Multiple sequence alignment - TraesCS2D01G292400

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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 TraesCS2D01G292400 chr2D 100.000 2453 0 0 1 2453 375026019 375028471 0.000000e+00 4530.0
1 TraesCS2D01G292400 chr2B 90.665 1789 89 33 638 2395 445172131 445173872 0.000000e+00 2307.0
2 TraesCS2D01G292400 chr2B 93.114 639 39 3 3 636 445171165 445171803 0.000000e+00 931.0
3 TraesCS2D01G292400 chr2B 92.500 40 1 2 535 572 568273878 568273917 3.410000e-04 56.5
4 TraesCS2D01G292400 chr2A 90.372 1693 86 36 749 2395 507376110 507377771 0.000000e+00 2152.0
5 TraesCS2D01G292400 chr2A 91.568 759 47 7 1 742 507374907 507375665 0.000000e+00 1031.0
6 TraesCS2D01G292400 chr3D 81.882 287 46 2 1154 1437 480850245 480850528 1.130000e-58 237.0
7 TraesCS2D01G292400 chr3B 81.752 274 44 2 1167 1437 641666763 641667033 8.830000e-55 224.0
8 TraesCS2D01G292400 chr3A 80.634 284 46 3 1154 1437 623616456 623616730 6.870000e-51 211.0
9 TraesCS2D01G292400 chr7B 95.122 41 1 1 536 575 218563174 218563214 2.040000e-06 63.9
10 TraesCS2D01G292400 chr7A 92.857 42 2 1 535 575 254882875 254882834 2.630000e-05 60.2
11 TraesCS2D01G292400 chr1A 97.143 35 1 0 535 569 306682982 306682948 2.630000e-05 60.2
12 TraesCS2D01G292400 chr1A 97.143 35 1 0 535 569 478625941 478625907 2.630000e-05 60.2
13 TraesCS2D01G292400 chr1A 97.059 34 1 0 535 568 347323119 347323152 9.470000e-05 58.4
14 TraesCS2D01G292400 chr1B 97.059 34 1 0 536 569 332093274 332093307 9.470000e-05 58.4


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 TraesCS2D01G292400 chr2D 375026019 375028471 2452 False 4530.0 4530 100.0000 1 2453 1 chr2D.!!$F1 2452
1 TraesCS2D01G292400 chr2B 445171165 445173872 2707 False 1619.0 2307 91.8895 3 2395 2 chr2B.!!$F2 2392
2 TraesCS2D01G292400 chr2A 507374907 507377771 2864 False 1591.5 2152 90.9700 1 2395 2 chr2A.!!$F1 2394

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
35 36 0.108138 AGATGCCGCGCTTACTCTTT 60.108 50.0 5.56 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 2449 0.59868 GATGGGCTCGACAGATTCCG 60.599 60.0 0.0 0.0 0.0 4.3 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
35 36 0.108138 AGATGCCGCGCTTACTCTTT 60.108 50.000 5.56 0.00 0.00 2.52
65 66 8.466798 GCATTACTTATGTTGTAAGGGTTTCAT 58.533 33.333 0.00 0.00 36.57 2.57
108 109 7.654022 TGTGGTGAAAAGGAAATCTAAAAGT 57.346 32.000 0.00 0.00 0.00 2.66
329 334 0.520404 CAGGCACTTGACTGTGATGC 59.480 55.000 3.69 0.00 45.99 3.91
391 400 4.931661 AATTGATCCATGCTCATCAACC 57.068 40.909 12.58 0.00 40.87 3.77
400 409 2.977914 TGCTCATCAACCAGCTTCTAC 58.022 47.619 0.00 0.00 36.53 2.59
407 416 4.785511 TCAACCAGCTTCTACTGTCTAC 57.214 45.455 0.00 0.00 35.83 2.59
460 473 3.308530 CTTTTTCATGCGAAAGGTGTCC 58.691 45.455 10.89 0.00 42.00 4.02
497 512 9.412460 TCATATTGCTTTCTTAGAAATGGATGT 57.588 29.630 7.92 0.00 32.86 3.06
564 581 6.528423 CCAAAACGTCTTACATTTGTGAACAA 59.472 34.615 7.22 0.00 32.29 2.83
623 641 5.043189 ACGCTTTACTTCATTTTAGCACC 57.957 39.130 0.00 0.00 0.00 5.01
636 654 3.673599 GCACCTGCTTTCAGACCC 58.326 61.111 0.00 0.00 42.95 4.46
679 1023 2.363306 TTGGTTGCTTGGTCACATCT 57.637 45.000 0.00 0.00 0.00 2.90
707 1051 6.006449 AGCTCAATCAACACCATACTTTCTT 58.994 36.000 0.00 0.00 0.00 2.52
722 1066 7.041098 CCATACTTTCTTAATAATTCCGCTGCT 60.041 37.037 0.00 0.00 0.00 4.24
742 1086 6.975772 GCTGCTGTATATAGTAGATAAGTGCC 59.024 42.308 16.87 0.00 32.88 5.01
759 1542 5.514500 AGTGCCTCTTTAAAATGGTCCTA 57.486 39.130 7.65 0.00 0.00 2.94
781 1564 8.058847 TCCTAGTAAAGCATAATTTTGGGACAT 58.941 33.333 0.00 0.00 39.30 3.06
798 1581 8.642935 TTGGGACATGTCTAATTGAATTGTTA 57.357 30.769 24.50 0.00 39.30 2.41
834 1618 8.983724 GCAGTGTAAAACCAATTTATTAAGCAA 58.016 29.630 0.00 0.00 35.98 3.91
856 1640 7.970061 AGCAACACATGTTAAGTATTATTGCAG 59.030 33.333 0.00 0.00 40.82 4.41
858 1642 7.630242 ACACATGTTAAGTATTATTGCAGCT 57.370 32.000 0.00 0.00 0.00 4.24
886 1670 3.966665 TGGAAATTCTGGGGCCAAATATC 59.033 43.478 4.39 0.00 0.00 1.63
899 1696 4.159506 GGCCAAATATCTGTGCCTGTAAAA 59.840 41.667 0.00 0.00 39.05 1.52
909 1706 5.473504 TCTGTGCCTGTAAAATCCTTCTTTC 59.526 40.000 0.00 0.00 0.00 2.62
911 1708 5.241506 TGTGCCTGTAAAATCCTTCTTTCTG 59.758 40.000 0.00 0.00 0.00 3.02
912 1709 5.241728 GTGCCTGTAAAATCCTTCTTTCTGT 59.758 40.000 0.00 0.00 0.00 3.41
913 1710 5.241506 TGCCTGTAAAATCCTTCTTTCTGTG 59.758 40.000 0.00 0.00 0.00 3.66
914 1711 5.473504 GCCTGTAAAATCCTTCTTTCTGTGA 59.526 40.000 0.00 0.00 0.00 3.58
922 1719 4.887748 TCCTTCTTTCTGTGATGTCTGTC 58.112 43.478 0.00 0.00 0.00 3.51
932 1732 6.276091 TCTGTGATGTCTGTCATTATAGCAC 58.724 40.000 0.00 0.00 36.83 4.40
941 1741 3.898123 TGTCATTATAGCACCTCCTCTCC 59.102 47.826 0.00 0.00 0.00 3.71
942 1742 3.057174 GTCATTATAGCACCTCCTCTCCG 60.057 52.174 0.00 0.00 0.00 4.63
943 1743 3.157881 CATTATAGCACCTCCTCTCCGA 58.842 50.000 0.00 0.00 0.00 4.55
944 1744 3.308035 TTATAGCACCTCCTCTCCGAA 57.692 47.619 0.00 0.00 0.00 4.30
945 1745 2.160721 ATAGCACCTCCTCTCCGAAA 57.839 50.000 0.00 0.00 0.00 3.46
946 1746 1.475403 TAGCACCTCCTCTCCGAAAG 58.525 55.000 0.00 0.00 0.00 2.62
947 1747 0.543174 AGCACCTCCTCTCCGAAAGT 60.543 55.000 0.00 0.00 0.00 2.66
948 1748 0.390472 GCACCTCCTCTCCGAAAGTG 60.390 60.000 0.00 0.00 0.00 3.16
949 1749 0.969894 CACCTCCTCTCCGAAAGTGT 59.030 55.000 0.00 0.00 0.00 3.55
950 1750 1.344763 CACCTCCTCTCCGAAAGTGTT 59.655 52.381 0.00 0.00 0.00 3.32
951 1751 2.047830 ACCTCCTCTCCGAAAGTGTTT 58.952 47.619 0.00 0.00 0.00 2.83
953 1753 2.037251 CCTCCTCTCCGAAAGTGTTTCA 59.963 50.000 0.68 0.00 39.63 2.69
954 1754 3.321497 CTCCTCTCCGAAAGTGTTTCAG 58.679 50.000 0.68 0.00 39.63 3.02
955 1755 2.963101 TCCTCTCCGAAAGTGTTTCAGA 59.037 45.455 0.68 0.00 39.63 3.27
956 1756 3.060602 CCTCTCCGAAAGTGTTTCAGAC 58.939 50.000 0.68 0.00 39.63 3.51
957 1757 3.243907 CCTCTCCGAAAGTGTTTCAGACT 60.244 47.826 0.68 0.00 39.63 3.24
958 1758 4.022242 CCTCTCCGAAAGTGTTTCAGACTA 60.022 45.833 0.68 0.00 39.63 2.59
959 1759 5.122512 TCTCCGAAAGTGTTTCAGACTAG 57.877 43.478 0.68 0.00 39.63 2.57
960 1760 4.583489 TCTCCGAAAGTGTTTCAGACTAGT 59.417 41.667 0.00 0.00 39.63 2.57
961 1761 5.766670 TCTCCGAAAGTGTTTCAGACTAGTA 59.233 40.000 0.00 0.00 39.63 1.82
962 1762 6.263842 TCTCCGAAAGTGTTTCAGACTAGTAA 59.736 38.462 0.00 0.00 39.63 2.24
963 1763 6.989659 TCCGAAAGTGTTTCAGACTAGTAAT 58.010 36.000 0.00 0.00 39.63 1.89
964 1764 7.439381 TCCGAAAGTGTTTCAGACTAGTAATT 58.561 34.615 0.00 0.00 39.63 1.40
965 1765 8.579006 TCCGAAAGTGTTTCAGACTAGTAATTA 58.421 33.333 0.00 0.00 39.63 1.40
966 1766 8.861101 CCGAAAGTGTTTCAGACTAGTAATTAG 58.139 37.037 0.00 0.00 39.63 1.73
967 1767 9.408069 CGAAAGTGTTTCAGACTAGTAATTAGT 57.592 33.333 0.00 0.00 41.21 2.24
1005 1805 1.645455 CAAAGCATCCGAGATGGCG 59.355 57.895 13.51 0.00 37.80 5.69
1135 1935 0.601046 CACGCTGACAGGCTCAAGAA 60.601 55.000 4.26 0.00 0.00 2.52
1142 1942 0.468226 ACAGGCTCAAGAACACGGAA 59.532 50.000 0.00 0.00 0.00 4.30
1347 2147 2.567049 GACCAGTCGGACCAGTCG 59.433 66.667 4.14 0.00 35.59 4.18
1423 2223 2.113433 ACCTCCGACCTCGTCATCG 61.113 63.158 0.00 0.00 37.74 3.84
1473 2276 2.029728 GCATGTAGCAGCACTAGTTTCG 59.970 50.000 0.00 0.00 44.79 3.46
1488 2291 4.228912 AGTTTCGTTCAATCTTTGGCAG 57.771 40.909 0.00 0.00 0.00 4.85
1593 2404 1.767759 ACCTGAGCAAGTGCACTTTT 58.232 45.000 29.23 19.88 45.16 2.27
1609 2420 8.611757 AGTGCACTTTTTATTTTCATTTTGTCC 58.388 29.630 15.25 0.00 0.00 4.02
1617 2428 9.677567 TTTTATTTTCATTTTGTCCTTCTCTCG 57.322 29.630 0.00 0.00 0.00 4.04
1619 2430 7.693969 ATTTTCATTTTGTCCTTCTCTCGAT 57.306 32.000 0.00 0.00 0.00 3.59
1638 2449 4.038042 TCGATGTTCTCATGTGGGTATCTC 59.962 45.833 0.00 0.00 34.06 2.75
1858 2673 3.535561 CAGAAAGGTGTGTCACTTGACT 58.464 45.455 10.63 0.00 44.99 3.41
1872 2687 4.600111 TCACTTGACTTGGGGGTAAAGTAT 59.400 41.667 0.00 0.00 38.46 2.12
1873 2688 5.786457 TCACTTGACTTGGGGGTAAAGTATA 59.214 40.000 0.00 0.00 38.46 1.47
1874 2689 5.878669 CACTTGACTTGGGGGTAAAGTATAC 59.121 44.000 0.00 0.00 38.46 1.47
1912 2727 1.209127 CACCGCCACGAAAACATCC 59.791 57.895 0.00 0.00 0.00 3.51
1940 2755 0.674895 AGCGCGAGGAGATGCTTTTT 60.675 50.000 12.10 0.00 32.89 1.94
1982 2797 4.024048 GTGATCTTTGGCGGTATATGTTGG 60.024 45.833 0.00 0.00 0.00 3.77
2011 2826 4.447054 TGGTTGGTGTATACGTACGTTTTG 59.553 41.667 27.92 0.00 33.36 2.44
2012 2827 4.447389 GGTTGGTGTATACGTACGTTTTGT 59.553 41.667 27.92 12.70 33.36 2.83
2021 2841 6.826893 ATACGTACGTTTTGTAAACACACT 57.173 33.333 27.92 0.00 34.07 3.55
2152 2972 2.395360 GCGTTAGGTGCGGCATTGA 61.395 57.895 5.72 0.00 0.00 2.57
2155 2975 0.676782 GTTAGGTGCGGCATTGAGGT 60.677 55.000 5.72 0.00 0.00 3.85
2156 2976 0.392461 TTAGGTGCGGCATTGAGGTC 60.392 55.000 5.72 0.00 0.00 3.85
2158 2978 2.434185 GTGCGGCATTGAGGTCGA 60.434 61.111 5.72 0.00 38.35 4.20
2160 2980 3.567797 GCGGCATTGAGGTCGAGC 61.568 66.667 6.48 6.48 38.35 5.03
2161 2981 2.125552 CGGCATTGAGGTCGAGCA 60.126 61.111 18.15 0.00 38.35 4.26
2164 2984 1.427020 GCATTGAGGTCGAGCAAGC 59.573 57.895 18.15 8.97 0.00 4.01
2302 3132 0.967380 AGGCGCCAAATGGAGGAAAG 60.967 55.000 31.54 0.00 37.39 2.62
2358 3188 5.579119 AGCGTATCGAATTATTGTTGTCACA 59.421 36.000 0.00 0.00 0.00 3.58
2389 3220 1.069204 CATAGGATCCAGTCGTGGGTG 59.931 57.143 15.82 0.00 45.11 4.61
2395 3226 2.734723 CAGTCGTGGGTGTGAGCG 60.735 66.667 0.00 0.00 0.00 5.03
2396 3227 2.910479 AGTCGTGGGTGTGAGCGA 60.910 61.111 0.00 0.00 0.00 4.93
2397 3228 2.430921 GTCGTGGGTGTGAGCGAG 60.431 66.667 0.00 0.00 33.90 5.03
2398 3229 2.910479 TCGTGGGTGTGAGCGAGT 60.910 61.111 0.00 0.00 0.00 4.18
2399 3230 1.601477 TCGTGGGTGTGAGCGAGTA 60.601 57.895 0.00 0.00 0.00 2.59
2400 3231 1.174078 TCGTGGGTGTGAGCGAGTAA 61.174 55.000 0.00 0.00 0.00 2.24
2401 3232 0.319211 CGTGGGTGTGAGCGAGTAAA 60.319 55.000 0.00 0.00 0.00 2.01
2402 3233 1.429463 GTGGGTGTGAGCGAGTAAAG 58.571 55.000 0.00 0.00 0.00 1.85
2403 3234 1.045407 TGGGTGTGAGCGAGTAAAGT 58.955 50.000 0.00 0.00 0.00 2.66
2404 3235 1.000506 TGGGTGTGAGCGAGTAAAGTC 59.999 52.381 0.00 0.00 0.00 3.01
2405 3236 1.272769 GGGTGTGAGCGAGTAAAGTCT 59.727 52.381 0.00 0.00 0.00 3.24
2406 3237 2.490903 GGGTGTGAGCGAGTAAAGTCTA 59.509 50.000 0.00 0.00 0.00 2.59
2407 3238 3.057033 GGGTGTGAGCGAGTAAAGTCTAA 60.057 47.826 0.00 0.00 0.00 2.10
2408 3239 4.553323 GGTGTGAGCGAGTAAAGTCTAAA 58.447 43.478 0.00 0.00 0.00 1.85
2409 3240 4.986659 GGTGTGAGCGAGTAAAGTCTAAAA 59.013 41.667 0.00 0.00 0.00 1.52
2410 3241 5.638234 GGTGTGAGCGAGTAAAGTCTAAAAT 59.362 40.000 0.00 0.00 0.00 1.82
2411 3242 6.810182 GGTGTGAGCGAGTAAAGTCTAAAATA 59.190 38.462 0.00 0.00 0.00 1.40
2412 3243 7.330208 GGTGTGAGCGAGTAAAGTCTAAAATAA 59.670 37.037 0.00 0.00 0.00 1.40
2413 3244 8.706035 GTGTGAGCGAGTAAAGTCTAAAATAAA 58.294 33.333 0.00 0.00 0.00 1.40
2414 3245 8.706035 TGTGAGCGAGTAAAGTCTAAAATAAAC 58.294 33.333 0.00 0.00 0.00 2.01
2415 3246 8.167345 GTGAGCGAGTAAAGTCTAAAATAAACC 58.833 37.037 0.00 0.00 0.00 3.27
2416 3247 8.092687 TGAGCGAGTAAAGTCTAAAATAAACCT 58.907 33.333 0.00 0.00 0.00 3.50
2417 3248 8.843885 AGCGAGTAAAGTCTAAAATAAACCTT 57.156 30.769 0.00 0.00 0.00 3.50
2418 3249 8.933807 AGCGAGTAAAGTCTAAAATAAACCTTC 58.066 33.333 0.00 0.00 0.00 3.46
2419 3250 8.715088 GCGAGTAAAGTCTAAAATAAACCTTCA 58.285 33.333 0.00 0.00 0.00 3.02
2431 3262 8.870075 AAAATAAACCTTCAACTCATAGAGCT 57.130 30.769 0.00 0.00 32.04 4.09
2432 3263 9.959721 AAAATAAACCTTCAACTCATAGAGCTA 57.040 29.630 0.00 0.00 32.04 3.32
2433 3264 9.606631 AAATAAACCTTCAACTCATAGAGCTAG 57.393 33.333 0.00 0.00 32.04 3.42
2434 3265 6.613153 AAACCTTCAACTCATAGAGCTAGT 57.387 37.500 0.00 0.00 32.04 2.57
2435 3266 5.845391 ACCTTCAACTCATAGAGCTAGTC 57.155 43.478 0.00 0.00 32.04 2.59
2436 3267 4.647399 ACCTTCAACTCATAGAGCTAGTCC 59.353 45.833 0.00 0.00 32.04 3.85
2437 3268 4.261405 CCTTCAACTCATAGAGCTAGTCCG 60.261 50.000 0.00 0.00 32.04 4.79
2438 3269 4.152284 TCAACTCATAGAGCTAGTCCGA 57.848 45.455 0.00 0.00 32.04 4.55
2439 3270 4.524053 TCAACTCATAGAGCTAGTCCGAA 58.476 43.478 0.00 0.00 32.04 4.30
2440 3271 5.133941 TCAACTCATAGAGCTAGTCCGAAT 58.866 41.667 0.00 0.00 32.04 3.34
2441 3272 5.239744 TCAACTCATAGAGCTAGTCCGAATC 59.760 44.000 0.00 0.00 32.04 2.52
2442 3273 4.720046 ACTCATAGAGCTAGTCCGAATCA 58.280 43.478 0.00 0.00 32.04 2.57
2443 3274 5.133941 ACTCATAGAGCTAGTCCGAATCAA 58.866 41.667 0.00 0.00 32.04 2.57
2444 3275 5.594725 ACTCATAGAGCTAGTCCGAATCAAA 59.405 40.000 0.00 0.00 32.04 2.69
2445 3276 5.833082 TCATAGAGCTAGTCCGAATCAAAC 58.167 41.667 0.00 0.00 0.00 2.93
2446 3277 3.528597 AGAGCTAGTCCGAATCAAACC 57.471 47.619 0.00 0.00 0.00 3.27
2447 3278 3.100671 AGAGCTAGTCCGAATCAAACCT 58.899 45.455 0.00 0.00 0.00 3.50
2448 3279 3.131400 AGAGCTAGTCCGAATCAAACCTC 59.869 47.826 0.00 0.00 0.00 3.85
2449 3280 2.159226 AGCTAGTCCGAATCAAACCTCG 60.159 50.000 0.00 0.00 34.83 4.63
2450 3281 2.159282 GCTAGTCCGAATCAAACCTCGA 60.159 50.000 0.00 0.00 37.23 4.04
2451 3282 3.675228 GCTAGTCCGAATCAAACCTCGAA 60.675 47.826 0.00 0.00 37.23 3.71
2452 3283 2.685100 AGTCCGAATCAAACCTCGAAC 58.315 47.619 0.00 0.00 37.23 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 5.587043 CCCTTACAACATAAGTAATGCCGAA 59.413 40.000 0.00 0.00 39.39 4.30
65 66 5.163301 ACCACAAAGCTCTTTCAGAGTAAGA 60.163 40.000 2.79 0.00 44.12 2.10
325 330 5.297776 ACATTAGAGTACAAGCAATGGCATC 59.702 40.000 0.00 0.00 44.61 3.91
329 334 5.185454 TGGACATTAGAGTACAAGCAATGG 58.815 41.667 0.00 0.00 32.20 3.16
371 380 3.889538 CTGGTTGATGAGCATGGATCAAT 59.110 43.478 0.00 0.00 39.97 2.57
391 400 6.253727 CCATAAAACGTAGACAGTAGAAGCTG 59.746 42.308 0.00 0.00 41.92 4.24
400 409 2.980568 TGGGCCATAAAACGTAGACAG 58.019 47.619 0.00 0.00 0.00 3.51
407 416 3.936585 CCGAATGGGCCATAAAACG 57.063 52.632 21.54 20.72 0.00 3.60
460 473 5.879223 AGAAAGCAATATGACTCTTCCACAG 59.121 40.000 0.00 0.00 0.00 3.66
497 512 5.800438 CGATATCGTCTTCACAGAAGTTTGA 59.200 40.000 17.06 4.38 30.95 2.69
564 581 2.127708 CCATCTTAGCAGGTACCCCTT 58.872 52.381 8.74 0.00 39.89 3.95
582 600 1.888512 GTCACAACTACGTCCTACCCA 59.111 52.381 0.00 0.00 0.00 4.51
603 621 4.859245 GCAGGTGCTAAAATGAAGTAAAGC 59.141 41.667 0.00 0.00 38.21 3.51
623 641 4.142513 GCTAGAAAATGGGTCTGAAAGCAG 60.143 45.833 0.00 0.00 43.67 4.24
663 1007 4.878397 AGCTATAAGATGTGACCAAGCAAC 59.122 41.667 0.00 0.00 0.00 4.17
679 1023 9.109393 GAAAGTATGGTGTTGATTGAGCTATAA 57.891 33.333 0.00 0.00 0.00 0.98
742 1086 8.561738 TGCTTTACTAGGACCATTTTAAAGAG 57.438 34.615 14.46 0.00 31.13 2.85
759 1542 7.397192 AGACATGTCCCAAAATTATGCTTTACT 59.603 33.333 22.21 0.00 0.00 2.24
793 1576 8.917655 GTTTTACACTGCTTCAAAACTTAACAA 58.082 29.630 0.00 0.00 37.70 2.83
798 1581 6.031751 TGGTTTTACACTGCTTCAAAACTT 57.968 33.333 8.24 0.00 39.61 2.66
834 1618 7.630242 AGCTGCAATAATACTTAACATGTGT 57.370 32.000 0.00 0.00 0.00 3.72
847 1631 9.895138 AGAATTTCCATTTTTAGCTGCAATAAT 57.105 25.926 1.02 0.00 0.00 1.28
856 1640 4.191544 GCCCCAGAATTTCCATTTTTAGC 58.808 43.478 0.00 0.00 0.00 3.09
858 1642 4.171234 TGGCCCCAGAATTTCCATTTTTA 58.829 39.130 0.00 0.00 0.00 1.52
872 1656 1.035139 GCACAGATATTTGGCCCCAG 58.965 55.000 0.00 0.00 0.00 4.45
886 1670 5.474876 AGAAAGAAGGATTTTACAGGCACAG 59.525 40.000 0.00 0.00 0.00 3.66
899 1696 5.012458 TGACAGACATCACAGAAAGAAGGAT 59.988 40.000 0.00 0.00 0.00 3.24
909 1706 5.464722 GGTGCTATAATGACAGACATCACAG 59.535 44.000 0.00 0.00 38.38 3.66
911 1708 5.605534 AGGTGCTATAATGACAGACATCAC 58.394 41.667 0.00 0.00 38.38 3.06
912 1709 5.221521 GGAGGTGCTATAATGACAGACATCA 60.222 44.000 0.00 0.00 38.38 3.07
913 1710 5.011533 AGGAGGTGCTATAATGACAGACATC 59.988 44.000 0.00 0.00 38.38 3.06
914 1711 4.904251 AGGAGGTGCTATAATGACAGACAT 59.096 41.667 0.00 0.00 41.45 3.06
922 1719 3.157881 TCGGAGAGGAGGTGCTATAATG 58.842 50.000 0.00 0.00 0.00 1.90
932 1732 2.037251 TGAAACACTTTCGGAGAGGAGG 59.963 50.000 0.31 0.00 42.55 4.30
941 1741 9.408069 ACTAATTACTAGTCTGAAACACTTTCG 57.592 33.333 0.00 0.00 38.20 3.46
978 1778 0.322456 CGGATGCTTTGGGGTCTGAA 60.322 55.000 0.00 0.00 0.00 3.02
979 1779 1.198094 TCGGATGCTTTGGGGTCTGA 61.198 55.000 0.00 0.00 0.00 3.27
984 1784 0.820891 CCATCTCGGATGCTTTGGGG 60.821 60.000 8.01 0.00 36.56 4.96
988 1788 0.811616 GTCGCCATCTCGGATGCTTT 60.812 55.000 8.01 0.00 36.56 3.51
994 1794 1.337071 GAATGTAGTCGCCATCTCGGA 59.663 52.381 0.00 0.00 36.56 4.55
1005 1805 1.803334 TTGGTGCCGTGAATGTAGTC 58.197 50.000 0.00 0.00 0.00 2.59
1423 2223 4.580835 GGACTCCTTGTGCGTCTC 57.419 61.111 0.00 0.00 0.00 3.36
1473 2276 3.817647 AGACAGACTGCCAAAGATTGAAC 59.182 43.478 1.25 0.00 0.00 3.18
1488 2291 1.269517 GGCGGATCAGATCAGACAGAC 60.270 57.143 14.20 0.00 32.33 3.51
1593 2404 8.615878 TCGAGAGAAGGACAAAATGAAAATAA 57.384 30.769 0.00 0.00 37.03 1.40
1617 2428 4.302455 CGAGATACCCACATGAGAACATC 58.698 47.826 0.00 0.00 34.15 3.06
1619 2430 2.430694 CCGAGATACCCACATGAGAACA 59.569 50.000 0.00 0.00 0.00 3.18
1638 2449 0.598680 GATGGGCTCGACAGATTCCG 60.599 60.000 0.00 0.00 0.00 4.30
1836 2651 2.032178 GTCAAGTGACACACCTTTCTGC 59.968 50.000 8.59 0.00 44.18 4.26
1858 2673 6.838612 ACGTATGTAGTATACTTTACCCCCAA 59.161 38.462 11.40 0.00 43.54 4.12
1872 2687 6.039270 GGTGGTGGTATGTTACGTATGTAGTA 59.961 42.308 0.00 0.00 0.00 1.82
1873 2688 5.163519 GGTGGTGGTATGTTACGTATGTAGT 60.164 44.000 0.00 0.00 0.00 2.73
1874 2689 5.284079 GGTGGTGGTATGTTACGTATGTAG 58.716 45.833 0.00 0.00 0.00 2.74
1888 2703 2.321263 TTTTCGTGGCGGTGGTGGTA 62.321 55.000 0.00 0.00 0.00 3.25
1940 2755 5.336150 TCACAGCAATTTTGGAGTTCAAA 57.664 34.783 0.00 0.00 42.98 2.69
1950 2765 3.319755 CGCCAAAGATCACAGCAATTTT 58.680 40.909 0.00 0.00 0.00 1.82
1982 2797 3.140623 ACGTATACACCAACCAACCAAC 58.859 45.455 3.32 0.00 0.00 3.77
2011 2826 7.411480 GCAAAAGGTCTTTTCAAGTGTGTTTAC 60.411 37.037 5.79 0.00 40.45 2.01
2012 2827 6.588373 GCAAAAGGTCTTTTCAAGTGTGTTTA 59.412 34.615 5.79 0.00 40.45 2.01
2021 2841 3.878160 AACCGCAAAAGGTCTTTTCAA 57.122 38.095 5.79 0.00 45.21 2.69
2149 2969 2.048222 CCGCTTGCTCGACCTCAA 60.048 61.111 0.00 0.00 0.00 3.02
2152 2972 2.992114 AGTCCGCTTGCTCGACCT 60.992 61.111 6.22 0.00 0.00 3.85
2155 2975 4.742201 GCCAGTCCGCTTGCTCGA 62.742 66.667 0.00 0.00 31.41 4.04
2358 3188 4.651503 ACTGGATCCTATGATTCGTGAGTT 59.348 41.667 14.23 0.00 0.00 3.01
2389 3220 8.167345 GGTTTATTTTAGACTTTACTCGCTCAC 58.833 37.037 0.00 0.00 0.00 3.51
2405 3236 9.959721 AGCTCTATGAGTTGAAGGTTTATTTTA 57.040 29.630 0.00 0.00 31.39 1.52
2406 3237 8.870075 AGCTCTATGAGTTGAAGGTTTATTTT 57.130 30.769 0.00 0.00 31.39 1.82
2407 3238 9.606631 CTAGCTCTATGAGTTGAAGGTTTATTT 57.393 33.333 0.00 0.00 31.39 1.40
2408 3239 8.763601 ACTAGCTCTATGAGTTGAAGGTTTATT 58.236 33.333 0.00 0.00 31.39 1.40
2409 3240 8.312669 ACTAGCTCTATGAGTTGAAGGTTTAT 57.687 34.615 0.00 0.00 31.39 1.40
2410 3241 7.147880 GGACTAGCTCTATGAGTTGAAGGTTTA 60.148 40.741 0.00 0.00 31.39 2.01
2411 3242 6.351456 GGACTAGCTCTATGAGTTGAAGGTTT 60.351 42.308 0.00 0.00 31.39 3.27
2412 3243 5.128008 GGACTAGCTCTATGAGTTGAAGGTT 59.872 44.000 0.00 0.00 31.39 3.50
2413 3244 4.647399 GGACTAGCTCTATGAGTTGAAGGT 59.353 45.833 0.00 0.00 31.39 3.50
2414 3245 4.261405 CGGACTAGCTCTATGAGTTGAAGG 60.261 50.000 0.00 0.00 31.39 3.46
2415 3246 4.576873 TCGGACTAGCTCTATGAGTTGAAG 59.423 45.833 0.00 0.00 31.39 3.02
2416 3247 4.524053 TCGGACTAGCTCTATGAGTTGAA 58.476 43.478 0.00 0.00 31.39 2.69
2417 3248 4.152284 TCGGACTAGCTCTATGAGTTGA 57.848 45.455 0.00 0.00 31.39 3.18
2418 3249 4.902443 TTCGGACTAGCTCTATGAGTTG 57.098 45.455 0.00 0.00 31.39 3.16
2419 3250 5.133941 TGATTCGGACTAGCTCTATGAGTT 58.866 41.667 0.00 0.00 31.39 3.01
2420 3251 4.720046 TGATTCGGACTAGCTCTATGAGT 58.280 43.478 0.00 0.00 31.39 3.41
2421 3252 5.697473 TTGATTCGGACTAGCTCTATGAG 57.303 43.478 0.00 0.00 0.00 2.90
2422 3253 5.221263 GGTTTGATTCGGACTAGCTCTATGA 60.221 44.000 0.00 0.00 0.00 2.15
2423 3254 4.985409 GGTTTGATTCGGACTAGCTCTATG 59.015 45.833 0.00 0.00 0.00 2.23
2424 3255 4.896482 AGGTTTGATTCGGACTAGCTCTAT 59.104 41.667 0.00 0.00 0.00 1.98
2425 3256 4.279145 AGGTTTGATTCGGACTAGCTCTA 58.721 43.478 0.00 0.00 0.00 2.43
2426 3257 3.100671 AGGTTTGATTCGGACTAGCTCT 58.899 45.455 0.00 0.00 0.00 4.09
2427 3258 3.449632 GAGGTTTGATTCGGACTAGCTC 58.550 50.000 0.00 0.00 0.00 4.09
2428 3259 2.159226 CGAGGTTTGATTCGGACTAGCT 60.159 50.000 0.00 0.00 33.39 3.32
2429 3260 2.159282 TCGAGGTTTGATTCGGACTAGC 60.159 50.000 0.00 0.00 37.42 3.42
2430 3261 3.777465 TCGAGGTTTGATTCGGACTAG 57.223 47.619 0.00 0.00 37.42 2.57
2431 3262 3.841643 GTTCGAGGTTTGATTCGGACTA 58.158 45.455 0.00 0.00 41.10 2.59
2432 3263 2.685100 GTTCGAGGTTTGATTCGGACT 58.315 47.619 0.00 0.00 41.10 3.85


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

AutoCloner maintained by Alex Coulton.