Multiple sequence alignment - TraesCS1D01G284400

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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 TraesCS1D01G284400 chr1D 100.000 4720 0 0 1 4720 382724187 382719468 0.000000e+00 8717
1 TraesCS1D01G284400 chr1A 93.856 4199 190 33 563 4719 482771833 482767661 0.000000e+00 6263
2 TraesCS1D01G284400 chr1A 95.390 282 7 3 1 281 482777806 482777530 1.210000e-120 444
3 TraesCS1D01G284400 chr1A 91.870 246 19 1 305 550 482772363 482772119 4.520000e-90 342
4 TraesCS1D01G284400 chr1B 92.687 4075 216 42 563 4592 512634488 512630451 0.000000e+00 5799
5 TraesCS1D01G284400 chr1B 92.740 551 33 4 1 550 512635319 512634775 0.000000e+00 789
6 TraesCS1D01G284400 chr1B 87.905 463 28 18 3947 4386 641523151 641523608 1.950000e-143 520
7 TraesCS1D01G284400 chr1B 97.638 127 3 0 4594 4720 512624143 512624017 7.950000e-53 219
8 TraesCS1D01G284400 chr3B 91.091 449 27 8 3942 4386 70580335 70580774 3.140000e-166 595
9 TraesCS1D01G284400 chr3D 89.888 445 35 6 3938 4375 45064148 45064589 8.870000e-157 564
10 TraesCS1D01G284400 chr3D 90.385 416 23 7 3951 4365 36822835 36822436 8.990000e-147 531
11 TraesCS1D01G284400 chr3D 89.435 407 26 11 3951 4356 50658038 50658428 9.120000e-137 497
12 TraesCS1D01G284400 chr4D 89.498 438 30 9 3949 4375 30195485 30195053 1.490000e-149 540
13 TraesCS1D01G284400 chr4D 88.196 449 27 13 3958 4387 352755079 352755520 3.260000e-141 512
14 TraesCS1D01G284400 chr4A 86.929 482 28 19 3958 4414 112767615 112767144 4.210000e-140 508
15 TraesCS1D01G284400 chr4B 87.973 449 28 13 3958 4387 436311863 436312304 1.520000e-139 507
16 TraesCS1D01G284400 chr3A 89.104 413 31 10 3948 4356 605179769 605180171 7.050000e-138 501


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 TraesCS1D01G284400 chr1D 382719468 382724187 4719 True 8717.0 8717 100.0000 1 4720 1 chr1D.!!$R1 4719
1 TraesCS1D01G284400 chr1A 482767661 482772363 4702 True 3302.5 6263 92.8630 305 4719 2 chr1A.!!$R2 4414
2 TraesCS1D01G284400 chr1B 512630451 512635319 4868 True 3294.0 5799 92.7135 1 4592 2 chr1B.!!$R2 4591

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
590 868 0.967662 TCCGTTAATGTGACCCACGA 59.032 50.0 0.0 0.0 37.14 4.35 F
2504 2793 0.374758 CATCGGTGGATCTTGTTGCG 59.625 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 2823 0.179111 TCGGGTCGATGATGCTTGAC 60.179 55.0 0.0 0.0 0.0 3.18 R
3942 4287 0.107116 TCACCTCCTCCTAGACGCTC 60.107 60.0 0.0 0.0 0.0 5.03 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
57 58 0.974383 ACCGGGAGAATGAACTTCGT 59.026 50.000 6.32 0.00 38.98 3.85
106 107 1.817099 CAGCGTGCCCCTCTTGATC 60.817 63.158 0.00 0.00 0.00 2.92
165 166 2.937433 GCCTAAAGTCAGCCAGAACTCC 60.937 54.545 0.00 0.00 0.00 3.85
187 188 4.952335 CCAAAACAGAAGGGCTATGAGAAT 59.048 41.667 0.00 0.00 0.00 2.40
214 215 7.867445 AACGCACCAGTTTATCTTTATTTTG 57.133 32.000 0.00 0.00 0.00 2.44
300 302 9.612620 GAGACTAAAAACTTATGTTTCCACATG 57.387 33.333 7.15 0.00 44.70 3.21
345 347 7.907389 AGGATCACTGTGACTAGAAATTGTTA 58.093 34.615 13.50 0.00 0.00 2.41
366 368 9.990360 TTGTTACTGATGTGTTAAGAGTTCATA 57.010 29.630 0.00 0.00 0.00 2.15
403 405 2.294233 CAGGGTGGAGTTTGTCATGTTG 59.706 50.000 0.00 0.00 0.00 3.33
492 494 3.066760 CCTGAAACTTTCCATAATCCCGC 59.933 47.826 0.00 0.00 0.00 6.13
497 499 3.660865 ACTTTCCATAATCCCGCGATAC 58.339 45.455 8.23 0.00 0.00 2.24
550 552 3.186409 GCTCTGTTGTGCTGAATTCGTAA 59.814 43.478 0.04 0.00 0.00 3.18
551 553 4.142816 GCTCTGTTGTGCTGAATTCGTAAT 60.143 41.667 0.04 0.00 0.00 1.89
585 863 5.019785 ACCTCTATTCCGTTAATGTGACC 57.980 43.478 0.00 0.00 0.00 4.02
586 864 4.141779 ACCTCTATTCCGTTAATGTGACCC 60.142 45.833 0.00 0.00 0.00 4.46
587 865 4.141801 CCTCTATTCCGTTAATGTGACCCA 60.142 45.833 0.00 0.00 0.00 4.51
588 866 4.761975 TCTATTCCGTTAATGTGACCCAC 58.238 43.478 0.00 0.00 34.56 4.61
589 867 1.798283 TTCCGTTAATGTGACCCACG 58.202 50.000 0.00 0.00 37.14 4.94
590 868 0.967662 TCCGTTAATGTGACCCACGA 59.032 50.000 0.00 0.00 37.14 4.35
591 869 1.067425 TCCGTTAATGTGACCCACGAG 60.067 52.381 0.00 0.00 37.14 4.18
592 870 1.355971 CGTTAATGTGACCCACGAGG 58.644 55.000 0.00 0.00 43.78 4.63
643 921 3.914312 AGTACATTGACCTGAGACGTTG 58.086 45.455 0.00 0.00 0.00 4.10
647 925 4.495422 ACATTGACCTGAGACGTTGATAC 58.505 43.478 0.00 0.00 0.00 2.24
672 950 7.041235 ACGTATTCGGTAGAAAACATCCAAAAA 60.041 33.333 0.00 0.00 40.15 1.94
682 960 7.381323 AGAAAACATCCAAAAATTCAGGCTAG 58.619 34.615 0.00 0.00 0.00 3.42
846 1125 2.233271 CTCAGAAACATGTGGCCAGTT 58.767 47.619 5.11 3.85 0.00 3.16
1208 1487 5.352284 AGTCTCAACAGTATAGGATTTGCG 58.648 41.667 0.00 0.00 0.00 4.85
1281 1560 1.064060 GGCGTCGAAATGATCCTTTGG 59.936 52.381 0.26 0.15 0.00 3.28
1485 1764 5.394738 AGGGAAAGGTAGGGAAAAAGAAAG 58.605 41.667 0.00 0.00 0.00 2.62
1561 1840 2.293677 CTGCTTGATCATGCCCATCTTC 59.706 50.000 25.74 2.25 0.00 2.87
1630 1910 7.014038 AGCCTCCATTATTCATTTCATCTTGTC 59.986 37.037 0.00 0.00 0.00 3.18
1734 2014 6.402222 ACCTTCATGTAAAGCAGACTCTAAG 58.598 40.000 0.00 0.00 0.00 2.18
1797 2077 0.950555 TCACATCGCCAGTGAGCAAC 60.951 55.000 0.00 0.00 40.80 4.17
1874 2160 6.928492 TCGATATACTGCATTTTCATGTAGCA 59.072 34.615 0.72 0.00 44.76 3.49
1878 2164 4.801891 ACTGCATTTTCATGTAGCAAGTG 58.198 39.130 0.72 0.00 44.76 3.16
1915 2201 4.813750 AAATTCAGGGCCTTCAAATGAG 57.186 40.909 1.32 0.00 0.00 2.90
1948 2235 7.985634 TTTTTCAAATGTAGTTGACTTCAGC 57.014 32.000 0.00 0.00 37.24 4.26
1989 2276 6.716628 TCATTCTTCTCCAGTTTGTTATTGCT 59.283 34.615 0.00 0.00 0.00 3.91
2163 2450 2.743636 TGTCTCCGGTCACAGAAATC 57.256 50.000 0.00 0.00 0.00 2.17
2179 2466 2.309528 AATCGGCGACATTTCAGCTA 57.690 45.000 13.76 0.00 0.00 3.32
2209 2496 5.597813 CACAGTGACAGTGGTAAAAGATC 57.402 43.478 14.70 0.00 33.43 2.75
2211 2498 5.760253 CACAGTGACAGTGGTAAAAGATCTT 59.240 40.000 14.70 0.88 33.43 2.40
2212 2499 6.929049 CACAGTGACAGTGGTAAAAGATCTTA 59.071 38.462 8.75 0.00 33.43 2.10
2213 2500 7.604164 CACAGTGACAGTGGTAAAAGATCTTAT 59.396 37.037 8.75 0.00 33.43 1.73
2214 2501 7.604164 ACAGTGACAGTGGTAAAAGATCTTATG 59.396 37.037 8.75 2.49 0.00 1.90
2215 2502 7.065085 CAGTGACAGTGGTAAAAGATCTTATGG 59.935 40.741 8.75 0.00 0.00 2.74
2220 2507 7.148018 ACAGTGGTAAAAGATCTTATGGCAATG 60.148 37.037 8.75 6.47 0.00 2.82
2221 2508 6.322201 AGTGGTAAAAGATCTTATGGCAATGG 59.678 38.462 8.75 0.00 0.00 3.16
2243 2530 2.936498 CCTTTGTTGCAGGGACTATACG 59.064 50.000 0.00 0.00 36.02 3.06
2256 2544 7.476667 CAGGGACTATACGATACTGATTGATC 58.523 42.308 0.00 0.00 36.02 2.92
2273 2561 8.777865 TGATTGATCAGGTTTGTAGTTCTTAG 57.222 34.615 0.00 0.00 32.11 2.18
2276 2564 7.962964 TGATCAGGTTTGTAGTTCTTAGTTG 57.037 36.000 0.00 0.00 0.00 3.16
2277 2565 7.506114 TGATCAGGTTTGTAGTTCTTAGTTGT 58.494 34.615 0.00 0.00 0.00 3.32
2278 2566 7.656137 TGATCAGGTTTGTAGTTCTTAGTTGTC 59.344 37.037 0.00 0.00 0.00 3.18
2280 2568 7.506114 TCAGGTTTGTAGTTCTTAGTTGTCAT 58.494 34.615 0.00 0.00 0.00 3.06
2282 2570 9.268268 CAGGTTTGTAGTTCTTAGTTGTCATAA 57.732 33.333 0.00 0.00 0.00 1.90
2415 2704 1.406614 CCAAGCCCAGTGATCTCAGAC 60.407 57.143 0.00 0.00 0.00 3.51
2471 2760 1.547901 GGTGGGGTGCTTAAAAGAGCT 60.548 52.381 0.00 0.00 43.11 4.09
2501 2790 0.620556 AGGCATCGGTGGATCTTGTT 59.379 50.000 0.00 0.00 0.00 2.83
2504 2793 0.374758 CATCGGTGGATCTTGTTGCG 59.625 55.000 0.00 0.00 0.00 4.85
2534 2823 4.280494 CGCCCCGTATCCGTCCTG 62.280 72.222 0.00 0.00 0.00 3.86
2539 2828 0.102481 CCCGTATCCGTCCTGTCAAG 59.898 60.000 0.00 0.00 0.00 3.02
2693 2982 7.946207 TGTGAACTTATTGCCTGTTTTATTCA 58.054 30.769 0.00 0.00 0.00 2.57
2700 2989 9.859427 CTTATTGCCTGTTTTATTCAGATTTGA 57.141 29.630 0.00 0.00 35.20 2.69
2718 3021 8.024865 CAGATTTGAATTGTACTGCTTGAATCA 58.975 33.333 0.00 0.00 0.00 2.57
2742 3045 8.156820 TCACTCTCCAAGATCAAACAGATAAAA 58.843 33.333 0.00 0.00 37.00 1.52
2951 3260 0.745845 ATGGAACTGAGCACATCGCC 60.746 55.000 0.00 0.00 44.04 5.54
2957 3266 4.166011 GAGCACATCGCCGTTGCC 62.166 66.667 4.86 0.00 44.04 4.52
2965 3274 0.606944 ATCGCCGTTGCCAAGGTAAA 60.607 50.000 0.00 0.00 0.00 2.01
3001 3310 3.362237 GTGTTTCTCTGACAGAACGATCG 59.638 47.826 14.88 14.88 41.13 3.69
3026 3335 1.569479 GAAACCAGTGAGCCACTCGC 61.569 60.000 5.02 0.00 43.43 5.03
3060 3388 3.093717 TCAATCTCCGGCGATCTTTAC 57.906 47.619 9.30 0.00 0.00 2.01
3061 3389 2.429250 TCAATCTCCGGCGATCTTTACA 59.571 45.455 9.30 0.00 0.00 2.41
3067 3395 2.028839 TCCGGCGATCTTTACAGTTTGA 60.029 45.455 9.30 0.00 0.00 2.69
3092 3420 1.758440 ATGTGCAGGGCGATATCGGT 61.758 55.000 25.51 0.00 40.23 4.69
3215 3543 3.082579 GCTGATCGAGAAGGCCGGT 62.083 63.158 1.90 0.00 0.00 5.28
3371 3699 4.246206 CGCGAGTACGGCATCGGA 62.246 66.667 0.00 0.00 41.39 4.55
3392 3720 3.368248 AGCCCAGGTACGTACTTGAATA 58.632 45.455 32.31 0.00 35.55 1.75
3394 3722 3.131755 GCCCAGGTACGTACTTGAATACT 59.868 47.826 32.31 14.49 35.55 2.12
3395 3723 4.339247 GCCCAGGTACGTACTTGAATACTA 59.661 45.833 32.31 0.00 35.55 1.82
3396 3724 5.163519 GCCCAGGTACGTACTTGAATACTAA 60.164 44.000 32.31 0.00 35.55 2.24
3454 3788 4.665451 TGTCTTGATGATTGATGGTGGTT 58.335 39.130 0.00 0.00 0.00 3.67
3466 3801 3.264193 TGATGGTGGTTATCTTGCTGTCT 59.736 43.478 0.00 0.00 0.00 3.41
3467 3802 4.469586 TGATGGTGGTTATCTTGCTGTCTA 59.530 41.667 0.00 0.00 0.00 2.59
3479 3814 7.789273 ATCTTGCTGTCTATTTCAGATTCTG 57.211 36.000 7.38 7.38 35.17 3.02
3742 4077 1.879737 TACACCCACCACACGATCCG 61.880 60.000 0.00 0.00 0.00 4.18
3745 4080 2.125147 CCACCACACGATCCGCAT 60.125 61.111 0.00 0.00 0.00 4.73
3891 4233 1.108132 AACTACGAGCCTCGATCCCC 61.108 60.000 22.80 0.00 43.74 4.81
3933 4278 1.716760 CGACGAGACGAGAGAAGGG 59.283 63.158 0.00 0.00 35.09 3.95
3934 4279 1.430228 GACGAGACGAGAGAAGGGC 59.570 63.158 0.00 0.00 0.00 5.19
3942 4287 4.806339 AGAGAAGGGCGGGGGAGG 62.806 72.222 0.00 0.00 0.00 4.30
4432 4790 2.527875 GGCGGGGAGGAGGATGAT 60.528 66.667 0.00 0.00 0.00 2.45
4502 4860 2.561478 TTGGATTTATAGAGGGGCGC 57.439 50.000 0.00 0.00 0.00 6.53
4533 4891 2.431047 ATTGGTGGAGGGGGTGAGGA 62.431 60.000 0.00 0.00 0.00 3.71
4567 4925 0.250513 GTGGAAGGATCTCAGGCGTT 59.749 55.000 0.00 0.00 0.00 4.84
4592 4950 0.762418 TGGTTGACGGTGAGGATTGT 59.238 50.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 2.281484 GTCGCAGGTTTGGCCTCA 60.281 61.111 3.32 0.00 46.96 3.86
121 122 2.642254 CCCACTGTTGGCTGGCATG 61.642 63.158 4.22 0.00 42.35 4.06
122 123 2.283388 CCCACTGTTGGCTGGCAT 60.283 61.111 4.22 0.00 42.35 4.40
153 154 2.575532 TCTGTTTTGGAGTTCTGGCTG 58.424 47.619 0.00 0.00 0.00 4.85
165 166 5.649395 TGATTCTCATAGCCCTTCTGTTTTG 59.351 40.000 0.00 0.00 0.00 2.44
187 188 6.811253 ATAAAGATAAACTGGTGCGTTTGA 57.189 33.333 0.00 0.00 37.63 2.69
192 193 6.861055 ACACAAAATAAAGATAAACTGGTGCG 59.139 34.615 0.00 0.00 0.00 5.34
243 245 7.550906 AGAATGGATCTCCTAATTAATTAGCGC 59.449 37.037 24.19 0.00 38.69 5.92
244 246 8.877779 CAGAATGGATCTCCTAATTAATTAGCG 58.122 37.037 24.19 18.30 36.35 4.26
327 329 8.438513 CACATCAGTAACAATTTCTAGTCACAG 58.561 37.037 0.00 0.00 0.00 3.66
366 368 4.443457 CCACCCTGTCAATGATCGATAAGT 60.443 45.833 0.00 0.00 0.00 2.24
371 373 1.482182 CTCCACCCTGTCAATGATCGA 59.518 52.381 0.00 0.00 0.00 3.59
403 405 3.868077 GGCCACATCGAAGCTATGATATC 59.132 47.826 0.00 0.00 0.00 1.63
435 437 1.652563 AAAAAGCTTCGTCGGGCAC 59.347 52.632 0.00 0.00 0.00 5.01
459 461 4.508584 GGAAAGTTTCAGGATACCCAAGGT 60.509 45.833 17.16 0.00 40.16 3.50
492 494 2.348872 GCCACATTGCATCTTCGTATCG 60.349 50.000 0.00 0.00 0.00 2.92
497 499 0.742505 ATGGCCACATTGCATCTTCG 59.257 50.000 8.16 0.00 32.00 3.79
550 552 9.955102 AACGGAATAGAGGTTAAAACTTCTTAT 57.045 29.630 12.05 3.14 41.91 1.73
573 851 1.355971 CCTCGTGGGTCACATTAACG 58.644 55.000 0.00 0.00 33.40 3.18
592 870 3.264897 ATGAAGCATCGTCGCGGC 61.265 61.111 6.13 1.93 36.85 6.53
619 897 5.916661 ACGTCTCAGGTCAATGTACTTAT 57.083 39.130 0.00 0.00 0.00 1.73
643 921 6.919662 TGGATGTTTTCTACCGAATACGTATC 59.080 38.462 8.86 2.01 34.90 2.24
647 925 6.411630 TTTGGATGTTTTCTACCGAATACG 57.588 37.500 0.00 0.00 34.90 3.06
656 934 7.301868 AGCCTGAATTTTTGGATGTTTTCTA 57.698 32.000 0.00 0.00 0.00 2.10
846 1125 1.599518 CCACGCAAGGTGTAGCCAA 60.600 57.895 0.00 0.00 45.52 4.52
928 1207 9.293404 TGTTTATATACCTCTATCGCTTGTACT 57.707 33.333 0.00 0.00 0.00 2.73
960 1239 2.488952 GATCTTCGGAAATCAGCTCCC 58.511 52.381 0.00 0.00 0.00 4.30
986 1265 3.233980 CCATCTGGCGATCCCCGA 61.234 66.667 0.00 0.00 41.76 5.14
1208 1487 6.357367 TCTTAAGCATCCCTTTCTGATAACC 58.643 40.000 0.00 0.00 34.95 2.85
1281 1560 1.087501 GGCCCATTCTTGTTCTCGTC 58.912 55.000 0.00 0.00 0.00 4.20
1316 1595 1.671379 GGAAGCACTGGACCCGTTC 60.671 63.158 0.00 0.00 0.00 3.95
1388 1667 4.530857 GGGTCACCCTCGGCATCG 62.531 72.222 5.22 0.00 41.34 3.84
1485 1764 7.875971 ACTATTTGTGTTCAGAAAATCAGGAC 58.124 34.615 0.00 0.00 0.00 3.85
1561 1840 5.004726 GCATATCTTTAAGCACCGCAAAAAG 59.995 40.000 6.69 6.69 35.42 2.27
1630 1910 6.036844 AGTGTGATTCATTCATCTTGTCATCG 59.963 38.462 0.00 0.00 36.54 3.84
1695 1975 7.672983 ACATGAAGGTACTCAATTACTTGTG 57.327 36.000 0.00 0.00 38.49 3.33
1698 1978 8.947115 GCTTTACATGAAGGTACTCAATTACTT 58.053 33.333 0.00 0.00 38.49 2.24
1734 2014 3.406764 CCTTGATAGTCCAAGCATAGCC 58.593 50.000 0.00 0.00 41.53 3.93
1826 2106 9.685828 TCGAATATCACGATATTGACATTGTTA 57.314 29.630 15.31 0.00 42.32 2.41
1874 2160 7.495279 TGAATTTTGAAGCAAGCAAATACACTT 59.505 29.630 0.00 0.00 35.41 3.16
1878 2164 6.128472 CCCTGAATTTTGAAGCAAGCAAATAC 60.128 38.462 0.00 0.00 35.41 1.89
1989 2276 2.753452 GTCACCCTTCTCGTCATCTACA 59.247 50.000 0.00 0.00 0.00 2.74
2163 2450 0.647410 CAGTAGCTGAAATGTCGCCG 59.353 55.000 0.00 0.00 32.44 6.46
2220 2507 0.251165 TAGTCCCTGCAACAAAGGCC 60.251 55.000 0.00 0.00 33.07 5.19
2221 2508 1.839424 ATAGTCCCTGCAACAAAGGC 58.161 50.000 0.00 0.00 33.07 4.35
2256 2544 7.730364 ATGACAACTAAGAACTACAAACCTG 57.270 36.000 0.00 0.00 0.00 4.00
2453 2742 1.547675 CCAGCTCTTTTAAGCACCCCA 60.548 52.381 0.00 0.00 45.00 4.96
2456 2745 0.528017 GCCCAGCTCTTTTAAGCACC 59.472 55.000 0.00 0.00 45.00 5.01
2462 2751 0.605319 CGGTGTGCCCAGCTCTTTTA 60.605 55.000 0.00 0.00 36.93 1.52
2471 2760 4.408821 GATGCCTCGGTGTGCCCA 62.409 66.667 0.00 0.00 0.00 5.36
2528 2817 0.926155 CGATGATGCTTGACAGGACG 59.074 55.000 0.00 0.00 0.00 4.79
2534 2823 0.179111 TCGGGTCGATGATGCTTGAC 60.179 55.000 0.00 0.00 0.00 3.18
2539 2828 0.876342 GTCCTTCGGGTCGATGATGC 60.876 60.000 0.00 0.00 35.23 3.91
2693 2982 8.025445 GTGATTCAAGCAGTACAATTCAAATCT 58.975 33.333 0.00 0.00 0.00 2.40
2700 2989 5.645497 GGAGAGTGATTCAAGCAGTACAATT 59.355 40.000 0.00 0.00 0.00 2.32
2703 3006 3.578282 TGGAGAGTGATTCAAGCAGTACA 59.422 43.478 0.00 0.00 0.00 2.90
2718 3021 8.378565 TCTTTTATCTGTTTGATCTTGGAGAGT 58.621 33.333 0.00 0.00 36.65 3.24
2742 3045 6.158695 TCCTAACCTAGCCATTTCTCATTTCT 59.841 38.462 0.00 0.00 0.00 2.52
2752 3055 8.669571 ACATGTAATTATCCTAACCTAGCCATT 58.330 33.333 0.00 0.00 0.00 3.16
2753 3056 8.219660 ACATGTAATTATCCTAACCTAGCCAT 57.780 34.615 0.00 0.00 0.00 4.40
2787 3091 7.552687 TGCTGAAATGAGATCGTATAAAAAGGT 59.447 33.333 0.00 0.00 0.00 3.50
2951 3260 3.866883 ATTCCATTTACCTTGGCAACG 57.133 42.857 0.00 0.00 42.51 4.10
2957 3266 7.209475 ACACAACAAGAATTCCATTTACCTTG 58.791 34.615 0.65 0.00 37.57 3.61
2965 3274 6.547141 TCAGAGAAACACAACAAGAATTCCAT 59.453 34.615 0.65 0.00 0.00 3.41
3001 3310 0.957888 GGCTCACTGGTTTCTGCTCC 60.958 60.000 0.00 0.00 0.00 4.70
3026 3335 3.423571 GAGATTGAATCGCACAAGCAAG 58.576 45.455 3.99 0.00 42.27 4.01
3030 3339 1.328680 CCGGAGATTGAATCGCACAAG 59.671 52.381 10.93 0.00 0.00 3.16
3092 3420 0.247460 CCAGCACGTCTTCTCCATCA 59.753 55.000 0.00 0.00 0.00 3.07
3188 3516 2.646445 CTCGATCAGCTGCATCGCG 61.646 63.158 28.53 23.26 42.42 5.87
3284 3612 1.523758 CTTGGTCCTGCAGGTTGTAC 58.476 55.000 31.58 21.67 36.34 2.90
3371 3699 1.636148 TTCAAGTACGTACCTGGGCT 58.364 50.000 21.80 0.00 0.00 5.19
3392 3720 6.959639 ATGTTAAATCCGCCATGAATTAGT 57.040 33.333 0.00 0.00 0.00 2.24
3394 3722 7.581213 AGAATGTTAAATCCGCCATGAATTA 57.419 32.000 0.00 0.00 0.00 1.40
3395 3723 6.469782 AGAATGTTAAATCCGCCATGAATT 57.530 33.333 0.00 0.00 0.00 2.17
3396 3724 6.275335 CAAGAATGTTAAATCCGCCATGAAT 58.725 36.000 0.00 0.00 0.00 2.57
3454 3788 8.699130 TCAGAATCTGAAATAGACAGCAAGATA 58.301 33.333 10.99 0.00 37.57 1.98
3466 3801 6.359804 CCAATGTCCCTCAGAATCTGAAATA 58.640 40.000 14.44 2.17 40.18 1.40
3467 3802 5.198965 CCAATGTCCCTCAGAATCTGAAAT 58.801 41.667 14.44 1.12 40.18 2.17
3479 3814 3.499737 CGCACGCCAATGTCCCTC 61.500 66.667 0.00 0.00 0.00 4.30
3891 4233 3.559657 GATGATCGTCTCGGCCCCG 62.560 68.421 7.73 0.00 41.35 5.73
3898 4240 1.253034 GTCGCGTTTGATGATCGTCTC 59.747 52.381 15.81 6.01 0.00 3.36
3934 4279 2.907917 CTAGACGCTCCTCCCCCG 60.908 72.222 0.00 0.00 0.00 5.73
3939 4284 0.536460 CCTCCTCCTAGACGCTCCTC 60.536 65.000 0.00 0.00 0.00 3.71
3940 4285 1.283381 ACCTCCTCCTAGACGCTCCT 61.283 60.000 0.00 0.00 0.00 3.69
3942 4287 0.107116 TCACCTCCTCCTAGACGCTC 60.107 60.000 0.00 0.00 0.00 5.03
4429 4787 0.972134 GCCCTCTCCGATCATCATCA 59.028 55.000 0.00 0.00 0.00 3.07
4432 4790 2.861101 GCGCCCTCTCCGATCATCA 61.861 63.158 0.00 0.00 0.00 3.07
4509 4867 0.850883 ACCCCCTCCACCAATCACAT 60.851 55.000 0.00 0.00 0.00 3.21
4533 4891 4.129737 CACCTCACCGATCCGCGT 62.130 66.667 4.92 0.00 38.67 6.01
4567 4925 0.038618 CTCACCGTCAACCACATCGA 60.039 55.000 0.00 0.00 0.00 3.59
4592 4950 1.180456 TAACTCTTCCCCACGCGTCA 61.180 55.000 9.86 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.