Multiple sequence alignment - TraesCS3A01G189600

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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 TraesCS3A01G189600 chr3A 100.000 6157 0 0 1 6157 234209473 234215629 0.000000e+00 11370
1 TraesCS3A01G189600 chr3B 92.420 2269 98 21 1840 4067 262190099 262192334 0.000000e+00 3169
2 TraesCS3A01G189600 chr3B 95.107 1267 47 4 4904 6157 262196957 262198221 0.000000e+00 1982
3 TraesCS3A01G189600 chr3B 94.300 807 29 3 4063 4867 262196162 262196953 0.000000e+00 1219
4 TraesCS3A01G189600 chr3B 91.874 603 32 5 757 1344 262188941 262189541 0.000000e+00 826
5 TraesCS3A01G189600 chr3B 96.581 351 12 0 1340 1690 262189738 262190088 3.200000e-162 582
6 TraesCS3A01G189600 chr3B 91.039 279 16 4 498 767 262188646 262188924 9.750000e-98 368
7 TraesCS3A01G189600 chr3B 85.253 217 14 10 21 219 262187984 262188200 2.250000e-49 207
8 TraesCS3A01G189600 chr3B 92.308 104 3 2 413 511 262188526 262188629 6.430000e-30 143
9 TraesCS3A01G189600 chr3D 96.976 1885 31 1 3141 4999 183740775 183742659 0.000000e+00 3142
10 TraesCS3A01G189600 chr3D 94.793 1210 45 6 4961 6157 183742657 183743861 0.000000e+00 1869
11 TraesCS3A01G189600 chr3D 92.784 1178 43 14 1975 3140 183739475 183740622 0.000000e+00 1666
12 TraesCS3A01G189600 chr3D 93.980 598 32 3 1340 1934 183738880 183739476 0.000000e+00 902
13 TraesCS3A01G189600 chr3D 93.729 590 23 5 758 1344 183738111 183738689 0.000000e+00 872
14 TraesCS3A01G189600 chr3D 88.394 629 24 17 20 635 183737428 183738020 0.000000e+00 712
15 TraesCS3A01G189600 chr3D 83.459 399 52 7 1760 2156 536983466 536983080 5.870000e-95 359
16 TraesCS3A01G189600 chrUn 100.000 421 0 0 3519 3939 476833311 476832891 0.000000e+00 778
17 TraesCS3A01G189600 chr1B 83.416 404 52 6 1761 2161 426453316 426452925 1.630000e-95 361
18 TraesCS3A01G189600 chr7B 83.797 395 45 11 1759 2151 145695008 145695385 2.110000e-94 357
19 TraesCS3A01G189600 chr7B 81.707 410 59 9 1750 2156 660642870 660643266 1.650000e-85 327
20 TraesCS3A01G189600 chr5B 83.544 395 50 12 1766 2157 701525022 701524640 7.590000e-94 355
21 TraesCS3A01G189600 chr5B 82.500 400 57 6 1759 2157 565891914 565892301 7.640000e-89 339
22 TraesCS3A01G189600 chr2A 83.000 400 52 9 1761 2156 584516390 584516777 1.270000e-91 348
23 TraesCS3A01G189600 chr6D 82.915 398 55 7 1755 2151 394935799 394935414 4.570000e-91 346
24 TraesCS3A01G189600 chr7A 81.095 402 58 13 1762 2160 81793001 81792615 7.750000e-79 305
25 TraesCS3A01G189600 chr7A 80.481 374 51 6 1760 2132 443957917 443958269 3.660000e-67 267
26 TraesCS3A01G189600 chr1A 80.798 401 60 10 1759 2156 291246122 291246508 1.300000e-76 298
27 TraesCS3A01G189600 chr7D 79.494 395 57 7 1760 2151 392257828 392258201 6.120000e-65 259
28 TraesCS3A01G189600 chr5D 80.526 190 35 2 1966 2155 32136068 32135881 1.790000e-30 145


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 TraesCS3A01G189600 chr3A 234209473 234215629 6156 False 11370.000000 11370 100.000000 1 6157 1 chr3A.!!$F1 6156
1 TraesCS3A01G189600 chr3B 262187984 262198221 10237 False 1062.000000 3169 92.360250 21 6157 8 chr3B.!!$F1 6136
2 TraesCS3A01G189600 chr3D 183737428 183743861 6433 False 1527.166667 3142 93.442667 20 6157 6 chr3D.!!$F1 6137

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
136 155 0.317603 ATTCGTTCGGTCGCCTATCG 60.318 55.000 0.00 0.0 40.15 2.92 F
1138 1418 0.255033 GGCCGAGGTTAGTTGGGAAT 59.745 55.000 0.00 0.0 0.00 3.01 F
1782 2271 0.036875 GGCCTGTTTGGTACTGCTCT 59.963 55.000 0.00 0.0 38.35 4.09 F
2490 2985 0.170339 GCAACCTACGTGGAAATGCC 59.830 55.000 0.00 0.0 37.42 4.40 F
3033 3533 1.280998 GTACCCTTGCACCATGGTAGT 59.719 52.381 19.28 10.6 34.17 2.73 F
3205 3861 1.892209 AAAGAAAGGGGCAGTACACG 58.108 50.000 0.00 0.0 0.00 4.49 F
4955 9472 1.974543 CCAATCCAGCGGCCTTTTT 59.025 52.632 0.00 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1140 1420 0.111639 CCCCGTCCAAGGAAAAGGAA 59.888 55.000 7.76 0.00 35.29 3.36 R
2276 2770 0.951558 ATGAGCACCGGTTTTGACAC 59.048 50.000 2.97 0.00 0.00 3.67 R
2874 3371 1.196104 CCGGTAAGTCCTTGACCCCA 61.196 60.000 0.00 0.00 32.18 4.96 R
4249 8765 0.251165 GAGGCCAAGGCAACAAGGTA 60.251 55.000 13.87 0.00 44.11 3.08 R
4258 8774 0.255890 TTATCACCAGAGGCCAAGGC 59.744 55.000 5.01 1.52 41.06 4.35 R
4962 9479 1.067495 GTCCTCTCCTGAAACGACTGG 60.067 57.143 0.00 0.00 0.00 4.00 R
5834 10400 0.815213 CTCCAGGGTGTGTGTGTGTG 60.815 60.000 0.00 0.00 0.00 3.82 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
36 37 2.037251 ACGGCGGCTGTAATCATATTCT 59.963 45.455 13.83 0.00 0.00 2.40
126 145 1.015085 TTGCACGGGTATTCGTTCGG 61.015 55.000 0.00 0.00 41.86 4.30
136 155 0.317603 ATTCGTTCGGTCGCCTATCG 60.318 55.000 0.00 0.00 40.15 2.92
208 229 6.687604 TCTTCGATCAAATGTCACTAGTGAA 58.312 36.000 26.74 16.79 41.85 3.18
268 456 3.072622 ACCTTCTGGAAAGGGTAGAACAC 59.927 47.826 8.58 0.00 41.71 3.32
361 549 0.996229 CATTTGCGCAAAAGCGACGA 60.996 50.000 36.42 14.46 40.67 4.20
570 793 7.658261 AGGACTAGTTGCAAAAATTTCTTACC 58.342 34.615 0.00 0.00 0.00 2.85
571 794 7.286775 AGGACTAGTTGCAAAAATTTCTTACCA 59.713 33.333 0.00 0.00 0.00 3.25
636 859 3.446161 CGTACCTGACCAATAAGTCCAGA 59.554 47.826 0.00 0.00 35.83 3.86
638 861 5.395324 CGTACCTGACCAATAAGTCCAGAAT 60.395 44.000 0.00 0.00 35.83 2.40
639 862 5.104259 ACCTGACCAATAAGTCCAGAATC 57.896 43.478 0.00 0.00 35.83 2.52
644 867 7.227512 CCTGACCAATAAGTCCAGAATCAATAC 59.772 40.741 0.00 0.00 35.83 1.89
680 908 7.010923 GCATAGGAGTACATGAAAAGAGAACAG 59.989 40.741 0.00 0.00 0.00 3.16
709 938 1.348775 ATCCTTACTCAGGCCCCTGC 61.349 60.000 9.48 0.00 43.55 4.85
751 980 7.508296 AGAGACTCAAAACAGGGTTAGTACTAA 59.492 37.037 11.38 11.38 0.00 2.24
754 983 9.933723 GACTCAAAACAGGGTTAGTACTAATAA 57.066 33.333 18.03 0.00 0.00 1.40
755 984 9.716531 ACTCAAAACAGGGTTAGTACTAATAAC 57.283 33.333 18.03 8.40 33.29 1.89
790 1049 2.132762 CGGGTTAGGATAATCGTGTGC 58.867 52.381 0.00 0.00 0.00 4.57
957 1216 4.475135 GGGACTTCCGGCTCCAGC 62.475 72.222 13.01 0.00 41.14 4.85
1028 1299 2.913117 GCCATACACCCACCACCCA 61.913 63.158 0.00 0.00 0.00 4.51
1132 1412 4.446413 CCGCGGCCGAGGTTAGTT 62.446 66.667 36.60 0.00 36.29 2.24
1133 1413 3.186047 CGCGGCCGAGGTTAGTTG 61.186 66.667 33.48 1.65 36.29 3.16
1134 1414 2.818274 GCGGCCGAGGTTAGTTGG 60.818 66.667 33.48 0.00 0.00 3.77
1135 1415 2.125269 CGGCCGAGGTTAGTTGGG 60.125 66.667 24.07 0.00 0.00 4.12
1136 1416 2.652095 CGGCCGAGGTTAGTTGGGA 61.652 63.158 24.07 0.00 0.00 4.37
1137 1417 1.681076 GGCCGAGGTTAGTTGGGAA 59.319 57.895 0.00 0.00 0.00 3.97
1138 1418 0.255033 GGCCGAGGTTAGTTGGGAAT 59.745 55.000 0.00 0.00 0.00 3.01
1139 1419 1.664873 GCCGAGGTTAGTTGGGAATC 58.335 55.000 0.00 0.00 0.00 2.52
1140 1420 1.209747 GCCGAGGTTAGTTGGGAATCT 59.790 52.381 0.00 0.00 0.00 2.40
1185 1465 2.224450 GGACTTCTCCGGTTCCTTTCAA 60.224 50.000 0.00 0.00 0.00 2.69
1204 1484 2.055310 ATTGCCGATGTGATGCGCTG 62.055 55.000 9.73 0.00 0.00 5.18
1237 1517 0.318955 GCGGCTTTTGTGCTGTCAAT 60.319 50.000 0.00 0.00 41.12 2.57
1327 1611 0.983378 CTCCGTCTTCCCCTCCCAAT 60.983 60.000 0.00 0.00 0.00 3.16
1430 1916 5.675684 TCATGCTATCTTTGTGTCCTACA 57.324 39.130 0.00 0.00 37.56 2.74
1559 2045 9.924650 TGTACTAAAAGGAAACAGTTCTCTATC 57.075 33.333 0.00 0.00 33.92 2.08
1633 2122 5.829391 AGCCTTTTCTTGCCAAATGAAAAAT 59.171 32.000 6.20 0.00 38.61 1.82
1659 2148 8.137437 TGGAACTTCAACTTCTTTGATCAAATC 58.863 33.333 20.76 10.63 43.99 2.17
1717 2206 8.752005 TCTTTATTAGTAAGACTAAGCCGGTA 57.248 34.615 1.90 0.00 43.17 4.02
1726 2215 0.661020 CTAAGCCGGTATTTTGCCCG 59.339 55.000 1.90 0.00 43.82 6.13
1774 2263 0.409484 ATGCTTAGGGCCTGTTTGGT 59.591 50.000 18.53 0.00 40.92 3.67
1782 2271 0.036875 GGCCTGTTTGGTACTGCTCT 59.963 55.000 0.00 0.00 38.35 4.09
1784 2273 1.160137 CCTGTTTGGTACTGCTCTGC 58.840 55.000 0.00 0.00 0.00 4.26
1804 2293 5.049680 TCTGCTCCACGAAAATCAGTTTTAC 60.050 40.000 0.00 0.00 37.65 2.01
1806 2295 5.298276 TGCTCCACGAAAATCAGTTTTACTT 59.702 36.000 0.00 0.00 37.65 2.24
1807 2296 5.851703 GCTCCACGAAAATCAGTTTTACTTC 59.148 40.000 0.00 0.00 37.65 3.01
1810 2299 6.540914 TCCACGAAAATCAGTTTTACTTCACT 59.459 34.615 0.00 0.00 37.65 3.41
1822 2311 9.450807 CAGTTTTACTTCACTAAATCCACTTTG 57.549 33.333 0.00 0.00 0.00 2.77
1834 2323 3.228188 TCCACTTTGGAGCAGTTTCAT 57.772 42.857 0.00 0.00 42.67 2.57
1907 2396 7.039011 TCCAGTTAACTCTAGCTTCAAGAATGA 60.039 37.037 4.77 0.00 0.00 2.57
1908 2397 7.277539 CCAGTTAACTCTAGCTTCAAGAATGAG 59.722 40.741 4.77 0.00 36.78 2.90
1918 2407 5.771666 AGCTTCAAGAATGAGAATTTGGTGA 59.228 36.000 0.00 0.00 36.78 4.02
1919 2408 6.266103 AGCTTCAAGAATGAGAATTTGGTGAA 59.734 34.615 0.00 0.00 36.78 3.18
1944 2433 4.384056 AGGATCTATTTGATTGGCTGACG 58.616 43.478 0.00 0.00 35.14 4.35
1961 2450 2.059541 GACGTGAGGAGAAACGAAAGG 58.940 52.381 0.00 0.00 42.32 3.11
2080 2569 3.916989 GGGAGTTGGACCCCATATTCTAT 59.083 47.826 0.00 0.00 42.24 1.98
2109 2598 2.710377 TGAAGCCGCATATTGTGAAGT 58.290 42.857 0.00 0.00 0.00 3.01
2112 2601 4.881273 TGAAGCCGCATATTGTGAAGTTAT 59.119 37.500 0.00 0.00 0.00 1.89
2139 2628 5.147162 GTTTGGCTTGTGTTTTCTAGATCG 58.853 41.667 0.00 0.00 0.00 3.69
2234 2728 3.333029 AGCTTGGTTTGCAAACAGTTT 57.667 38.095 35.95 18.80 40.63 2.66
2276 2770 7.678947 ATCAGTTTATGTCTTGTCTTTGGAG 57.321 36.000 0.00 0.00 0.00 3.86
2286 2780 4.398044 TCTTGTCTTTGGAGTGTCAAAACC 59.602 41.667 0.00 0.00 36.37 3.27
2490 2985 0.170339 GCAACCTACGTGGAAATGCC 59.830 55.000 0.00 0.00 37.42 4.40
2716 3211 5.766150 TGTCTGATTGTTACAAAGGGTTG 57.234 39.130 0.66 0.00 40.84 3.77
2812 3309 8.844441 TTGTTAAAACAAGTATAGTGTGTTGC 57.156 30.769 4.19 0.00 43.45 4.17
2816 3313 9.550406 TTAAAACAAGTATAGTGTGTTGCTAGT 57.450 29.630 8.13 0.00 35.70 2.57
2818 3315 9.720769 AAAACAAGTATAGTGTGTTGCTAGTAT 57.279 29.630 8.13 0.00 35.70 2.12
2819 3316 9.720769 AAACAAGTATAGTGTGTTGCTAGTATT 57.279 29.630 8.13 0.00 35.70 1.89
2820 3317 9.720769 AACAAGTATAGTGTGTTGCTAGTATTT 57.279 29.630 7.09 0.00 34.28 1.40
2874 3371 9.661954 AAATGATATATAGATAGGGACCGTGAT 57.338 33.333 0.00 0.00 0.00 3.06
3033 3533 1.280998 GTACCCTTGCACCATGGTAGT 59.719 52.381 19.28 10.60 34.17 2.73
3205 3861 1.892209 AAAGAAAGGGGCAGTACACG 58.108 50.000 0.00 0.00 0.00 4.49
3410 4066 8.082852 GCTATGATAAAATCTTCCGTAGTCTCA 58.917 37.037 0.00 0.00 0.00 3.27
4165 8680 6.957020 TCTTCCAGGGCCAATTAAAGAAAATA 59.043 34.615 6.18 0.00 0.00 1.40
4215 8730 2.683362 GCCAGTTTGTAAGCCTATGTCC 59.317 50.000 0.00 0.00 0.00 4.02
4807 9324 9.401058 CTAAAACTCTAAGAATTGATGACCCAT 57.599 33.333 0.00 0.00 0.00 4.00
4867 9384 3.795688 TCAAACCTGATGAGAAAGGCT 57.204 42.857 0.00 0.00 37.03 4.58
4955 9472 1.974543 CCAATCCAGCGGCCTTTTT 59.025 52.632 0.00 0.00 0.00 1.94
4968 9485 1.207593 CTTTTTGCGCTCCCAGTCG 59.792 57.895 9.73 0.00 0.00 4.18
5033 9586 0.251698 TGCCATCAGCCACCAATGAA 60.252 50.000 0.00 0.00 42.71 2.57
5040 9593 2.964464 TCAGCCACCAATGAATGTTGTT 59.036 40.909 0.00 0.00 0.00 2.83
5279 9841 2.397597 AGTTTGGAAAGTGGCATGGTT 58.602 42.857 0.00 0.00 0.00 3.67
5313 9875 6.043411 GGTCAGCGAAACATAGAGAACTATT 58.957 40.000 0.00 0.00 37.24 1.73
5333 9895 1.348696 TGTCTGCTGGAATTCAGAGCA 59.651 47.619 22.96 22.96 46.18 4.26
5377 9939 6.084738 AGACCTATAGCCCTTACATTGATGA 58.915 40.000 0.00 0.00 0.00 2.92
5491 10053 7.471721 TGAAATGATTGTTATGCTAACCTTCG 58.528 34.615 4.35 0.00 0.00 3.79
5529 10091 2.626266 GGAACCGAAATGGAACCAACTT 59.374 45.455 0.00 0.00 42.00 2.66
5782 10348 1.341080 CCAGGGCACAAATTCTTGGT 58.659 50.000 0.00 0.00 36.82 3.67
5808 10374 7.801315 TCGTCAACAATTTCTATTTCCTTTTCG 59.199 33.333 0.00 0.00 0.00 3.46
5811 10377 7.865385 TCAACAATTTCTATTTCCTTTTCGGTG 59.135 33.333 0.00 0.00 0.00 4.94
5854 10420 0.980754 ACACACACACACCCTGGAGA 60.981 55.000 0.00 0.00 0.00 3.71
5898 10464 1.134340 TGAATGGCCCGTATACACACC 60.134 52.381 0.00 1.07 0.00 4.16
5920 10486 2.863401 AAGGGCAGAAACGAACAAAC 57.137 45.000 0.00 0.00 0.00 2.93
5938 10504 9.037417 CGAACAAACGAAACAGAATATAAGAAC 57.963 33.333 0.00 0.00 35.09 3.01
5939 10505 9.872757 GAACAAACGAAACAGAATATAAGAACA 57.127 29.630 0.00 0.00 0.00 3.18
5940 10506 9.878599 AACAAACGAAACAGAATATAAGAACAG 57.121 29.630 0.00 0.00 0.00 3.16
5941 10507 9.052759 ACAAACGAAACAGAATATAAGAACAGT 57.947 29.630 0.00 0.00 0.00 3.55
5945 10511 8.857216 ACGAAACAGAATATAAGAACAGTAACG 58.143 33.333 0.00 0.00 0.00 3.18
5946 10512 7.839837 CGAAACAGAATATAAGAACAGTAACGC 59.160 37.037 0.00 0.00 0.00 4.84
5947 10513 8.773404 AAACAGAATATAAGAACAGTAACGCT 57.227 30.769 0.00 0.00 0.00 5.07
5948 10514 9.865321 AAACAGAATATAAGAACAGTAACGCTA 57.135 29.630 0.00 0.00 0.00 4.26
6104 10674 3.620472 GCCTTGATTGCAAAATGTGGGAT 60.620 43.478 1.71 0.00 32.73 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.093514 GCCGCCGTTATTAAGAAAAAGAC 58.906 43.478 0.00 0.00 0.00 3.01
1 2 4.004982 AGCCGCCGTTATTAAGAAAAAGA 58.995 39.130 0.00 0.00 0.00 2.52
2 3 4.095610 CAGCCGCCGTTATTAAGAAAAAG 58.904 43.478 0.00 0.00 0.00 2.27
3 4 3.502979 ACAGCCGCCGTTATTAAGAAAAA 59.497 39.130 0.00 0.00 0.00 1.94
4 5 3.075884 ACAGCCGCCGTTATTAAGAAAA 58.924 40.909 0.00 0.00 0.00 2.29
5 6 2.702261 ACAGCCGCCGTTATTAAGAAA 58.298 42.857 0.00 0.00 0.00 2.52
6 7 2.389962 ACAGCCGCCGTTATTAAGAA 57.610 45.000 0.00 0.00 0.00 2.52
7 8 3.523606 TTACAGCCGCCGTTATTAAGA 57.476 42.857 0.00 0.00 0.00 2.10
8 9 3.805422 TGATTACAGCCGCCGTTATTAAG 59.195 43.478 0.00 0.00 0.00 1.85
9 10 3.794717 TGATTACAGCCGCCGTTATTAA 58.205 40.909 0.00 0.00 0.00 1.40
10 11 3.455990 TGATTACAGCCGCCGTTATTA 57.544 42.857 0.00 0.00 0.00 0.98
11 12 2.319136 TGATTACAGCCGCCGTTATT 57.681 45.000 0.00 0.00 0.00 1.40
12 13 2.543777 ATGATTACAGCCGCCGTTAT 57.456 45.000 0.00 0.00 0.00 1.89
13 14 3.671008 ATATGATTACAGCCGCCGTTA 57.329 42.857 0.00 0.00 0.00 3.18
14 15 2.543777 ATATGATTACAGCCGCCGTT 57.456 45.000 0.00 0.00 0.00 4.44
15 16 2.037251 AGAATATGATTACAGCCGCCGT 59.963 45.455 0.00 0.00 0.00 5.68
16 17 2.688507 AGAATATGATTACAGCCGCCG 58.311 47.619 0.00 0.00 0.00 6.46
17 18 4.377431 CGAAAGAATATGATTACAGCCGCC 60.377 45.833 0.00 0.00 0.00 6.13
18 19 4.211374 ACGAAAGAATATGATTACAGCCGC 59.789 41.667 0.00 0.00 0.00 6.53
36 37 0.394938 TGCCCTAGCACTCAACGAAA 59.605 50.000 0.00 0.00 46.52 3.46
109 128 1.416050 GACCGAACGAATACCCGTGC 61.416 60.000 0.00 0.00 42.54 5.34
208 229 7.504574 CCCTCTTGGTTCGGGTTATAATAAAAT 59.495 37.037 0.00 0.00 33.16 1.82
243 431 3.870559 TCTACCCTTTCCAGAAGGTTCT 58.129 45.455 4.29 0.00 38.25 3.01
268 456 8.525290 AATCAATTCTATTTTACTCCTGGTGG 57.475 34.615 0.33 0.00 0.00 4.61
308 496 1.668151 GGACAAAGCGCTTCCTCGT 60.668 57.895 25.24 17.70 0.00 4.18
379 567 4.765449 TTGCGAGCCGATGCAGCT 62.765 61.111 0.00 0.00 45.23 4.24
380 568 2.801113 TTTTTGCGAGCCGATGCAGC 62.801 55.000 0.00 0.00 42.89 5.25
381 569 0.795735 CTTTTTGCGAGCCGATGCAG 60.796 55.000 0.00 0.00 42.89 4.41
382 570 1.209898 CTTTTTGCGAGCCGATGCA 59.790 52.632 0.00 0.00 41.13 3.96
383 571 2.154569 GCTTTTTGCGAGCCGATGC 61.155 57.895 0.00 0.00 34.06 3.91
384 572 4.062183 GCTTTTTGCGAGCCGATG 57.938 55.556 0.00 0.00 34.06 3.84
603 826 1.756950 CAGGTACGAGGCCTAGGCA 60.757 63.158 34.09 11.63 44.11 4.75
644 867 9.764363 TTCATGTACTCCTATGCAATAAACTAG 57.236 33.333 0.00 0.00 0.00 2.57
709 938 5.243730 TGAGTCTCTAATTTTGGCTTTTGGG 59.756 40.000 0.65 0.00 0.00 4.12
751 980 3.016736 CCGAGCAAGTCCATTTGGTTAT 58.983 45.455 0.00 0.00 38.76 1.89
754 983 0.609131 CCCGAGCAAGTCCATTTGGT 60.609 55.000 0.00 0.00 41.12 3.67
755 984 0.609131 ACCCGAGCAAGTCCATTTGG 60.609 55.000 0.00 0.00 0.00 3.28
765 1024 2.696707 ACGATTATCCTAACCCGAGCAA 59.303 45.455 0.00 0.00 0.00 3.91
790 1049 6.672147 ACTTTCTTTCTTCCAATGAATCACG 58.328 36.000 0.00 0.00 0.00 4.35
891 1150 2.012673 CAAAAGTGCAGCCTAGCCTAG 58.987 52.381 0.00 0.00 0.00 3.02
949 1208 4.828925 GGTGAGCGAGCTGGAGCC 62.829 72.222 0.84 0.00 43.38 4.70
1135 1415 3.440522 CCGTCCAAGGAAAAGGAAGATTC 59.559 47.826 0.00 0.00 35.74 2.52
1136 1416 3.421844 CCGTCCAAGGAAAAGGAAGATT 58.578 45.455 0.00 0.00 35.74 2.40
1137 1417 2.290960 CCCGTCCAAGGAAAAGGAAGAT 60.291 50.000 7.76 0.00 35.74 2.40
1138 1418 1.073284 CCCGTCCAAGGAAAAGGAAGA 59.927 52.381 7.76 0.00 35.74 2.87
1139 1419 1.534729 CCCGTCCAAGGAAAAGGAAG 58.465 55.000 7.76 0.00 35.29 3.46
1140 1420 0.111639 CCCCGTCCAAGGAAAAGGAA 59.888 55.000 7.76 0.00 35.29 3.36
1185 1465 1.820906 AGCGCATCACATCGGCAAT 60.821 52.632 11.47 0.00 0.00 3.56
1204 1484 1.239347 AGCCGCCAAGAAAGAAGAAC 58.761 50.000 0.00 0.00 0.00 3.01
1237 1517 1.066303 CTAACAAAACCAGCCGCACAA 59.934 47.619 0.00 0.00 0.00 3.33
1430 1916 0.252103 TCAAGAAGGCCCTCGGTAGT 60.252 55.000 0.00 0.00 0.00 2.73
1559 2045 7.695201 GGATTTATTTAACCGTTTCCTTTCTCG 59.305 37.037 0.00 0.00 0.00 4.04
1616 2105 5.927819 AGTTCCATTTTTCATTTGGCAAGA 58.072 33.333 0.00 0.00 0.00 3.02
1659 2148 4.213270 TCTTAACAATCTCAGTGCAAACGG 59.787 41.667 0.00 0.00 0.00 4.44
1737 2226 6.890979 AAGCATTTAGATTCTATTGGGCTC 57.109 37.500 8.94 0.00 0.00 4.70
1745 2234 5.369699 ACAGGCCCTAAGCATTTAGATTCTA 59.630 40.000 0.00 0.00 46.50 2.10
1774 2263 0.966179 TTTCGTGGAGCAGAGCAGTA 59.034 50.000 0.00 0.00 0.00 2.74
1782 2271 4.819630 AGTAAAACTGATTTTCGTGGAGCA 59.180 37.500 0.00 0.00 38.91 4.26
1784 2273 6.851330 GTGAAGTAAAACTGATTTTCGTGGAG 59.149 38.462 0.00 0.00 38.91 3.86
1815 2304 3.820467 TGTATGAAACTGCTCCAAAGTGG 59.180 43.478 0.00 0.00 39.43 4.00
1822 2311 3.618690 ACTCCTGTATGAAACTGCTCC 57.381 47.619 0.00 0.00 0.00 4.70
1907 2396 9.933723 CAAATAGATCCTTTTTCACCAAATTCT 57.066 29.630 0.00 0.00 0.00 2.40
1908 2397 9.927668 TCAAATAGATCCTTTTTCACCAAATTC 57.072 29.630 0.00 0.00 0.00 2.17
1918 2407 7.550712 GTCAGCCAATCAAATAGATCCTTTTT 58.449 34.615 0.00 0.00 35.39 1.94
1919 2408 6.183360 CGTCAGCCAATCAAATAGATCCTTTT 60.183 38.462 0.00 0.00 35.39 2.27
1944 2433 2.545537 ACCCTTTCGTTTCTCCTCAC 57.454 50.000 0.00 0.00 0.00 3.51
2095 2584 3.807622 ACGGGATAACTTCACAATATGCG 59.192 43.478 0.00 0.00 0.00 4.73
2109 2598 2.279935 ACACAAGCCAAACGGGATAA 57.720 45.000 0.00 0.00 40.01 1.75
2112 2601 1.135333 GAAAACACAAGCCAAACGGGA 59.865 47.619 0.00 0.00 40.01 5.14
2139 2628 9.875691 AATTATTGTTTCCTAAAATTCAGCTCC 57.124 29.630 0.00 0.00 0.00 4.70
2234 2728 4.263905 ACTGATTTTGGAGGTCCATAGCAA 60.264 41.667 0.00 0.00 46.97 3.91
2276 2770 0.951558 ATGAGCACCGGTTTTGACAC 59.048 50.000 2.97 0.00 0.00 3.67
2286 2780 5.174398 GCATAAATGAATTTCATGAGCACCG 59.826 40.000 12.50 0.67 37.15 4.94
2364 2858 8.139989 TGTTGATCAGTATCTATGACAGATGTG 58.860 37.037 0.00 0.00 44.10 3.21
2456 2951 4.420522 AGGTTGCAAAATCATTTGGTGT 57.579 36.364 0.00 0.00 44.93 4.16
2490 2985 3.431233 CGATATGCACATGAGTAGGCTTG 59.569 47.826 0.00 0.00 0.00 4.01
2793 3290 9.720769 AATACTAGCAACACACTATACTTGTTT 57.279 29.630 0.00 0.00 30.98 2.83
2816 3313 8.568676 TTGCACAACTGCCTAAATAGTAAATA 57.431 30.769 0.00 0.00 43.51 1.40
2817 3314 7.461182 TTGCACAACTGCCTAAATAGTAAAT 57.539 32.000 0.00 0.00 43.51 1.40
2818 3315 6.885952 TTGCACAACTGCCTAAATAGTAAA 57.114 33.333 0.00 0.00 43.51 2.01
2819 3316 6.885952 TTTGCACAACTGCCTAAATAGTAA 57.114 33.333 0.00 0.00 43.51 2.24
2820 3317 6.885952 TTTTGCACAACTGCCTAAATAGTA 57.114 33.333 0.00 0.00 43.51 1.82
2821 3318 5.782893 TTTTGCACAACTGCCTAAATAGT 57.217 34.783 0.00 0.00 43.51 2.12
2822 3319 5.634859 CCTTTTTGCACAACTGCCTAAATAG 59.365 40.000 0.00 0.00 43.51 1.73
2874 3371 1.196104 CCGGTAAGTCCTTGACCCCA 61.196 60.000 0.00 0.00 32.18 4.96
3033 3533 4.650972 AAAGCACTAATCCAAGGTGGTA 57.349 40.909 0.00 0.00 40.14 3.25
3205 3861 6.314917 ACTCATATCACCAATAATTTCCCCC 58.685 40.000 0.00 0.00 0.00 5.40
3314 3970 7.432869 AGCTGATTTAAACAAGCAACACATTA 58.567 30.769 20.35 0.00 0.00 1.90
3410 4066 2.036475 CACCGCTGGCATAAGAGAGTAT 59.964 50.000 0.00 0.00 0.00 2.12
3517 4199 7.801716 AGTTCATGTTGAGTTAGCTACAAAA 57.198 32.000 0.00 0.00 0.00 2.44
4086 8601 4.227982 TGGATCTCATTGGAAACATCTCCA 59.772 41.667 0.00 0.00 43.99 3.86
4165 8680 5.866207 AGATCCGAACTCCTTTACTGTTTT 58.134 37.500 0.00 0.00 0.00 2.43
4249 8765 0.251165 GAGGCCAAGGCAACAAGGTA 60.251 55.000 13.87 0.00 44.11 3.08
4258 8774 0.255890 TTATCACCAGAGGCCAAGGC 59.744 55.000 5.01 1.52 41.06 4.35
4362 8878 5.179452 AGTATCCTAACACATTGCTTGGT 57.821 39.130 0.00 0.00 0.00 3.67
4667 9183 4.782156 TGATTTTGTTTGGAGGGCCATTAT 59.218 37.500 6.18 0.00 45.46 1.28
4738 9254 4.161189 CCTATTCTCTTCTTGCAGGTCTGA 59.839 45.833 1.65 0.00 0.00 3.27
4807 9324 1.270305 CGAACTCTTTGTGGCCTCAGA 60.270 52.381 7.68 2.50 0.00 3.27
4867 9384 5.241506 CCTTCATCTGTAAAGGCTCAAACAA 59.758 40.000 0.00 0.00 35.95 2.83
4955 9472 2.357034 GAAACGACTGGGAGCGCA 60.357 61.111 11.47 0.00 0.00 6.09
4962 9479 1.067495 GTCCTCTCCTGAAACGACTGG 60.067 57.143 0.00 0.00 0.00 4.00
4968 9485 4.565022 CTTCTCAAGTCCTCTCCTGAAAC 58.435 47.826 0.00 0.00 0.00 2.78
5033 9586 2.086610 GGCATATCCCCCAACAACAT 57.913 50.000 0.00 0.00 0.00 2.71
5228 9790 3.726190 GCTTAGAAAACTCGCTGCATGTC 60.726 47.826 0.00 0.00 0.00 3.06
5279 9841 2.378445 TTCGCTGACCATTTCGATGA 57.622 45.000 0.00 0.00 0.00 2.92
5313 9875 1.348696 TGCTCTGAATTCCAGCAGACA 59.651 47.619 20.10 8.32 42.62 3.41
5491 10053 4.183865 GGTTCCTGAATTAAGCATTTGGC 58.816 43.478 0.00 0.00 45.30 4.52
5575 10137 0.968901 CAATGGGCACATGAGCACCT 60.969 55.000 15.10 1.67 37.02 4.00
5717 10283 4.657814 AAGGTGAATGGGTGAATACTGT 57.342 40.909 0.00 0.00 0.00 3.55
5782 10348 7.801315 CGAAAAGGAAATAGAAATTGTTGACGA 59.199 33.333 0.00 0.00 0.00 4.20
5834 10400 0.815213 CTCCAGGGTGTGTGTGTGTG 60.815 60.000 0.00 0.00 0.00 3.82
5838 10404 1.338107 TAGTCTCCAGGGTGTGTGTG 58.662 55.000 0.00 0.00 0.00 3.82
5854 10420 8.952278 TCATTTGTTAACGGCAATAGATTTAGT 58.048 29.630 0.26 0.00 0.00 2.24
5898 10464 0.941542 TGTTCGTTTCTGCCCTTTCG 59.058 50.000 0.00 0.00 0.00 3.46
5907 10473 4.932268 TCTGTTTCGTTTGTTCGTTTCT 57.068 36.364 0.00 0.00 0.00 2.52
5920 10486 7.839837 GCGTTACTGTTCTTATATTCTGTTTCG 59.160 37.037 0.00 0.00 0.00 3.46
5945 10511 2.517959 TGCAGGGGAATTGCATATAGC 58.482 47.619 0.00 0.00 45.89 2.97


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

AutoCloner maintained by Alex Coulton.