Multiple sequence alignment - TraesCS3A01G274000

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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 TraesCS3A01G274000 chr3A 100.000 4420 0 0 1 4420 502835457 502839876 0.000000e+00 8163.0
1 TraesCS3A01G274000 chr3D 94.161 3100 134 29 779 3853 378922760 378925837 0.000000e+00 4678.0
2 TraesCS3A01G274000 chr3D 93.394 439 21 4 3856 4294 378925950 378926380 1.040000e-180 643.0
3 TraesCS3A01G274000 chr3D 83.884 726 44 28 2 710 378921849 378922518 3.750000e-175 625.0
4 TraesCS3A01G274000 chr3D 86.667 120 1 4 4313 4420 378926448 378926564 7.770000e-23 119.0
5 TraesCS3A01G274000 chr3D 96.226 53 2 0 729 781 378922686 378922738 2.190000e-13 87.9
6 TraesCS3A01G274000 chr3B 93.492 1552 80 11 779 2326 494070133 494071667 0.000000e+00 2287.0
7 TraesCS3A01G274000 chr3B 92.918 1299 45 17 3001 4294 494072937 494074193 0.000000e+00 1845.0
8 TraesCS3A01G274000 chr3B 94.915 590 16 4 2351 2937 494071660 494072238 0.000000e+00 911.0
9 TraesCS3A01G274000 chr3B 84.246 749 38 40 1 710 494069177 494069884 0.000000e+00 656.0
10 TraesCS3A01G274000 chr3B 87.143 140 6 1 4293 4420 494074241 494074380 9.900000e-32 148.0
11 TraesCS3A01G274000 chr3B 87.179 78 6 1 704 781 494070038 494070111 7.880000e-13 86.1
12 TraesCS3A01G274000 chr7A 79.839 124 17 7 3913 4033 7876910 7876792 2.830000e-12 84.2
13 TraesCS3A01G274000 chr2D 77.857 140 25 5 3909 4046 580978193 580978058 1.020000e-11 82.4
14 TraesCS3A01G274000 chr6A 82.500 80 11 2 3995 4074 49086193 49086269 2.850000e-07 67.6
15 TraesCS3A01G274000 chr2B 74.830 147 31 5 3913 4057 50738397 50738255 1.330000e-05 62.1


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 TraesCS3A01G274000 chr3A 502835457 502839876 4419 False 8163.00 8163 100.000000 1 4420 1 chr3A.!!$F1 4419
1 TraesCS3A01G274000 chr3D 378921849 378926564 4715 False 1230.58 4678 90.866400 2 4420 5 chr3D.!!$F1 4418
2 TraesCS3A01G274000 chr3B 494069177 494074380 5203 False 988.85 2287 89.982167 1 4420 6 chr3B.!!$F1 4419

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
989 1236 0.107508 CCACTGCATCGGTCCATCTT 60.108 55.0 0.00 0.0 0.00 2.40 F
1531 1778 0.186386 TCCTTTCCCGGCCAAGAAAA 59.814 50.0 15.83 4.5 31.91 2.29 F
1695 1942 0.671781 CCAGCAAGAGGTTCTCCACG 60.672 60.0 0.00 0.0 35.89 4.94 F
1844 2091 0.924090 GCAACGAAGGTGCTCGATAG 59.076 55.0 2.42 0.0 41.44 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 2182 0.107410 TGAACTTGACAGCAACGGGT 60.107 50.000 0.0 0.0 0.00 5.28 R
2710 2964 0.389817 CGTTCGCCAGAGGATCACAA 60.390 55.000 0.0 0.0 37.82 3.33 R
2734 2988 1.064463 GCCATCCATCTGAAAGTCCCA 60.064 52.381 0.0 0.0 33.76 4.37 R
3709 4610 0.117340 AGAGGCCCAGGTGTACTTCT 59.883 55.000 0.0 0.0 0.00 2.85 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
59 60 7.669304 TCTCTCATGATTGACCCATAAACAAAA 59.331 33.333 0.00 0.00 0.00 2.44
164 165 4.832823 CCCCCTGCCCTATTTATTTTACAG 59.167 45.833 0.00 0.00 0.00 2.74
168 169 3.002862 TGCCCTATTTATTTTACAGCGCG 59.997 43.478 0.00 0.00 0.00 6.86
169 170 3.608474 GCCCTATTTATTTTACAGCGCGG 60.608 47.826 8.83 5.83 0.00 6.46
170 171 3.810941 CCCTATTTATTTTACAGCGCGGA 59.189 43.478 16.26 0.00 0.00 5.54
171 172 4.273969 CCCTATTTATTTTACAGCGCGGAA 59.726 41.667 16.26 3.32 0.00 4.30
172 173 5.440685 CCTATTTATTTTACAGCGCGGAAG 58.559 41.667 16.26 2.24 0.00 3.46
246 259 3.332187 AGGAAAAGGAGGAGAAAGGAAGG 59.668 47.826 0.00 0.00 0.00 3.46
248 261 0.995803 AAGGAGGAGAAAGGAAGGGC 59.004 55.000 0.00 0.00 0.00 5.19
249 262 1.222113 GGAGGAGAAAGGAAGGGCG 59.778 63.158 0.00 0.00 0.00 6.13
250 263 1.450491 GAGGAGAAAGGAAGGGCGC 60.450 63.158 0.00 0.00 0.00 6.53
252 265 2.438614 GAGAAAGGAAGGGCGCCC 60.439 66.667 39.29 39.29 0.00 6.13
253 266 4.410400 AGAAAGGAAGGGCGCCCG 62.410 66.667 38.88 0.00 41.95 6.13
358 384 1.241327 CATCCATCCCTCCCTCCCT 59.759 63.158 0.00 0.00 0.00 4.20
359 385 0.839853 CATCCATCCCTCCCTCCCTC 60.840 65.000 0.00 0.00 0.00 4.30
360 386 2.054834 ATCCATCCCTCCCTCCCTCC 62.055 65.000 0.00 0.00 0.00 4.30
361 387 2.705410 CATCCCTCCCTCCCTCCA 59.295 66.667 0.00 0.00 0.00 3.86
362 388 1.768077 CATCCCTCCCTCCCTCCAC 60.768 68.421 0.00 0.00 0.00 4.02
363 389 3.041297 ATCCCTCCCTCCCTCCACC 62.041 68.421 0.00 0.00 0.00 4.61
364 390 4.825679 CCCTCCCTCCCTCCACCC 62.826 77.778 0.00 0.00 0.00 4.61
365 391 4.825679 CCTCCCTCCCTCCACCCC 62.826 77.778 0.00 0.00 0.00 4.95
366 392 3.700350 CTCCCTCCCTCCACCCCT 61.700 72.222 0.00 0.00 0.00 4.79
367 393 3.695825 TCCCTCCCTCCACCCCTC 61.696 72.222 0.00 0.00 0.00 4.30
368 394 4.825679 CCCTCCCTCCACCCCTCC 62.826 77.778 0.00 0.00 0.00 4.30
369 395 4.825679 CCTCCCTCCACCCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
385 411 2.126110 CCGGCAAATTCCAACGCC 60.126 61.111 0.00 0.00 41.30 5.68
454 480 3.391382 CGGTTCTCTCCCCGCCTT 61.391 66.667 0.00 0.00 37.43 4.35
455 481 2.056223 CGGTTCTCTCCCCGCCTTA 61.056 63.158 0.00 0.00 37.43 2.69
456 482 1.610554 CGGTTCTCTCCCCGCCTTAA 61.611 60.000 0.00 0.00 37.43 1.85
485 541 2.771762 GCTGCTCCCTCCCTCCAT 60.772 66.667 0.00 0.00 0.00 3.41
486 542 2.817056 GCTGCTCCCTCCCTCCATC 61.817 68.421 0.00 0.00 0.00 3.51
487 543 2.040464 TGCTCCCTCCCTCCATCC 60.040 66.667 0.00 0.00 0.00 3.51
488 544 2.851588 GCTCCCTCCCTCCATCCC 60.852 72.222 0.00 0.00 0.00 3.85
489 545 3.041365 CTCCCTCCCTCCATCCCT 58.959 66.667 0.00 0.00 0.00 4.20
490 546 1.152139 CTCCCTCCCTCCATCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
491 547 2.122189 CCCTCCCTCCATCCCTCC 60.122 72.222 0.00 0.00 0.00 4.30
505 561 2.342279 CTCCACGTTCTTGGCCGA 59.658 61.111 0.00 0.00 36.48 5.54
568 625 1.657804 AGATTCGGGTGTTCCTTCCT 58.342 50.000 0.00 0.00 0.00 3.36
569 626 1.985895 AGATTCGGGTGTTCCTTCCTT 59.014 47.619 0.00 0.00 0.00 3.36
570 627 2.027100 AGATTCGGGTGTTCCTTCCTTC 60.027 50.000 0.00 0.00 0.00 3.46
571 628 0.399075 TTCGGGTGTTCCTTCCTTCC 59.601 55.000 0.00 0.00 0.00 3.46
656 713 4.244802 CACCGGTTGCGTTGCGTT 62.245 61.111 2.97 0.00 0.00 4.84
657 714 3.944233 ACCGGTTGCGTTGCGTTC 61.944 61.111 0.00 0.00 0.00 3.95
705 927 1.065928 CGAATTCCGAGGTCTCCCG 59.934 63.158 0.00 0.00 41.76 5.14
712 934 2.835705 CGAGGTCTCCCGATCGTGG 61.836 68.421 15.09 14.68 35.12 4.94
714 936 3.148279 GGTCTCCCGATCGTGGCT 61.148 66.667 15.09 0.00 0.00 4.75
719 941 1.079405 TCCCGATCGTGGCTTTCAC 60.079 57.895 15.09 0.00 42.74 3.18
746 968 4.237724 CTGTGTGTGTGTATTGATCTCGT 58.762 43.478 0.00 0.00 0.00 4.18
777 999 2.833943 GCTTTTGAATTGATCCAGGGGT 59.166 45.455 0.00 0.00 0.00 4.95
781 1003 0.756815 GAATTGATCCAGGGGTGGCC 60.757 60.000 0.00 0.00 0.00 5.36
828 1075 2.289002 GAGGCATGCCATAAGAAGAACG 59.711 50.000 37.18 0.00 38.92 3.95
917 1164 2.224066 CGTCCAGGTTCCTATAAGCCTG 60.224 54.545 0.00 0.00 45.86 4.85
973 1220 2.874701 CGAATCAAGTCCATCCATCCAC 59.125 50.000 0.00 0.00 0.00 4.02
989 1236 0.107508 CCACTGCATCGGTCCATCTT 60.108 55.000 0.00 0.00 0.00 2.40
1146 1393 1.079057 GAACAAGGGCTCCGACTCC 60.079 63.158 0.00 0.00 0.00 3.85
1284 1531 1.033746 ATGCCTTCTCCAACGCCATG 61.034 55.000 0.00 0.00 0.00 3.66
1419 1666 2.896443 GAGCCCGAGGTTCAGGAG 59.104 66.667 2.65 0.00 33.06 3.69
1423 1670 4.148825 CCGAGGTTCAGGAGCCGG 62.149 72.222 0.00 0.00 36.74 6.13
1467 1714 0.903454 TCGAGTTCTCCTTCCACCCC 60.903 60.000 0.00 0.00 0.00 4.95
1470 1717 0.905337 AGTTCTCCTTCCACCCCGAG 60.905 60.000 0.00 0.00 0.00 4.63
1531 1778 0.186386 TCCTTTCCCGGCCAAGAAAA 59.814 50.000 15.83 4.50 31.91 2.29
1637 1884 4.581391 GAGGTCCCCTCTCCCAAA 57.419 61.111 2.98 0.00 46.41 3.28
1641 1888 3.327404 TCCCCTCTCCCAAACCGC 61.327 66.667 0.00 0.00 0.00 5.68
1694 1941 0.957888 GCCAGCAAGAGGTTCTCCAC 60.958 60.000 0.00 0.00 35.89 4.02
1695 1942 0.671781 CCAGCAAGAGGTTCTCCACG 60.672 60.000 0.00 0.00 35.89 4.94
1696 1943 1.004440 AGCAAGAGGTTCTCCACGC 60.004 57.895 0.00 0.00 35.89 5.34
1731 1978 1.146358 GGAAATCTTCGTCTCCGCCG 61.146 60.000 0.00 0.00 0.00 6.46
1807 2054 0.951040 GAAGGAGCACTGGGACAACG 60.951 60.000 0.00 0.00 38.70 4.10
1842 2089 2.094659 CGCAACGAAGGTGCTCGAT 61.095 57.895 8.48 0.00 41.44 3.59
1844 2091 0.924090 GCAACGAAGGTGCTCGATAG 59.076 55.000 2.42 0.00 41.44 2.08
1935 2182 4.890988 TCCATGGAATCTACAAGGAGGTA 58.109 43.478 13.46 0.00 31.39 3.08
1974 2221 2.031163 AGGCAGCCTGACGTTGAC 59.969 61.111 15.24 0.00 29.57 3.18
2085 2335 2.354503 GGTAACTTCCCGAGTTTCCTCC 60.355 54.545 7.16 0.00 46.34 4.30
2086 2336 1.430992 AACTTCCCGAGTTTCCTCCA 58.569 50.000 0.00 0.00 46.34 3.86
2097 2347 5.648092 CCGAGTTTCCTCCACAGAAATATTT 59.352 40.000 0.00 0.00 35.77 1.40
2098 2348 6.403636 CCGAGTTTCCTCCACAGAAATATTTG 60.404 42.308 5.17 0.00 35.77 2.32
2103 2353 7.610580 TTCCTCCACAGAAATATTTGGTTTT 57.389 32.000 5.17 0.00 0.00 2.43
2154 2404 9.809096 TGTATTTATCAAACAAGCTTGAAACAA 57.191 25.926 32.50 14.48 38.75 2.83
2157 2407 7.945033 TTATCAAACAAGCTTGAAACAATCC 57.055 32.000 32.50 0.00 38.75 3.01
2159 2409 5.108517 TCAAACAAGCTTGAAACAATCCAC 58.891 37.500 32.50 0.00 32.39 4.02
2164 2414 4.647424 AGCTTGAAACAATCCACGAAAA 57.353 36.364 0.00 0.00 0.00 2.29
2211 2461 4.874396 AGTAATCCTTACGTTTAGCCTTGC 59.126 41.667 0.00 0.00 41.01 4.01
2225 2475 1.364626 CCTTGCGCCAGCTGACTTAG 61.365 60.000 17.39 5.62 45.42 2.18
2260 2510 5.472137 TGAAATGGCAAGTTTCTGGTACTAC 59.528 40.000 13.14 0.00 36.71 2.73
2266 2516 4.748600 GCAAGTTTCTGGTACTACGTTTCT 59.251 41.667 0.00 0.00 0.00 2.52
2270 2520 6.549952 AGTTTCTGGTACTACGTTTCTATCG 58.450 40.000 0.00 0.00 0.00 2.92
2285 2535 6.128553 CGTTTCTATCGGTACCTAGCGTTATA 60.129 42.308 10.90 0.00 46.22 0.98
2286 2536 6.727824 TTCTATCGGTACCTAGCGTTATAC 57.272 41.667 10.90 0.00 46.22 1.47
2288 2538 6.467677 TCTATCGGTACCTAGCGTTATACTT 58.532 40.000 10.90 0.00 46.22 2.24
2302 2553 5.622914 GCGTTATACTTCAGGTGTTCCTACA 60.623 44.000 0.00 0.00 43.07 2.74
2396 2647 6.264744 GTGATCCCATCTTTGATGTGATCATT 59.735 38.462 26.02 2.63 39.39 2.57
2464 2715 2.570181 GTTGGAGCATGCACCAGC 59.430 61.111 31.27 30.15 34.66 4.85
2638 2889 2.236741 TCGTACATCGTGACGTGAAG 57.763 50.000 4.40 0.00 40.00 3.02
2710 2964 3.692257 ATAGCCTGCGAAGAAGCATAT 57.308 42.857 0.00 0.00 46.97 1.78
2716 2970 3.562973 CCTGCGAAGAAGCATATTGTGAT 59.437 43.478 0.00 0.00 46.97 3.06
2734 2988 0.757188 ATCCTCTGGCGAACGATCCT 60.757 55.000 0.00 0.00 0.00 3.24
2740 2994 2.722201 GGCGAACGATCCTGGGACT 61.722 63.158 0.00 0.00 0.00 3.85
2932 3186 0.991920 TCCCATTTCTGTCCCTGTCC 59.008 55.000 0.00 0.00 0.00 4.02
2949 3455 5.585047 CCCTGTCCAGTAATACTTTGTTAGC 59.415 44.000 0.00 0.00 0.00 3.09
2988 3494 2.755686 TCCAGATGGAGAGAGCATGAA 58.244 47.619 0.00 0.00 39.78 2.57
2993 3499 4.882427 CAGATGGAGAGAGCATGAAATTGT 59.118 41.667 0.00 0.00 0.00 2.71
2994 3500 6.053650 CAGATGGAGAGAGCATGAAATTGTA 58.946 40.000 0.00 0.00 0.00 2.41
2995 3501 6.018098 CAGATGGAGAGAGCATGAAATTGTAC 60.018 42.308 0.00 0.00 0.00 2.90
2996 3502 5.164620 TGGAGAGAGCATGAAATTGTACA 57.835 39.130 0.00 0.00 0.00 2.90
2997 3503 5.748402 TGGAGAGAGCATGAAATTGTACAT 58.252 37.500 0.00 0.00 0.00 2.29
2998 3504 5.819379 TGGAGAGAGCATGAAATTGTACATC 59.181 40.000 0.00 0.00 0.00 3.06
2999 3505 6.054295 GGAGAGAGCATGAAATTGTACATCT 58.946 40.000 0.00 0.00 0.00 2.90
3002 3891 8.604640 AGAGAGCATGAAATTGTACATCTATG 57.395 34.615 0.00 0.00 0.00 2.23
3073 3962 5.650703 TCTCGAACAGTCCATGTACATTCTA 59.349 40.000 5.37 0.00 43.00 2.10
3410 4300 0.250901 CTGGACCTCCACCACCAAAG 60.251 60.000 0.00 0.00 42.01 2.77
3464 4354 6.068971 TCTGTTCTAGTCCAGGTAGTCCTTAT 60.069 42.308 10.22 0.00 43.07 1.73
3531 4424 6.173427 AGTCCCATTTGCTTGTATTTGTTT 57.827 33.333 0.00 0.00 0.00 2.83
3577 4475 9.231297 CTTCTCTGGGTTCAACTTGATTTATTA 57.769 33.333 0.00 0.00 0.00 0.98
3709 4610 5.974751 CCAAAAGAAAAATCGAACTTCGGAA 59.025 36.000 11.21 0.00 40.88 4.30
3723 4624 1.263356 TCGGAAGAAGTACACCTGGG 58.737 55.000 0.00 0.00 37.03 4.45
3828 4730 1.447489 CTGAGCAGAGCACCTTCCG 60.447 63.158 0.00 0.00 0.00 4.30
3839 4741 1.790755 CACCTTCCGATTGTTGTCGA 58.209 50.000 0.00 0.00 44.06 4.20
3890 4902 5.473039 CCAAGGTGAATTGAATGTTTCCTC 58.527 41.667 0.00 0.00 31.55 3.71
3891 4903 5.473039 CAAGGTGAATTGAATGTTTCCTCC 58.527 41.667 0.00 0.00 31.55 4.30
3892 4904 4.089361 AGGTGAATTGAATGTTTCCTCCC 58.911 43.478 0.00 0.00 0.00 4.30
3893 4905 4.089361 GGTGAATTGAATGTTTCCTCCCT 58.911 43.478 0.00 0.00 0.00 4.20
3906 4918 5.012768 TGTTTCCTCCCTTGTAGTAAAGAGG 59.987 44.000 0.00 0.00 0.00 3.69
3907 4919 4.687262 TCCTCCCTTGTAGTAAAGAGGA 57.313 45.455 2.48 2.48 31.21 3.71
3908 4920 5.019657 TCCTCCCTTGTAGTAAAGAGGAA 57.980 43.478 4.12 0.00 30.91 3.36
3909 4921 5.408824 TCCTCCCTTGTAGTAAAGAGGAAA 58.591 41.667 4.12 0.00 30.91 3.13
3960 4973 6.732531 TCTTCACAGAGTGCATATTTTCTG 57.267 37.500 11.22 11.22 42.07 3.02
3971 4984 8.045176 AGTGCATATTTTCTGTCTTAACTTCC 57.955 34.615 0.00 0.00 0.00 3.46
3973 4986 6.093495 TGCATATTTTCTGTCTTAACTTCCGG 59.907 38.462 0.00 0.00 0.00 5.14
3992 5005 2.223688 CGGACCAGACATTTTGCAACAA 60.224 45.455 0.00 0.00 0.00 2.83
4085 5098 4.513692 CCGTTTTGACCAATCAACACTCTA 59.486 41.667 5.16 0.00 44.66 2.43
4098 5111 7.986085 ATCAACACTCTAATGCAAACTACTT 57.014 32.000 0.00 0.00 0.00 2.24
4101 5114 8.364894 TCAACACTCTAATGCAAACTACTTAGA 58.635 33.333 0.00 0.00 0.00 2.10
4119 5132 7.582435 ACTTAGATTGTACACATCAACTTCG 57.418 36.000 15.69 0.00 0.00 3.79
4152 5165 6.064060 GTCCACATCCATATCATCCTCAAAA 58.936 40.000 0.00 0.00 0.00 2.44
4165 5178 5.072329 TCATCCTCAAAAGTCACTCTCCTTT 59.928 40.000 0.00 0.00 32.44 3.11
4210 5223 4.211125 TCAACAAAAATGTCAGCTACCCA 58.789 39.130 0.00 0.00 0.00 4.51
4246 5259 1.005450 GTTTGCCATCCTCTACCCCAA 59.995 52.381 0.00 0.00 0.00 4.12
4300 5362 2.636830 ACTGAAGCTGCACATGGATAC 58.363 47.619 1.02 0.00 0.00 2.24
4383 5457 1.017387 GCAGCCAATCCGTTCCTAAG 58.983 55.000 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.231478 TCATGAGAGACGACTTTGGGAC 59.769 50.000 0.00 0.00 0.00 4.46
71 72 5.652452 CCCCGGAATACAATTCTTTCTTTCT 59.348 40.000 0.73 0.00 0.00 2.52
72 73 5.650703 TCCCCGGAATACAATTCTTTCTTTC 59.349 40.000 0.73 0.00 0.00 2.62
73 74 5.576128 TCCCCGGAATACAATTCTTTCTTT 58.424 37.500 0.73 0.00 0.00 2.52
74 75 5.187621 TCCCCGGAATACAATTCTTTCTT 57.812 39.130 0.73 0.00 0.00 2.52
75 76 4.855298 TCCCCGGAATACAATTCTTTCT 57.145 40.909 0.73 0.00 0.00 2.52
142 143 4.280929 GCTGTAAAATAAATAGGGCAGGGG 59.719 45.833 0.00 0.00 0.00 4.79
168 169 1.416030 GAATCCTCTGCCCTCTCTTCC 59.584 57.143 0.00 0.00 0.00 3.46
169 170 2.397597 AGAATCCTCTGCCCTCTCTTC 58.602 52.381 0.00 0.00 0.00 2.87
170 171 2.566708 AGAATCCTCTGCCCTCTCTT 57.433 50.000 0.00 0.00 0.00 2.85
171 172 2.397597 GAAGAATCCTCTGCCCTCTCT 58.602 52.381 0.00 0.00 30.03 3.10
172 173 1.416030 GGAAGAATCCTCTGCCCTCTC 59.584 57.143 0.00 0.00 41.32 3.20
226 239 3.691575 CCCTTCCTTTCTCCTCCTTTTC 58.308 50.000 0.00 0.00 0.00 2.29
231 244 1.222113 CGCCCTTCCTTTCTCCTCC 59.778 63.158 0.00 0.00 0.00 4.30
232 245 1.450491 GCGCCCTTCCTTTCTCCTC 60.450 63.158 0.00 0.00 0.00 3.71
345 371 2.706071 GTGGAGGGAGGGAGGGAT 59.294 66.667 0.00 0.00 0.00 3.85
365 391 1.506262 CGTTGGAATTTGCCGGGAG 59.494 57.895 2.18 0.00 0.00 4.30
366 392 2.631580 GCGTTGGAATTTGCCGGGA 61.632 57.895 2.18 0.00 0.00 5.14
367 393 2.126110 GCGTTGGAATTTGCCGGG 60.126 61.111 2.18 0.00 0.00 5.73
368 394 2.126110 GGCGTTGGAATTTGCCGG 60.126 61.111 0.00 0.00 37.81 6.13
439 465 0.107800 GGTTAAGGCGGGGAGAGAAC 60.108 60.000 0.00 0.00 0.00 3.01
444 470 2.271173 GTGGGTTAAGGCGGGGAG 59.729 66.667 0.00 0.00 0.00 4.30
450 476 3.122971 GGCGACGTGGGTTAAGGC 61.123 66.667 0.00 0.00 0.00 4.35
480 536 0.905357 AAGAACGTGGAGGGATGGAG 59.095 55.000 0.00 0.00 0.00 3.86
481 537 0.613260 CAAGAACGTGGAGGGATGGA 59.387 55.000 0.00 0.00 0.00 3.41
482 538 0.392998 CCAAGAACGTGGAGGGATGG 60.393 60.000 0.71 0.00 41.65 3.51
483 539 1.026718 GCCAAGAACGTGGAGGGATG 61.027 60.000 10.64 0.00 41.65 3.51
484 540 1.299976 GCCAAGAACGTGGAGGGAT 59.700 57.895 10.64 0.00 41.65 3.85
485 541 2.747686 GCCAAGAACGTGGAGGGA 59.252 61.111 10.64 0.00 41.65 4.20
486 542 2.359975 GGCCAAGAACGTGGAGGG 60.360 66.667 10.64 0.00 41.65 4.30
487 543 2.742372 CGGCCAAGAACGTGGAGG 60.742 66.667 2.24 0.00 41.65 4.30
488 544 2.027625 GTCGGCCAAGAACGTGGAG 61.028 63.158 2.24 4.18 41.65 3.86
489 545 2.029964 GTCGGCCAAGAACGTGGA 59.970 61.111 2.24 0.00 41.65 4.02
490 546 3.047877 GGTCGGCCAAGAACGTGG 61.048 66.667 0.00 2.60 42.05 4.94
491 547 3.411351 CGGTCGGCCAAGAACGTG 61.411 66.667 6.96 0.00 45.37 4.49
538 595 0.456312 CCCGAATCTATCTACGCCGC 60.456 60.000 0.00 0.00 0.00 6.53
543 600 5.509332 GGAAGGAACACCCGAATCTATCTAC 60.509 48.000 0.00 0.00 40.87 2.59
599 656 1.475213 GGCCCTCCTAATCTGAAACCG 60.475 57.143 0.00 0.00 0.00 4.44
653 710 4.789123 AAATCCCCCGGCCGAACG 62.789 66.667 30.73 13.59 0.00 3.95
655 712 4.434354 CCAAATCCCCCGGCCGAA 62.434 66.667 30.73 9.56 0.00 4.30
661 718 3.802227 TATTCCACGCCAAATCCCCCG 62.802 57.143 0.00 0.00 0.00 5.73
662 719 0.106419 TATTCCACGCCAAATCCCCC 60.106 55.000 0.00 0.00 0.00 5.40
719 941 4.550577 TCAATACACACACACAGCTTTG 57.449 40.909 0.00 0.00 0.00 2.77
732 954 6.299604 CAAAACACTCACGAGATCAATACAC 58.700 40.000 0.00 0.00 0.00 2.90
733 955 5.107104 GCAAAACACTCACGAGATCAATACA 60.107 40.000 0.00 0.00 0.00 2.29
734 956 5.120830 AGCAAAACACTCACGAGATCAATAC 59.879 40.000 0.00 0.00 0.00 1.89
735 957 5.237815 AGCAAAACACTCACGAGATCAATA 58.762 37.500 0.00 0.00 0.00 1.90
746 968 6.479660 GGATCAATTCAAAAGCAAAACACTCA 59.520 34.615 0.00 0.00 0.00 3.41
781 1003 1.328680 CTCTGAATTCACCCGCAATCG 59.671 52.381 3.38 0.00 0.00 3.34
789 1036 2.611292 CCTCGATTGCTCTGAATTCACC 59.389 50.000 3.38 0.00 0.00 4.02
828 1075 0.332972 ACATTTGCTCCCCCTCTTCC 59.667 55.000 0.00 0.00 0.00 3.46
953 1200 3.881688 CAGTGGATGGATGGACTTGATTC 59.118 47.826 0.00 0.00 0.00 2.52
973 1220 1.293924 GACAAGATGGACCGATGCAG 58.706 55.000 0.00 0.00 0.00 4.41
989 1236 4.429212 CGTCCATGCCGACCGACA 62.429 66.667 0.00 0.00 0.00 4.35
1035 1282 3.793060 ACGGAGTGGGAGAACCTG 58.207 61.111 0.00 0.00 42.51 4.00
1146 1393 2.742372 CCGTGGAGCTTGAACCCG 60.742 66.667 0.00 0.00 0.00 5.28
1219 1466 1.587043 CTCAGCGACCTTGTCCTCGA 61.587 60.000 0.00 0.00 31.24 4.04
1284 1531 2.511373 TCGTGATGATGCACCGGC 60.511 61.111 0.00 0.00 41.68 6.13
1342 1589 1.008538 CGTTGGCAGAGTTGTTGGC 60.009 57.895 0.00 0.00 41.12 4.52
1467 1714 1.067749 CCTCATGCTCTGCTCCTCG 59.932 63.158 0.00 0.00 0.00 4.63
1569 1816 1.671901 GGAGGACCCTGAGCGAAGAG 61.672 65.000 0.00 0.00 0.00 2.85
1607 1854 2.364842 ACCTCGCCCTCAGCATCT 60.365 61.111 0.00 0.00 44.04 2.90
1828 2075 1.135083 CCAACTATCGAGCACCTTCGT 60.135 52.381 0.00 0.00 41.22 3.85
1829 2076 1.134367 TCCAACTATCGAGCACCTTCG 59.866 52.381 0.00 0.00 41.79 3.79
1842 2089 1.252215 TGCGATCCACCGTCCAACTA 61.252 55.000 0.00 0.00 0.00 2.24
1844 2091 1.635663 CTTGCGATCCACCGTCCAAC 61.636 60.000 0.00 0.00 0.00 3.77
1935 2182 0.107410 TGAACTTGACAGCAACGGGT 60.107 50.000 0.00 0.00 0.00 5.28
2085 2335 8.776376 ATTGCCTAAAACCAAATATTTCTGTG 57.224 30.769 0.00 0.00 0.00 3.66
2086 2336 9.791801 AAATTGCCTAAAACCAAATATTTCTGT 57.208 25.926 0.00 0.00 0.00 3.41
2127 2377 9.979578 TGTTTCAAGCTTGTTTGATAAATACAT 57.020 25.926 25.19 0.00 36.97 2.29
2128 2378 9.809096 TTGTTTCAAGCTTGTTTGATAAATACA 57.191 25.926 25.19 11.91 36.97 2.29
2190 2440 3.866910 CGCAAGGCTAAACGTAAGGATTA 59.133 43.478 0.00 0.00 46.39 1.75
2211 2461 2.898705 AGAAATCTAAGTCAGCTGGCG 58.101 47.619 13.66 0.00 0.00 5.69
2225 2475 4.806640 TTGCCATTTCAGGGAAGAAATC 57.193 40.909 0.00 0.00 44.16 2.17
2260 2510 2.289002 ACGCTAGGTACCGATAGAAACG 59.711 50.000 6.18 5.83 39.76 3.60
2266 2516 6.230472 TGAAGTATAACGCTAGGTACCGATA 58.770 40.000 6.18 0.00 0.00 2.92
2270 2520 4.582240 ACCTGAAGTATAACGCTAGGTACC 59.418 45.833 2.73 2.73 35.45 3.34
2285 2535 4.836825 CATGATGTAGGAACACCTGAAGT 58.163 43.478 0.00 0.00 38.78 3.01
2286 2536 3.624861 GCATGATGTAGGAACACCTGAAG 59.375 47.826 0.00 0.00 38.78 3.02
2288 2538 2.092968 GGCATGATGTAGGAACACCTGA 60.093 50.000 0.00 0.00 38.78 3.86
2302 2553 4.278669 CAGGACTACTACGTTAGGCATGAT 59.721 45.833 8.74 0.00 35.31 2.45
2396 2647 7.930325 TGGATCAATAATTGACTTTGTTTTGCA 59.070 29.630 0.00 0.00 43.48 4.08
2464 2715 4.379243 ACGCAGAAGACTGGCGGG 62.379 66.667 17.26 2.13 42.81 6.13
2638 2889 3.059597 CGTCAAATATGATGTTCTCCGGC 60.060 47.826 0.00 0.00 38.01 6.13
2710 2964 0.389817 CGTTCGCCAGAGGATCACAA 60.390 55.000 0.00 0.00 37.82 3.33
2716 2970 1.379977 AGGATCGTTCGCCAGAGGA 60.380 57.895 0.00 0.00 0.00 3.71
2734 2988 1.064463 GCCATCCATCTGAAAGTCCCA 60.064 52.381 0.00 0.00 33.76 4.37
2966 3472 2.433604 TCATGCTCTCTCCATCTGGAAC 59.566 50.000 0.00 0.00 44.91 3.62
2988 3494 9.466497 AGAAAATGTCCACATAGATGTACAATT 57.534 29.630 0.00 0.00 39.39 2.32
3064 3953 9.495754 GCACAGAATCAGAAATTTAGAATGTAC 57.504 33.333 0.00 0.00 0.00 2.90
3073 3962 7.230108 TCTCAGAAAGCACAGAATCAGAAATTT 59.770 33.333 0.00 0.00 0.00 1.82
3410 4300 7.704899 GGAAGAGAGAAGATTAGTTACAGAAGC 59.295 40.741 0.00 0.00 0.00 3.86
3531 4424 9.998106 AGAGAAGTACTTACTATGCTTTGAAAA 57.002 29.630 8.42 0.00 34.99 2.29
3537 4430 5.958987 ACCCAGAGAAGTACTTACTATGCTT 59.041 40.000 8.42 2.78 34.99 3.91
3577 4475 4.094739 GCACAAGCAACACAAAAGGAAAAT 59.905 37.500 0.00 0.00 41.58 1.82
3709 4610 0.117340 AGAGGCCCAGGTGTACTTCT 59.883 55.000 0.00 0.00 0.00 2.85
3723 4624 1.760029 CTAGGGAGTCCAGAAAGAGGC 59.240 57.143 12.30 0.00 34.83 4.70
3752 4654 5.247792 CAGATTATCCTGATGAGTGATGGGA 59.752 44.000 0.00 0.00 36.29 4.37
3754 4656 6.210984 TCTCAGATTATCCTGATGAGTGATGG 59.789 42.308 8.41 0.00 41.79 3.51
3828 4730 6.757010 AGGAGTACAATACATCGACAACAATC 59.243 38.462 0.00 0.00 0.00 2.67
3839 4741 7.813331 TCCACTCTACTAGGAGTACAATACAT 58.187 38.462 0.78 0.00 43.75 2.29
3927 4940 4.829968 CACTCTGTGAAGAGTTGATGGAT 58.170 43.478 5.66 0.00 45.94 3.41
3960 4973 2.298163 TGTCTGGTCCGGAAGTTAAGAC 59.702 50.000 5.23 15.01 34.52 3.01
3971 4984 1.336440 TGTTGCAAAATGTCTGGTCCG 59.664 47.619 0.00 0.00 0.00 4.79
3973 4986 6.215845 AGTTATTGTTGCAAAATGTCTGGTC 58.784 36.000 0.00 0.00 0.00 4.02
3992 5005 4.969484 ACTTGTCCGGTTTGAAGAGTTAT 58.031 39.130 0.00 0.00 0.00 1.89
4085 5098 8.615878 TGTGTACAATCTAAGTAGTTTGCATT 57.384 30.769 0.00 0.00 36.80 3.56
4098 5111 7.654116 TGTTTCGAAGTTGATGTGTACAATCTA 59.346 33.333 0.00 0.00 0.00 1.98
4101 5114 6.260050 ACTGTTTCGAAGTTGATGTGTACAAT 59.740 34.615 0.00 0.00 0.00 2.71
4119 5132 6.582636 TGATATGGATGTGGACTACTGTTTC 58.417 40.000 0.00 0.00 0.00 2.78
4152 5165 2.103263 AGCGAAACAAAGGAGAGTGACT 59.897 45.455 0.00 0.00 0.00 3.41
4210 5223 5.815581 TGGCAAACAACATAGTAGAGGAAT 58.184 37.500 0.00 0.00 0.00 3.01
4246 5259 7.062957 CCCTGGAAAAGAACTACATAATGGAT 58.937 38.462 0.00 0.00 0.00 3.41
4300 5362 7.010460 TCACACGTCATGCTAGAGAAAATATTG 59.990 37.037 0.00 0.00 0.00 1.90
4301 5363 7.010552 GTCACACGTCATGCTAGAGAAAATATT 59.989 37.037 0.00 0.00 0.00 1.28
4303 5365 5.805486 GTCACACGTCATGCTAGAGAAAATA 59.195 40.000 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.