Multiple sequence alignment - TraesCS5A01G082700

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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 TraesCS5A01G082700 chr5A 100.000 2677 0 0 1 2677 107446975 107444299 0.000000e+00 4944
1 TraesCS5A01G082700 chr5A 95.000 80 3 1 2279 2358 107444623 107444545 1.010000e-24 124
2 TraesCS5A01G082700 chr5A 95.000 80 3 1 2353 2431 107444697 107444618 1.010000e-24 124
3 TraesCS5A01G082700 chr5B 93.502 1739 76 18 636 2358 114125454 114123737 0.000000e+00 2551
4 TraesCS5A01G082700 chr5B 88.672 256 27 2 2353 2606 114123817 114123562 7.200000e-81 311
5 TraesCS5A01G082700 chr5D 96.203 1317 33 6 636 1949 104481026 104479724 0.000000e+00 2139
6 TraesCS5A01G082700 chr5D 87.792 385 36 5 1979 2354 104479728 104479346 8.800000e-120 440
7 TraesCS5A01G082700 chr5D 83.025 324 32 5 2356 2677 104479418 104479116 3.400000e-69 272
8 TraesCS5A01G082700 chr4B 99.371 636 4 0 1 636 411540868 411541503 0.000000e+00 1153
9 TraesCS5A01G082700 chr4A 99.371 636 4 0 1 636 210989060 210989695 0.000000e+00 1153
10 TraesCS5A01G082700 chr4A 99.214 636 5 0 1 636 637928788 637929423 0.000000e+00 1147
11 TraesCS5A01G082700 chr2B 99.215 637 5 0 1 637 593645689 593646325 0.000000e+00 1149
12 TraesCS5A01G082700 chr3B 99.060 638 6 0 1 638 592657223 592657860 0.000000e+00 1146
13 TraesCS5A01G082700 chrUn 99.058 637 6 0 1 637 128498584 128499220 0.000000e+00 1144
14 TraesCS5A01G082700 chrUn 99.057 636 6 0 1 636 49779571 49778936 0.000000e+00 1142
15 TraesCS5A01G082700 chr1A 99.058 637 6 0 1 637 203812398 203811762 0.000000e+00 1144
16 TraesCS5A01G082700 chr7A 98.905 639 7 0 1 639 564613340 564612702 0.000000e+00 1142


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 TraesCS5A01G082700 chr5A 107444299 107446975 2676 True 1730.666667 4944 96.666667 1 2677 3 chr5A.!!$R1 2676
1 TraesCS5A01G082700 chr5B 114123562 114125454 1892 True 1431.000000 2551 91.087000 636 2606 2 chr5B.!!$R1 1970
2 TraesCS5A01G082700 chr5D 104479116 104481026 1910 True 950.333333 2139 89.006667 636 2677 3 chr5D.!!$R1 2041
3 TraesCS5A01G082700 chr4B 411540868 411541503 635 False 1153.000000 1153 99.371000 1 636 1 chr4B.!!$F1 635
4 TraesCS5A01G082700 chr4A 210989060 210989695 635 False 1153.000000 1153 99.371000 1 636 1 chr4A.!!$F1 635
5 TraesCS5A01G082700 chr4A 637928788 637929423 635 False 1147.000000 1147 99.214000 1 636 1 chr4A.!!$F2 635
6 TraesCS5A01G082700 chr2B 593645689 593646325 636 False 1149.000000 1149 99.215000 1 637 1 chr2B.!!$F1 636
7 TraesCS5A01G082700 chr3B 592657223 592657860 637 False 1146.000000 1146 99.060000 1 638 1 chr3B.!!$F1 637
8 TraesCS5A01G082700 chrUn 128498584 128499220 636 False 1144.000000 1144 99.058000 1 637 1 chrUn.!!$F1 636
9 TraesCS5A01G082700 chrUn 49778936 49779571 635 True 1142.000000 1142 99.057000 1 636 1 chrUn.!!$R1 635
10 TraesCS5A01G082700 chr1A 203811762 203812398 636 True 1144.000000 1144 99.058000 1 637 1 chr1A.!!$R1 636
11 TraesCS5A01G082700 chr7A 564612702 564613340 638 True 1142.000000 1142 98.905000 1 639 1 chr7A.!!$R1 638

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
93 94 0.904865 TCCTTCTGGAGTGCGGTGAT 60.905 55.0 0.0 0.0 37.46 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1920 0.106708 AACACACTCGTCATGCACCT 59.893 50.0 0.0 0.0 0.0 4.0 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
93 94 0.904865 TCCTTCTGGAGTGCGGTGAT 60.905 55.000 0.00 0.00 37.46 3.06
738 739 1.081892 CATCACAAGCTCCGAACAGG 58.918 55.000 0.00 0.00 42.97 4.00
864 865 4.736896 GTGTGGGTCCGACGCTCC 62.737 72.222 15.82 7.75 31.67 4.70
912 913 2.044352 TCGCCTCTCCCGTGATCA 60.044 61.111 0.00 0.00 0.00 2.92
1029 1030 1.883084 GCTGCGTAACGGGGATCAG 60.883 63.158 0.00 0.00 0.00 2.90
1030 1031 1.227263 CTGCGTAACGGGGATCAGG 60.227 63.158 0.00 0.00 0.00 3.86
1031 1032 2.588034 GCGTAACGGGGATCAGGC 60.588 66.667 0.00 0.00 0.00 4.85
1032 1033 2.279252 CGTAACGGGGATCAGGCG 60.279 66.667 0.00 0.00 0.00 5.52
1033 1034 2.108362 GTAACGGGGATCAGGCGG 59.892 66.667 0.00 0.00 0.00 6.13
1034 1035 3.857038 TAACGGGGATCAGGCGGC 61.857 66.667 0.00 0.00 0.00 6.53
1370 1377 1.410517 AGTTGCATCTGGTCGATCGAT 59.589 47.619 22.50 0.00 0.00 3.59
1386 1393 2.687370 TCGATCACACACATGGAGTTG 58.313 47.619 0.00 0.00 0.00 3.16
1398 1405 7.286775 ACACACATGGAGTTGGTTAACTAATTT 59.713 33.333 7.72 0.00 46.79 1.82
1409 1416 7.193377 TGGTTAACTAATTTCGGAGTTGTTC 57.807 36.000 5.42 0.00 36.58 3.18
1413 1420 9.326339 GTTAACTAATTTCGGAGTTGTTCATTC 57.674 33.333 0.00 0.00 36.58 2.67
1460 1467 4.794648 GGGTACATGGCGCTGGCA 62.795 66.667 7.64 7.20 43.52 4.92
1705 1718 1.697394 TGGGGCCATGGAGCATACT 60.697 57.895 18.40 0.00 0.00 2.12
1706 1719 1.288508 TGGGGCCATGGAGCATACTT 61.289 55.000 18.40 0.00 0.00 2.24
1772 1785 2.468831 CTAGCCAGAGCACTTCGATTC 58.531 52.381 0.00 0.00 43.56 2.52
1825 1838 7.169308 GTGATTATTACAGTATGCACTACGCTT 59.831 37.037 0.00 0.00 42.53 4.68
1902 1920 5.245301 CGGGATATACCAGTGAAACATAGGA 59.755 44.000 4.43 0.00 41.20 2.94
1917 1935 0.817654 TAGGAGGTGCATGACGAGTG 59.182 55.000 0.00 0.00 0.00 3.51
1948 1966 6.713762 TCATTTTGGGTTTGCTATATCTGG 57.286 37.500 0.00 0.00 0.00 3.86
2016 2034 2.615912 CGAGAATTTGGGGAGCTTCATC 59.384 50.000 0.00 0.00 0.00 2.92
2018 2036 1.678101 GAATTTGGGGAGCTTCATCGG 59.322 52.381 0.00 0.00 0.00 4.18
2023 2043 1.843851 TGGGGAGCTTCATCGGTAATT 59.156 47.619 0.00 0.00 0.00 1.40
2085 2105 2.590575 AACGTTCGTGTGGCCAGG 60.591 61.111 5.11 0.00 0.00 4.45
2087 2107 2.280524 CGTTCGTGTGGCCAGGAA 60.281 61.111 5.11 7.81 41.72 3.36
2088 2108 1.890041 CGTTCGTGTGGCCAGGAAA 60.890 57.895 5.11 0.00 44.46 3.13
2090 2110 1.527380 TTCGTGTGGCCAGGAAACC 60.527 57.895 5.11 0.00 41.20 3.27
2101 2127 1.336755 CCAGGAAACCAACAAGGAACG 59.663 52.381 0.00 0.00 41.22 3.95
2176 2203 8.736244 TGTCTAACAGAAAAACTAAAACTTGCT 58.264 29.630 0.00 0.00 0.00 3.91
2196 2223 8.055181 ACTTGCTGATTTTCCCTCTATTTCATA 58.945 33.333 0.00 0.00 0.00 2.15
2232 2259 7.914871 TGCCACAATTGATCAAGAATTATAACG 59.085 33.333 13.59 0.00 0.00 3.18
2239 2266 7.946655 TGATCAAGAATTATAACGCGAAGAT 57.053 32.000 15.93 5.15 0.00 2.40
2242 2269 7.764695 TCAAGAATTATAACGCGAAGATCAA 57.235 32.000 15.93 0.00 0.00 2.57
2284 2311 0.238289 CCACTTTCATCACCACGTGC 59.762 55.000 10.91 0.00 32.98 5.34
2290 2317 0.388520 TCATCACCACGTGCGAGAAG 60.389 55.000 10.91 4.62 32.98 2.85
2302 2329 2.301577 GCGAGAAGCCTCATAGTTGT 57.698 50.000 0.00 0.00 39.39 3.32
2303 2330 1.929836 GCGAGAAGCCTCATAGTTGTG 59.070 52.381 0.00 0.00 39.39 3.33
2304 2331 1.929836 CGAGAAGCCTCATAGTTGTGC 59.070 52.381 0.00 0.00 39.39 4.57
2305 2332 2.675032 CGAGAAGCCTCATAGTTGTGCA 60.675 50.000 0.00 0.00 39.39 4.57
2306 2333 3.338249 GAGAAGCCTCATAGTTGTGCAA 58.662 45.455 0.00 0.00 39.24 4.08
2307 2334 3.753272 GAGAAGCCTCATAGTTGTGCAAA 59.247 43.478 0.00 0.00 39.24 3.68
2308 2335 4.144297 AGAAGCCTCATAGTTGTGCAAAA 58.856 39.130 0.00 0.00 0.00 2.44
2309 2336 4.584325 AGAAGCCTCATAGTTGTGCAAAAA 59.416 37.500 0.00 0.00 0.00 1.94
2310 2337 5.244626 AGAAGCCTCATAGTTGTGCAAAAAT 59.755 36.000 0.00 0.00 0.00 1.82
2311 2338 6.434028 AGAAGCCTCATAGTTGTGCAAAAATA 59.566 34.615 0.00 0.00 0.00 1.40
2312 2339 6.588719 AGCCTCATAGTTGTGCAAAAATAA 57.411 33.333 0.12 0.00 0.00 1.40
2313 2340 6.389906 AGCCTCATAGTTGTGCAAAAATAAC 58.610 36.000 0.12 0.00 0.00 1.89
2314 2341 5.286082 GCCTCATAGTTGTGCAAAAATAACG 59.714 40.000 0.12 0.00 0.00 3.18
2315 2342 5.286082 CCTCATAGTTGTGCAAAAATAACGC 59.714 40.000 0.12 0.00 0.00 4.84
2316 2343 5.157781 TCATAGTTGTGCAAAAATAACGCC 58.842 37.500 0.12 0.00 0.00 5.68
2317 2344 3.726291 AGTTGTGCAAAAATAACGCCT 57.274 38.095 0.00 0.00 0.00 5.52
2318 2345 4.053469 AGTTGTGCAAAAATAACGCCTT 57.947 36.364 0.00 0.00 0.00 4.35
2319 2346 4.438148 AGTTGTGCAAAAATAACGCCTTT 58.562 34.783 0.00 0.00 0.00 3.11
2320 2347 4.873259 AGTTGTGCAAAAATAACGCCTTTT 59.127 33.333 0.00 0.00 0.00 2.27
2321 2348 5.006261 AGTTGTGCAAAAATAACGCCTTTTC 59.994 36.000 0.00 0.00 0.00 2.29
2322 2349 3.487574 TGTGCAAAAATAACGCCTTTTCG 59.512 39.130 0.00 0.00 0.00 3.46
2323 2350 3.731717 GTGCAAAAATAACGCCTTTTCGA 59.268 39.130 0.00 0.00 0.00 3.71
2324 2351 4.207429 GTGCAAAAATAACGCCTTTTCGAA 59.793 37.500 0.00 0.00 0.00 3.71
2325 2352 4.442733 TGCAAAAATAACGCCTTTTCGAAG 59.557 37.500 0.00 0.00 0.00 3.79
2326 2353 4.443063 GCAAAAATAACGCCTTTTCGAAGT 59.557 37.500 0.00 0.00 0.00 3.01
2327 2354 5.609483 GCAAAAATAACGCCTTTTCGAAGTG 60.609 40.000 0.00 0.00 0.00 3.16
2328 2355 2.894307 ATAACGCCTTTTCGAAGTGC 57.106 45.000 0.00 1.76 0.00 4.40
2329 2356 0.869730 TAACGCCTTTTCGAAGTGCC 59.130 50.000 0.00 0.00 0.00 5.01
2330 2357 1.098712 AACGCCTTTTCGAAGTGCCA 61.099 50.000 0.00 0.00 0.00 4.92
2331 2358 0.889186 ACGCCTTTTCGAAGTGCCAT 60.889 50.000 0.00 0.00 0.00 4.40
2332 2359 0.454957 CGCCTTTTCGAAGTGCCATG 60.455 55.000 0.00 0.00 0.00 3.66
2333 2360 0.881118 GCCTTTTCGAAGTGCCATGA 59.119 50.000 0.00 0.00 0.00 3.07
2334 2361 1.401539 GCCTTTTCGAAGTGCCATGAC 60.402 52.381 0.00 0.00 0.00 3.06
2335 2362 2.154462 CCTTTTCGAAGTGCCATGACT 58.846 47.619 0.00 0.00 0.00 3.41
2336 2363 2.554032 CCTTTTCGAAGTGCCATGACTT 59.446 45.455 0.00 0.00 38.94 3.01
2337 2364 3.004734 CCTTTTCGAAGTGCCATGACTTT 59.995 43.478 0.00 0.00 36.27 2.66
2338 2365 3.624326 TTTCGAAGTGCCATGACTTTG 57.376 42.857 7.82 7.82 36.27 2.77
2339 2366 1.522668 TCGAAGTGCCATGACTTTGG 58.477 50.000 12.38 4.63 37.76 3.28
2351 2378 6.949352 CCATGACTTTGGCAATAACTAGAT 57.051 37.500 0.00 0.00 0.00 1.98
2352 2379 6.963796 CCATGACTTTGGCAATAACTAGATC 58.036 40.000 0.00 0.00 0.00 2.75
2353 2380 6.543465 CCATGACTTTGGCAATAACTAGATCA 59.457 38.462 0.00 2.71 0.00 2.92
2354 2381 6.985188 TGACTTTGGCAATAACTAGATCAC 57.015 37.500 0.00 0.00 0.00 3.06
2385 2413 6.434028 AGAAGCCTCATAGTTGTGCAAAAATA 59.566 34.615 0.00 0.00 0.00 1.40
2396 2424 3.242518 GTGCAAAAATAACGCCTTCTCC 58.757 45.455 0.00 0.00 0.00 3.71
2397 2425 2.887783 TGCAAAAATAACGCCTTCTCCA 59.112 40.909 0.00 0.00 0.00 3.86
2407 2435 0.322816 GCCTTCTCCAAGTGCCATGA 60.323 55.000 0.00 0.00 0.00 3.07
2412 2440 4.326826 CTTCTCCAAGTGCCATGACTTTA 58.673 43.478 0.00 0.00 33.75 1.85
2422 2450 6.414732 AGTGCCATGACTTTAGCAATAACTA 58.585 36.000 0.00 0.00 36.91 2.24
2438 2466 6.226787 CAATAACTAGATCAGTGACCCCATC 58.773 44.000 0.00 0.00 37.63 3.51
2461 2489 1.003233 AGGGTTTACTCCAAGCTTCCG 59.997 52.381 0.00 0.00 0.00 4.30
2491 2521 2.063015 ATGGGACCGAGTTGCACCAA 62.063 55.000 0.00 0.00 0.00 3.67
2501 2531 0.398318 GTTGCACCAACTCCTCCTCT 59.602 55.000 0.00 0.00 40.73 3.69
2534 2564 0.167908 TCAATGTTGATTGCGCCGAC 59.832 50.000 4.18 0.00 39.16 4.79
2539 2569 1.739929 TTGATTGCGCCGACGATGT 60.740 52.632 4.18 0.00 43.93 3.06
2559 2589 9.046296 ACGATGTTGATTTTCTATCTAACATCC 57.954 33.333 21.14 12.82 45.58 3.51
2561 2591 9.261180 GATGTTGATTTTCTATCTAACATCCGA 57.739 33.333 19.05 0.00 44.00 4.55
2563 2593 8.879759 TGTTGATTTTCTATCTAACATCCGAAC 58.120 33.333 0.00 0.00 0.00 3.95
2581 2611 1.447838 CGTCGCCAACACTAGCCAT 60.448 57.895 0.00 0.00 0.00 4.40
2593 2623 1.459348 TAGCCATCAGGGATGCCGA 60.459 57.895 0.00 0.00 38.59 5.54
2611 2641 1.620822 GAGTTGGGACTTTGGCATGT 58.379 50.000 0.00 0.00 35.88 3.21
2613 2643 0.240945 GTTGGGACTTTGGCATGTCG 59.759 55.000 12.73 0.00 34.31 4.35
2614 2644 0.109532 TTGGGACTTTGGCATGTCGA 59.890 50.000 12.73 0.00 34.31 4.20
2631 2661 4.848757 TGTCGAGTATCAACAGATCATCG 58.151 43.478 0.00 0.00 34.10 3.84
2644 2674 1.453524 GATCATCGCGGATTGTCTTCG 59.546 52.381 6.13 0.00 0.00 3.79
2645 2675 1.145759 TCATCGCGGATTGTCTTCGC 61.146 55.000 6.13 0.00 45.15 4.70
2660 2690 3.802139 GTCTTCGCCGAATGAACATATCA 59.198 43.478 0.00 0.00 43.67 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 3.680786 CGTCCCTGCAGTCGTCCA 61.681 66.667 13.81 0.00 0.00 4.02
1370 1377 2.727123 AACCAACTCCATGTGTGTGA 57.273 45.000 0.00 0.00 0.00 3.58
1386 1393 7.193377 TGAACAACTCCGAAATTAGTTAACC 57.807 36.000 0.88 0.00 34.23 2.85
1398 1405 2.094906 ACGATCGAATGAACAACTCCGA 60.095 45.455 24.34 0.00 0.00 4.55
1409 1416 0.246873 CACGCACACACGATCGAATG 60.247 55.000 24.34 20.32 36.70 2.67
1413 1420 4.468545 CGCACGCACACACGATCG 62.469 66.667 14.88 14.88 36.70 3.69
1705 1718 3.551890 CGAGTAGCTACTACGTACGGAAA 59.448 47.826 26.11 0.70 41.37 3.13
1706 1719 3.116300 CGAGTAGCTACTACGTACGGAA 58.884 50.000 26.11 6.30 41.37 4.30
1772 1785 2.029244 CGATCGATCAAAACCACCGAAG 59.971 50.000 24.40 0.25 32.84 3.79
1825 1838 8.122472 TCCATCTAATATTGTCGAGCTAATCA 57.878 34.615 0.00 0.00 0.00 2.57
1902 1920 0.106708 AACACACTCGTCATGCACCT 59.893 50.000 0.00 0.00 0.00 4.00
2016 2034 9.525007 GCTAATTGTAATCGAATGTAATTACCG 57.475 33.333 13.01 9.39 36.07 4.02
2018 2036 9.821662 GGGCTAATTGTAATCGAATGTAATTAC 57.178 33.333 8.75 8.75 36.07 1.89
2023 2043 6.822442 TCAGGGCTAATTGTAATCGAATGTA 58.178 36.000 0.00 0.00 0.00 2.29
2085 2105 1.535226 GGCACGTTCCTTGTTGGTTTC 60.535 52.381 0.00 0.00 37.07 2.78
2087 2107 0.395173 AGGCACGTTCCTTGTTGGTT 60.395 50.000 0.00 0.00 37.07 3.67
2088 2108 1.101049 CAGGCACGTTCCTTGTTGGT 61.101 55.000 3.17 0.00 33.25 3.67
2090 2110 1.008538 GCAGGCACGTTCCTTGTTG 60.009 57.895 3.17 0.00 33.25 3.33
2196 2223 8.929260 TTGATCAATTGTGGCATCTATCTTAT 57.071 30.769 3.38 0.00 0.00 1.73
2206 2233 7.914871 CGTTATAATTCTTGATCAATTGTGGCA 59.085 33.333 8.96 0.00 0.00 4.92
2284 2311 1.929836 GCACAACTATGAGGCTTCTCG 59.070 52.381 0.00 0.00 40.31 4.04
2290 2317 5.286082 CGTTATTTTTGCACAACTATGAGGC 59.714 40.000 0.00 0.00 0.00 4.70
2291 2318 5.286082 GCGTTATTTTTGCACAACTATGAGG 59.714 40.000 0.00 0.00 0.00 3.86
2292 2319 5.286082 GGCGTTATTTTTGCACAACTATGAG 59.714 40.000 0.00 0.00 0.00 2.90
2293 2320 5.048364 AGGCGTTATTTTTGCACAACTATGA 60.048 36.000 0.00 0.00 0.00 2.15
2294 2321 5.160641 AGGCGTTATTTTTGCACAACTATG 58.839 37.500 0.00 0.00 0.00 2.23
2295 2322 5.385509 AGGCGTTATTTTTGCACAACTAT 57.614 34.783 0.00 0.00 0.00 2.12
2296 2323 4.839668 AGGCGTTATTTTTGCACAACTA 57.160 36.364 0.00 0.00 0.00 2.24
2297 2324 3.726291 AGGCGTTATTTTTGCACAACT 57.274 38.095 0.00 0.00 0.00 3.16
2298 2325 4.787381 AAAGGCGTTATTTTTGCACAAC 57.213 36.364 0.00 0.00 0.00 3.32
2299 2326 4.026475 CGAAAAGGCGTTATTTTTGCACAA 60.026 37.500 0.00 0.00 30.22 3.33
2300 2327 3.487574 CGAAAAGGCGTTATTTTTGCACA 59.512 39.130 0.00 0.00 30.22 4.57
2301 2328 3.731717 TCGAAAAGGCGTTATTTTTGCAC 59.268 39.130 0.00 0.00 33.05 4.57
2302 2329 3.966154 TCGAAAAGGCGTTATTTTTGCA 58.034 36.364 0.00 0.00 33.05 4.08
2303 2330 4.443063 ACTTCGAAAAGGCGTTATTTTTGC 59.557 37.500 0.00 0.00 36.78 3.68
2304 2331 5.609483 GCACTTCGAAAAGGCGTTATTTTTG 60.609 40.000 0.00 0.00 36.78 2.44
2305 2332 4.443063 GCACTTCGAAAAGGCGTTATTTTT 59.557 37.500 0.00 0.00 36.78 1.94
2306 2333 3.978855 GCACTTCGAAAAGGCGTTATTTT 59.021 39.130 0.00 0.00 36.78 1.82
2307 2334 3.561503 GCACTTCGAAAAGGCGTTATTT 58.438 40.909 0.00 0.00 36.78 1.40
2308 2335 2.095415 GGCACTTCGAAAAGGCGTTATT 60.095 45.455 0.00 0.00 36.78 1.40
2309 2336 1.467342 GGCACTTCGAAAAGGCGTTAT 59.533 47.619 0.00 0.00 36.78 1.89
2310 2337 0.869730 GGCACTTCGAAAAGGCGTTA 59.130 50.000 0.00 0.00 36.78 3.18
2311 2338 1.098712 TGGCACTTCGAAAAGGCGTT 61.099 50.000 15.22 0.00 36.78 4.84
2312 2339 0.889186 ATGGCACTTCGAAAAGGCGT 60.889 50.000 15.22 13.04 36.78 5.68
2313 2340 0.454957 CATGGCACTTCGAAAAGGCG 60.455 55.000 15.22 0.03 36.78 5.52
2314 2341 0.881118 TCATGGCACTTCGAAAAGGC 59.119 50.000 13.91 13.91 36.78 4.35
2315 2342 2.154462 AGTCATGGCACTTCGAAAAGG 58.846 47.619 0.00 0.00 36.78 3.11
2316 2343 3.904136 AAGTCATGGCACTTCGAAAAG 57.096 42.857 0.00 0.00 38.54 2.27
2317 2344 3.243367 CCAAAGTCATGGCACTTCGAAAA 60.243 43.478 0.00 0.00 35.45 2.29
2318 2345 2.293122 CCAAAGTCATGGCACTTCGAAA 59.707 45.455 0.00 0.00 35.45 3.46
2319 2346 1.879380 CCAAAGTCATGGCACTTCGAA 59.121 47.619 0.00 0.00 35.45 3.71
2320 2347 1.522668 CCAAAGTCATGGCACTTCGA 58.477 50.000 0.00 0.00 35.45 3.71
2328 2355 6.543465 TGATCTAGTTATTGCCAAAGTCATGG 59.457 38.462 0.00 0.00 43.70 3.66
2329 2356 7.412853 GTGATCTAGTTATTGCCAAAGTCATG 58.587 38.462 0.00 0.00 0.00 3.07
2330 2357 6.258727 CGTGATCTAGTTATTGCCAAAGTCAT 59.741 38.462 0.00 0.00 0.00 3.06
2331 2358 5.580691 CGTGATCTAGTTATTGCCAAAGTCA 59.419 40.000 0.00 0.00 0.00 3.41
2332 2359 5.581085 ACGTGATCTAGTTATTGCCAAAGTC 59.419 40.000 0.00 0.00 0.00 3.01
2333 2360 5.351465 CACGTGATCTAGTTATTGCCAAAGT 59.649 40.000 10.90 0.00 0.00 2.66
2334 2361 5.727791 GCACGTGATCTAGTTATTGCCAAAG 60.728 44.000 22.23 0.00 0.00 2.77
2335 2362 4.094294 GCACGTGATCTAGTTATTGCCAAA 59.906 41.667 22.23 0.00 0.00 3.28
2336 2363 3.621268 GCACGTGATCTAGTTATTGCCAA 59.379 43.478 22.23 0.00 0.00 4.52
2337 2364 3.194861 GCACGTGATCTAGTTATTGCCA 58.805 45.455 22.23 0.00 0.00 4.92
2338 2365 2.218759 CGCACGTGATCTAGTTATTGCC 59.781 50.000 22.23 0.00 0.00 4.52
2339 2366 3.113322 TCGCACGTGATCTAGTTATTGC 58.887 45.455 22.23 0.00 0.00 3.56
2340 2367 4.598062 TCTCGCACGTGATCTAGTTATTG 58.402 43.478 22.23 0.00 0.00 1.90
2341 2368 4.895224 TCTCGCACGTGATCTAGTTATT 57.105 40.909 22.23 0.00 0.00 1.40
2342 2369 4.790123 GCTTCTCGCACGTGATCTAGTTAT 60.790 45.833 22.23 0.00 38.92 1.89
2343 2370 3.487042 GCTTCTCGCACGTGATCTAGTTA 60.487 47.826 22.23 2.79 38.92 2.24
2344 2371 2.732597 GCTTCTCGCACGTGATCTAGTT 60.733 50.000 22.23 0.00 38.92 2.24
2345 2372 1.202200 GCTTCTCGCACGTGATCTAGT 60.202 52.381 22.23 0.00 38.92 2.57
2346 2373 1.471964 GCTTCTCGCACGTGATCTAG 58.528 55.000 22.23 9.98 38.92 2.43
2347 2374 0.100682 GGCTTCTCGCACGTGATCTA 59.899 55.000 22.23 0.00 41.67 1.98
2348 2375 1.153745 GGCTTCTCGCACGTGATCT 60.154 57.895 22.23 0.00 41.67 2.75
2349 2376 1.142778 GAGGCTTCTCGCACGTGATC 61.143 60.000 22.23 0.56 41.67 2.92
2350 2377 1.153745 GAGGCTTCTCGCACGTGAT 60.154 57.895 22.23 0.00 41.67 3.06
2351 2378 1.877576 ATGAGGCTTCTCGCACGTGA 61.878 55.000 22.23 0.00 40.31 4.35
2352 2379 0.179137 TATGAGGCTTCTCGCACGTG 60.179 55.000 12.28 12.28 40.31 4.49
2353 2380 0.101399 CTATGAGGCTTCTCGCACGT 59.899 55.000 0.00 0.00 40.31 4.49
2354 2381 0.101399 ACTATGAGGCTTCTCGCACG 59.899 55.000 0.00 0.00 40.31 5.34
2385 2413 1.600916 GGCACTTGGAGAAGGCGTT 60.601 57.895 0.00 0.00 32.95 4.84
2396 2424 3.921119 TTGCTAAAGTCATGGCACTTG 57.079 42.857 0.00 0.00 36.69 3.16
2397 2425 5.711976 AGTTATTGCTAAAGTCATGGCACTT 59.288 36.000 0.00 0.00 38.30 3.16
2407 2435 7.982354 GGTCACTGATCTAGTTATTGCTAAAGT 59.018 37.037 0.00 0.00 37.60 2.66
2412 2440 4.101741 GGGGTCACTGATCTAGTTATTGCT 59.898 45.833 0.00 0.00 37.60 3.91
2422 2450 1.759445 CTTCGATGGGGTCACTGATCT 59.241 52.381 0.00 0.00 0.00 2.75
2438 2466 2.474410 AGCTTGGAGTAAACCCTTCG 57.526 50.000 0.00 0.00 0.00 3.79
2461 2489 2.297597 CTCGGTCCCATCTATCCTTCAC 59.702 54.545 0.00 0.00 0.00 3.18
2491 2521 0.900647 CGGTGTGGAAGAGGAGGAGT 60.901 60.000 0.00 0.00 0.00 3.85
2501 2531 1.202758 ACATTGAAGCTCGGTGTGGAA 60.203 47.619 0.00 0.00 0.00 3.53
2534 2564 8.217115 CGGATGTTAGATAGAAAATCAACATCG 58.783 37.037 21.05 16.77 46.72 3.84
2539 2569 7.762615 ACGTTCGGATGTTAGATAGAAAATCAA 59.237 33.333 0.00 0.00 0.00 2.57
2559 2589 1.941476 GCTAGTGTTGGCGACGTTCG 61.941 60.000 0.00 0.00 43.89 3.95
2561 2591 1.666872 GGCTAGTGTTGGCGACGTT 60.667 57.895 0.00 0.00 0.00 3.99
2563 2593 1.421410 GATGGCTAGTGTTGGCGACG 61.421 60.000 0.00 0.00 0.00 5.12
2581 2611 2.669133 CCCAACTCGGCATCCCTGA 61.669 63.158 0.00 0.00 0.00 3.86
2593 2623 1.620822 GACATGCCAAAGTCCCAACT 58.379 50.000 0.00 0.00 37.32 3.16
2611 2641 3.607078 CGCGATGATCTGTTGATACTCGA 60.607 47.826 0.00 0.00 38.17 4.04
2613 2643 2.983136 CCGCGATGATCTGTTGATACTC 59.017 50.000 8.23 0.00 32.19 2.59
2614 2644 2.623416 TCCGCGATGATCTGTTGATACT 59.377 45.455 8.23 0.00 32.19 2.12
2644 2674 3.466836 TCAGGTGATATGTTCATTCGGC 58.533 45.455 0.00 0.00 36.54 5.54
2645 2675 5.049198 CCATTCAGGTGATATGTTCATTCGG 60.049 44.000 0.00 0.00 36.54 4.30


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

AutoCloner maintained by Alex Coulton.