.00 4.00
1906 2323 1.479323 CACCTGGAGATGGCAAAATGG 59.521 52.381 0.00 0.00 0.00 3.16
1959 2376 9.722056 GTAGCGAAAGATCAACAATGATAAATT 57.278 29.630 0.00 0.00 46.30 1.82
1961 2378 9.294030 AGCGAAAGATCAACAATGATAAATTTC 57.706 29.630 0.00 10.53 46.30 2.17
1962 2379 8.534778 GCGAAAGATCAACAATGATAAATTTCC 58.465 33.333 0.00 0.00 46.30 3.13
1989 2410 2.842208 TTCTTGCTTTGTTCACCACG 57.158 45.000 0.00 0.00 0.00 4.94
2030 2451 8.761689 TGCATGGCTAGAAACAGATCATATATA 58.238 33.333 0.00 0.00 0.00 0.86
2031 2452 9.775854 GCATGGCTAGAAACAGATCATATATAT 57.224 33.333 0.00 0.00 0.00 0.86
2071 2492 2.230508 TCACGCCTAGTACTGTCAAAGG 59.769 50.000 5.39 4.87 0.00 3.11
2080 2501 6.154706 CCTAGTACTGTCAAAGGGTCAATAGT 59.845 42.308 5.39 0.00 0.00 2.12
2140 2561 5.473504 ACAGATTCAACGCCAGAAAATAGTT 59.526 36.000 0.00 0.00 0.00 2.24
2166 2587 3.397439 GCTCTGCCTCTGCTCCCA 61.397 66.667 0.00 0.00 38.71 4.37
2169 2590 0.392729 CTCTGCCTCTGCTCCCAAAG 60.393 60.000 0.00 0.00 38.71 2.77
2178 2614 1.889170 CTGCTCCCAAAGAAAGGAACC 59.111 52.381 0.00 0.00 0.00 3.62
2181 2617 2.035961 GCTCCCAAAGAAAGGAACCAAC 59.964 50.000 0.00 0.00 0.00 3.77
2468 2904 9.645059 TCTCTGAACACTTGAAAGAATATACTG 57.355 33.333 0.00 0.00 0.00 2.74
2505 2941 2.822561 ACTTTCTGTCAGCTGATCGAGA 59.177 45.455 21.47 17.76 0.00 4.04
2507 2943 0.729690 TCTGTCAGCTGATCGAGACG 59.270 55.000 21.47 3.84 33.83 4.18
2758 3194 6.985117 ACATCATTTTACACTCATTGCTTGT 58.015 32.000 0.00 0.00 0.00 3.16
2818 3254 6.223120 ACAAGTTGATAAAGTTTTGGATGCC 58.777 36.000 10.54 0.00 0.00 4.40
2834 3270 2.601240 TGCCATGAACTGGGATTTGA 57.399 45.000 0.00 0.00 46.06 2.69
2877 3313 9.736414 AAATATAATTGAGCTAGCATGATGAGT 57.264 29.630 18.83 0.00 0.00 3.41
2878 3314 8.719560 ATATAATTGAGCTAGCATGATGAGTG 57.280 34.615 18.83 0.00 0.00 3.51
2879 3315 4.684484 ATTGAGCTAGCATGATGAGTGA 57.316 40.909 18.83 0.00 0.00 3.41
2880 3316 4.684484 TTGAGCTAGCATGATGAGTGAT 57.316 40.909 18.83 0.00 0.00 3.06
2881 3317 3.991367 TGAGCTAGCATGATGAGTGATG 58.009 45.455 18.83 0.00 0.00 3.07
2914 3350 3.067180 CCATGTGCAGGTATGGTTCATTC 59.933 47.826 13.75 0.00 39.18 2.67
2962 3398 2.447047 AGTGGAGATGGTGGAAGGTTTT 59.553 45.455 0.00 0.00 0.00 2.43
2986 3422 6.088719 GAGATTGCTCTCAAGAAACTAACG 57.911 41.667 0.00 0.00 46.13 3.18
3078 3514 4.041740 GGTGAGACCAAAAACTGAAACC 57.958 45.455 0.00 0.00 38.42 3.27
3134 3570 9.744468 GACAACCAACAGATTAAATTTACAAGT 57.256 29.630 0.00 0.00 0.00 3.16
3176 3612 3.980775 CACATAAACAAACTTTCAGGGCG 59.019 43.478 0.00 0.00 0.00 6.13
3280 3716 2.224137 CGGACTACAGCATGATGGACAT 60.224 50.000 16.55 0.00 39.69 3.06
3503 3939 2.897969 GTGGAACCACTTCCTCTACTCA 59.102 50.000 15.69 0.00 45.87 3.41
3745 4190 0.958091 TGTTCATTTTGGAGGCGTGG 59.042 50.000 0.00 0.00 0.00 4.94
3864 4309 9.788960 GAAGTTGATTATTAATCTCAAACCCAC 57.211 33.333 15.57 4.32 38.72 4.61
3887 4420 3.314307 TTGGTGTGTGGTGGGAATTAA 57.686 42.857 0.00 0.00 0.00 1.40
3893 4426 3.446873 TGTGTGGTGGGAATTAATGATGC 59.553 43.478 0.00 0.00 0.00 3.91
3905 4438 7.255242 GGGAATTAATGATGCGAATTTGAGAGA 60.255 37.037 0.00 0.00 0.00 3.10
3907 4440 9.167239 GAATTAATGATGCGAATTTGAGAGAAG 57.833 33.333 0.00 0.00 0.00 2.85
3908 4441 7.615582 TTAATGATGCGAATTTGAGAGAAGT 57.384 32.000 0.00 0.00 0.00 3.01
3911 4444 5.931532 TGATGCGAATTTGAGAGAAGTTTC 58.068 37.500 0.00 0.00 0.00 2.78
3912 4445 4.389664 TGCGAATTTGAGAGAAGTTTCG 57.610 40.909 0.00 0.00 39.03 3.46
3952 4486 4.279145 AGGGATTAGTGAGTCGAAAGCTA 58.721 43.478 0.00 0.00 0.00 3.32
3953 4487 4.339814 AGGGATTAGTGAGTCGAAAGCTAG 59.660 45.833 0.00 0.00 0.00 3.42
3954 4488 4.098196 GGGATTAGTGAGTCGAAAGCTAGT 59.902 45.833 0.00 0.00 0.00 2.57
3961 4498 5.474189 AGTGAGTCGAAAGCTAGTCTAACTT 59.526 40.000 0.00 0.00 0.00 2.66
3964 4501 5.867166 AGTCGAAAGCTAGTCTAACTTACG 58.133 41.667 0.00 0.00 0.00 3.18
3967 4504 7.279758 AGTCGAAAGCTAGTCTAACTTACGTAT 59.720 37.037 0.00 0.00 0.00 3.06
3968 4505 8.543774 GTCGAAAGCTAGTCTAACTTACGTATA 58.456 37.037 0.00 0.00 0.00 1.47
4015 4557 6.072508 GGTGTTGCAAGAGTTGATTAGATCAA 60.073 38.462 0.00 0.00 46.30 2.57
4066 4646 8.436200 GTTATGTCTTATAAAGCCAATCTAGCG 58.564 37.037 0.00 0.00 34.64 4.26
4067 4647 5.297547 TGTCTTATAAAGCCAATCTAGCGG 58.702 41.667 0.00 0.00 34.64 5.52
4125 5754 1.966451 GTGAGGACTTTGGCCACCG 60.966 63.158 3.88 0.83 0.00 4.94
4134 5763 1.750778 CTTTGGCCACCGCTTTGATAT 59.249 47.619 3.88 0.00 34.44 1.63
4263 5892 2.675348 CCATCGAAGAAGTCTTGGAAGC 59.325 50.000 9.43 0.00 42.47 3.86
4293 5922 1.601166 AGTTGGTTTAACGAGGTGCC 58.399 50.000 0.00 0.00 44.15 5.01
4364 6001 7.150783 AGAAATCATGTTTAGTTTCCTGCTC 57.849 36.000 0.00 0.00 32.43 4.26
4393 6030 1.203441 AGCATCAAGGGTGGAGAGCA 61.203 55.000 0.00 0.00 0.00 4.26
4402 6039 2.038813 TGGAGAGCACGGGGATGA 59.961 61.111 0.00 0.00 0.00 2.92
4426 6063 4.041691 TGGTTGGATAAATAGAGGCTAGGC 59.958 45.833 8.55 8.55 0.00 3.93
4438 6076 2.102588 GAGGCTAGGCGAAGTTCCAATA 59.897 50.000 11.10 0.00 0.00 1.90
4457 6095 0.339859 AGGTGGGAGCTATGGAGTCA 59.660 55.000 0.00 0.00 0.00 3.41
4458 6096 0.755686 GGTGGGAGCTATGGAGTCAG 59.244 60.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 85 1.673400 CAAACACCACACGACCAATGA 59.327 47.619 0.00 0.00 0.00 2.57
89 91 3.503749 TGGCAAACACCACACGAC 58.496 55.556 0.00 0.00 33.75 4.34
206 208 4.201647 CGTCTTAACGTGTGTTTGTCTGTT 60.202 41.667 0.00 0.00 43.94 3.16
257 266 6.260493 ACTTATCTGTTACTGCCGTCTACTAG 59.740 42.308 0.00 0.00 0.00 2.57
365 379 9.890629 AATTCTTTATCAGTTGATGTAGCAGTA 57.109 29.630 4.90 0.00 36.05 2.74
648 983 1.537202 GAGTCACACCAGCCATTCAAC 59.463 52.381 0.00 0.00 0.00 3.18
890 1235 4.036027 TGAAAGTTTGAAGCTGCAAGAGAG 59.964 41.667 7.32 0.00 34.07 3.20
949 1310 4.802918 GCAACCTCCTGTAAGCTAACTCAA 60.803 45.833 0.00 0.00 0.00 3.02
1079 1446 3.826729 GCTGTCCCCTCTTTTATTGTTGT 59.173 43.478 0.00 0.00 0.00 3.32
1080 1447 3.119849 CGCTGTCCCCTCTTTTATTGTTG 60.120 47.826 0.00 0.00 0.00 3.33
1081 1448 3.081804 CGCTGTCCCCTCTTTTATTGTT 58.918 45.455 0.00 0.00 0.00 2.83
1144 1514 0.598065 GTGGTCATCTTGTTGTGGGC 59.402 55.000 0.00 0.00 0.00 5.36
1536 1906 2.815945 ATCGGGCTGCCATCTCCAG 61.816 63.158 22.05 2.45 0.00 3.86
1747 2124 6.366061 CCCCAAGAGTTCAATTTCGAAATTTC 59.634 38.462 28.91 23.28 36.52 2.17
1821 2198 0.833287 TAGAGGCCAAGCAGCTAAGG 59.167 55.000 5.01 9.08 0.00 2.69
1829 2206 1.377536 CTTTCAGCTAGAGGCCAAGC 58.622 55.000 14.96 14.96 43.05 4.01
1830 2207 1.377536 GCTTTCAGCTAGAGGCCAAG 58.622 55.000 5.01 0.00 43.05 3.61
1831 2208 0.035056 GGCTTTCAGCTAGAGGCCAA 60.035 55.000 5.01 0.00 42.61 4.52
1833 2210 0.254462 AAGGCTTTCAGCTAGAGGCC 59.746 55.000 12.19 12.19 41.99 5.19
1834 2211 2.990066 TAAGGCTTTCAGCTAGAGGC 57.010 50.000 4.45 8.19 41.99 4.70
1836 2213 4.579869 TGGTTTAAGGCTTTCAGCTAGAG 58.420 43.478 4.45 0.00 41.99 2.43
1838 2215 5.335976 CCTTTGGTTTAAGGCTTTCAGCTAG 60.336 44.000 4.45 4.60 41.99 3.42
1839 2216 4.522789 CCTTTGGTTTAAGGCTTTCAGCTA 59.477 41.667 4.45 0.00 41.99 3.32
1840 2217 3.321968 CCTTTGGTTTAAGGCTTTCAGCT 59.678 43.478 4.45 0.00 41.99 4.24
1841 2218 3.320826 TCCTTTGGTTTAAGGCTTTCAGC 59.679 43.478 4.45 2.70 43.62 4.26
1845 2222 3.645687 TGCATCCTTTGGTTTAAGGCTTT 59.354 39.130 4.45 0.00 43.62 3.51
1846 2223 3.238597 TGCATCCTTTGGTTTAAGGCTT 58.761 40.909 4.58 4.58 43.62 4.35
1847 2224 2.888212 TGCATCCTTTGGTTTAAGGCT 58.112 42.857 0.00 0.00 43.62 4.58
1848 2225 3.195396 TCATGCATCCTTTGGTTTAAGGC 59.805 43.478 0.00 0.00 43.62 4.35
1849 2226 5.603170 ATCATGCATCCTTTGGTTTAAGG 57.397 39.130 0.00 0.00 45.01 2.69
1852 2229 7.013274 GCTAGTTATCATGCATCCTTTGGTTTA 59.987 37.037 0.00 0.00 0.00 2.01
1874 2251 3.942829 TCTCCAGGTGTTCAATTGCTAG 58.057 45.455 0.00 0.00 0.00 3.42
1882 2269 0.770499 TTGCCATCTCCAGGTGTTCA 59.230 50.000 0.00 0.00 0.00 3.18
1888 2275 1.117150 CCCATTTTGCCATCTCCAGG 58.883 55.000 0.00 0.00 0.00 4.45
1889 2276 1.479323 CACCCATTTTGCCATCTCCAG 59.521 52.381 0.00 0.00 0.00 3.86
1891 2278 0.826062 CCACCCATTTTGCCATCTCC 59.174 55.000 0.00 0.00 0.00 3.71
1906 2323 2.757099 CAGCAGGCCAATCCCACC 60.757 66.667 5.01 0.00 34.51 4.61
1988 2409 1.093972 TGCAGGTGTATGGAATTGCG 58.906 50.000 0.00 0.00 34.44 4.85
1989 2410 3.088194 CATGCAGGTGTATGGAATTGC 57.912 47.619 0.00 0.00 35.01 3.56
2030 2451 0.187606 ATGACTGGATGCCATGCCAT 59.812 50.000 0.00 0.00 32.89 4.40
2031 2452 0.032912 AATGACTGGATGCCATGCCA 60.033 50.000 0.00 0.00 30.82 4.92
2071 2492 5.501715 CGCATGTCACAAATACTATTGACC 58.498 41.667 0.00 0.00 38.06 4.02
2080 2501 2.700722 TAGCCCGCATGTCACAAATA 57.299 45.000 0.00 0.00 0.00 1.40
2140 2561 3.581770 AGCAGAGGCAGAGCAATCATATA 59.418 43.478 0.00 0.00 44.61 0.86
2166 2587 4.760204 CACTATCCGTTGGTTCCTTTCTTT 59.240 41.667 0.00 0.00 0.00 2.52
2169 2590 3.934068 TCACTATCCGTTGGTTCCTTTC 58.066 45.455 0.00 0.00 0.00 2.62
2178 2614 6.045318 ACTCATGATCTTTCACTATCCGTTG 58.955 40.000 0.00 0.00 33.85 4.10
2181 2617 6.019237 CACAACTCATGATCTTTCACTATCCG 60.019 42.308 0.00 0.00 33.85 4.18
2236 2672 6.767524 AACCTGTTTCACAGTTTCAACATA 57.232 33.333 3.30 0.00 44.50 2.29
2436 2872 5.994054 TCTTTCAAGTGTTCAGAGATTGAGG 59.006 40.000 0.00 0.00 37.07 3.86
2468 2904 1.839424 AAGTGGCATGCCTTACTTCC 58.161 50.000 35.53 14.95 29.67 3.46
2505 2941 3.120321 TGTATTCCTGAAACAGTGCGT 57.880 42.857 0.00 0.00 0.00 5.24
2507 2943 4.168760 GCATTGTATTCCTGAAACAGTGC 58.831 43.478 17.54 17.54 45.39 4.40
2758 3194 8.746052 TTCAGATAACTCTTTCCTTTTGTTGA 57.254 30.769 0.00 0.00 0.00 3.18
2818 3254 9.573133 GTTACTAATTTCAAATCCCAGTTCATG 57.427 33.333 0.00 0.00 0.00 3.07
2878 3314 3.441222 TGCACATGGTGAAGATGTTCATC 59.559 43.478 8.72 8.80 44.58 2.92
2879 3315 3.423749 TGCACATGGTGAAGATGTTCAT 58.576 40.909 8.72 0.00 44.58 2.57
2880 3316 2.815503 CTGCACATGGTGAAGATGTTCA 59.184 45.455 0.23 0.23 41.52 3.18
2881 3317 2.163010 CCTGCACATGGTGAAGATGTTC 59.837 50.000 5.92 0.00 41.52 3.18
2914 3350 0.379669 GCTTTGCATCACCATCCTCG 59.620 55.000 0.00 0.00 0.00 4.63
2962 3398 5.635280 CGTTAGTTTCTTGAGAGCAATCTCA 59.365 40.000 3.88 3.88 44.15 3.27
2986 3422 3.319198 TTCGCTCCCACCCACTCC 61.319 66.667 0.00 0.00 0.00 3.85
3078 3514 5.293569 GTCAGGTTTAACGGTTGATGGATAG 59.706 44.000 3.07 0.00 0.00 2.08
3503 3939 8.613060 ATTTACATCATTTCTGCACGAGATAT 57.387 30.769 0.00 0.00 0.00 1.63
3643 4079 5.654497 CAAGTGCAGAGAAACCTTCTTTTT 58.346 37.500 0.00 0.00 40.87 1.94
3745 4190 7.282585 TGCAGGCTGGATTATATATATGTTCC 58.717 38.462 17.64 14.51 0.00 3.62
3864 4309 1.032657 TTCCCACCACACACCAAACG 61.033 55.000 0.00 0.00 0.00 3.60
3887 4420 6.506500 AAACTTCTCTCAAATTCGCATCAT 57.493 33.333 0.00 0.00 0.00 2.45
3893 4426 4.143094 GGGACGAAACTTCTCTCAAATTCG 60.143 45.833 4.39 4.39 43.65 3.34
3912 4445 2.199236 CCTTATTAGTTCACGCGGGAC 58.801 52.381 12.52 6.71 0.00 4.46
4063 4643 2.678934 TCTTAGTCCACGGCCGCT 60.679 61.111 28.58 17.06 0.00 5.52
4066 4646 1.049289 ATCCCTCTTAGTCCACGGCC 61.049 60.000 0.00 0.00 0.00 6.13
4067 4647 1.700955 TATCCCTCTTAGTCCACGGC 58.299 55.000 0.00 0.00 0.00 5.68
4125 5754 5.346822 CACTTCAAAACTGCCATATCAAAGC 59.653 40.000 0.00 0.00 0.00 3.51
4134 5763 2.886523 CCATCTCACTTCAAAACTGCCA 59.113 45.455 0.00 0.00 0.00 4.92
4263 5892 5.413213 TCGTTAAACCAACTATCACCCAATG 59.587 40.000 0.00 0.00 34.77 2.82
4293 5922 3.467803 ACGACTTTGACCCTTTCTTCTG 58.532 45.455 0.00 0.00 0.00 3.02
4364 6001 2.821969 ACCCTTGATGCTGCTTTTACTG 59.178 45.455 0.00 0.00 0.00 2.74
4393 6030 1.814429 TATCCAACCATCATCCCCGT 58.186 50.000 0.00 0.00 0.00 5.28
4402 6039 5.280727 GCCTAGCCTCTATTTATCCAACCAT 60.281 44.000 0.00 0.00 0.00 3.55
4438 6076 0.339859 TGACTCCATAGCTCCCACCT 59.660 55.000 0.00 0.00 0.00 4.00
4443 6081 4.953940 AAATCTCTGACTCCATAGCTCC 57.046 45.455 0.00 0.00 0.00 4.70
4451 6089 6.930731 AGTCTTCACTAAAATCTCTGACTCC 58.069 40.000 0.00 0.00 0.00 3.85
4457 6095 7.220030 TCAAGCAAGTCTTCACTAAAATCTCT 58.780 34.615 0.00 0.00 31.27 3.10
4458 6096 7.360776 CCTCAAGCAAGTCTTCACTAAAATCTC 60.361 40.741 0.00 0.00 31.27 2.75


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

AutoCloner maintained by Alex Coulton.