Multiple sequence alignment - TraesCS6A01G120800

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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 TraesCS6A01G120800 chr6A 100.000 2526 0 0 1 2526 92854660 92852135 0.000000e+00 4665.0
1 TraesCS6A01G120800 chr6D 92.847 713 35 5 1454 2166 77524556 77523860 0.000000e+00 1020.0
2 TraesCS6A01G120800 chr6D 93.379 589 20 6 189 774 77526591 77526019 0.000000e+00 854.0
3 TraesCS6A01G120800 chr6D 92.479 585 20 10 775 1341 77525235 77524657 0.000000e+00 815.0
4 TraesCS6A01G120800 chr6D 92.670 191 11 3 2336 2524 77519960 77519771 3.200000e-69 272.0
5 TraesCS6A01G120800 chr6D 98.750 80 1 0 1329 1408 77524637 77524558 2.620000e-30 143.0
6 TraesCS6A01G120800 chr6B 91.725 713 35 8 1454 2166 150151536 150150848 0.000000e+00 968.0
7 TraesCS6A01G120800 chr6B 92.972 498 26 6 278 773 150153474 150152984 0.000000e+00 717.0
8 TraesCS6A01G120800 chr6B 94.340 424 14 2 991 1408 150151957 150151538 2.120000e-180 641.0
9 TraesCS6A01G120800 chr6B 95.312 192 8 1 2336 2526 150150824 150150633 1.140000e-78 303.0
10 TraesCS6A01G120800 chr6B 89.048 210 8 4 775 973 150152150 150151945 1.940000e-61 246.0
11 TraesCS6A01G120800 chr6B 88.679 212 4 8 1 192 150154473 150154262 9.030000e-60 241.0
12 TraesCS6A01G120800 chr6B 96.262 107 3 1 193 298 150154232 150154126 9.290000e-40 174.0
13 TraesCS6A01G120800 chr7B 93.333 165 11 0 2173 2337 96812007 96812171 6.980000e-61 244.0
14 TraesCS6A01G120800 chr7B 76.437 174 31 10 1794 1962 617553412 617553244 4.480000e-13 86.1
15 TraesCS6A01G120800 chr5D 91.279 172 15 0 2169 2340 25040148 25039977 4.200000e-58 235.0
16 TraesCS6A01G120800 chr5D 91.071 168 15 0 2170 2337 311349685 311349852 7.030000e-56 228.0
17 TraesCS6A01G120800 chr3B 76.972 469 73 16 2083 2525 787996713 787996254 4.200000e-58 235.0
18 TraesCS6A01G120800 chr1D 90.805 174 16 0 2167 2340 206955531 206955704 1.510000e-57 233.0
19 TraesCS6A01G120800 chr1D 80.769 156 24 4 1744 1898 470934666 470934816 1.590000e-22 117.0
20 TraesCS6A01G120800 chr3A 91.617 167 14 0 2173 2339 52732309 52732143 5.430000e-57 231.0
21 TraesCS6A01G120800 chr2D 91.124 169 14 1 2173 2340 32474468 32474300 7.030000e-56 228.0
22 TraesCS6A01G120800 chr1B 90.286 175 16 1 2166 2340 37639103 37639276 7.030000e-56 228.0
23 TraesCS6A01G120800 chr3D 90.173 173 17 0 2170 2342 424623436 424623608 2.530000e-55 226.0
24 TraesCS6A01G120800 chr7A 80.682 176 26 7 1741 1913 638488910 638489080 2.040000e-26 130.0
25 TraesCS6A01G120800 chr7D 79.191 173 29 6 1742 1912 45576443 45576276 2.050000e-21 113.0
26 TraesCS6A01G120800 chr2B 78.182 165 29 4 1741 1904 449466746 449466904 5.750000e-17 99.0


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 TraesCS6A01G120800 chr6A 92852135 92854660 2525 True 4665.0 4665 100.000000 1 2526 1 chr6A.!!$R1 2525
1 TraesCS6A01G120800 chr6D 77519771 77526591 6820 True 620.8 1020 94.025000 189 2524 5 chr6D.!!$R1 2335
2 TraesCS6A01G120800 chr6B 150150633 150154473 3840 True 470.0 968 92.619714 1 2526 7 chr6B.!!$R1 2525

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
354 1075 0.87439 TTGCTGAAATCGCTGGACAC 59.126 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 3533 0.740737 AAAATGCATAGCCCGAGTGC 59.259 50.0 0.0 0.0 39.26 4.4 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
215 265 3.425659 AGCCAAGAGAAGGAAATCAACC 58.574 45.455 0.00 0.00 0.00 3.77
284 335 7.433680 AGCAACCGTTTTGAAAGAGAAATAAT 58.566 30.769 0.00 0.00 0.00 1.28
313 1034 5.163509 GCAGTTTCTCTTGAAAGGAAAAGGT 60.164 40.000 7.72 0.00 42.15 3.50
350 1071 1.468565 CCATGTTGCTGAAATCGCTGG 60.469 52.381 0.00 0.00 0.00 4.85
354 1075 0.874390 TTGCTGAAATCGCTGGACAC 59.126 50.000 0.00 0.00 0.00 3.67
389 1110 1.298340 CATGGGCCTTGTACGACCA 59.702 57.895 11.13 0.00 35.39 4.02
508 1230 1.805945 CGAAGGCGACTACCTGTGC 60.806 63.158 0.00 0.00 42.68 4.57
565 1288 8.331740 AGGAGAACATCATTTATTTCCTTCTGA 58.668 33.333 0.00 0.00 29.85 3.27
597 1320 3.088532 TGGGCACATATGAAAGGTGTTC 58.911 45.455 10.38 0.00 35.05 3.18
598 1321 2.427095 GGGCACATATGAAAGGTGTTCC 59.573 50.000 10.38 0.19 35.05 3.62
637 1360 3.286329 TGCTGTACTGCATCCATCATT 57.714 42.857 21.93 0.00 38.12 2.57
638 1361 4.420522 TGCTGTACTGCATCCATCATTA 57.579 40.909 21.93 0.00 38.12 1.90
639 1362 4.976864 TGCTGTACTGCATCCATCATTAT 58.023 39.130 21.93 0.00 38.12 1.28
662 1385 4.202749 TGGGTCTAGTCCTCTTGTAAGGAA 60.203 45.833 5.97 0.00 46.90 3.36
707 1430 2.257207 TGGAAGTAGACCTCCCAACAG 58.743 52.381 0.00 0.00 0.00 3.16
716 1439 1.339151 ACCTCCCAACAGCGATCTTTC 60.339 52.381 0.00 0.00 0.00 2.62
811 2371 8.755028 TCAGTTTGGCTTAGTACACTATTATGA 58.245 33.333 0.00 0.00 0.00 2.15
814 2374 9.542462 GTTTGGCTTAGTACACTATTATGATCA 57.458 33.333 0.00 0.00 0.00 2.92
874 2444 3.058501 CCGAAAATAAACGACTGGCAACT 60.059 43.478 0.00 0.00 37.61 3.16
881 2451 1.238439 ACGACTGGCAACTCCAAATG 58.762 50.000 0.00 0.00 46.01 2.32
1143 2715 4.430765 GTCCGTGATGGCGTCGGT 62.431 66.667 6.72 0.00 43.94 4.69
1321 2899 3.057019 GTTGCACAACAGATGAGACGTA 58.943 45.455 8.61 0.00 40.84 3.57
1322 2900 2.672714 TGCACAACAGATGAGACGTAC 58.327 47.619 0.00 0.00 0.00 3.67
1323 2901 1.649171 GCACAACAGATGAGACGTACG 59.351 52.381 15.01 15.01 0.00 3.67
1324 2902 2.921069 GCACAACAGATGAGACGTACGT 60.921 50.000 23.04 23.04 0.00 3.57
1418 3028 3.041940 CGCACAACCCACTCCGTC 61.042 66.667 0.00 0.00 0.00 4.79
1419 3029 2.426023 GCACAACCCACTCCGTCT 59.574 61.111 0.00 0.00 0.00 4.18
1420 3030 1.227853 GCACAACCCACTCCGTCTT 60.228 57.895 0.00 0.00 0.00 3.01
1421 3031 0.818040 GCACAACCCACTCCGTCTTT 60.818 55.000 0.00 0.00 0.00 2.52
1422 3032 0.944386 CACAACCCACTCCGTCTTTG 59.056 55.000 0.00 0.00 0.00 2.77
1423 3033 0.544697 ACAACCCACTCCGTCTTTGT 59.455 50.000 0.00 0.00 0.00 2.83
1424 3034 1.064979 ACAACCCACTCCGTCTTTGTT 60.065 47.619 0.00 0.00 0.00 2.83
1425 3035 1.602377 CAACCCACTCCGTCTTTGTTC 59.398 52.381 0.00 0.00 0.00 3.18
1426 3036 0.249741 ACCCACTCCGTCTTTGTTCG 60.250 55.000 0.00 0.00 0.00 3.95
1427 3037 0.249741 CCCACTCCGTCTTTGTTCGT 60.250 55.000 0.00 0.00 0.00 3.85
1428 3038 0.859232 CCACTCCGTCTTTGTTCGTG 59.141 55.000 0.00 0.00 0.00 4.35
1429 3039 1.537348 CCACTCCGTCTTTGTTCGTGA 60.537 52.381 0.00 0.00 0.00 4.35
1430 3040 2.404215 CACTCCGTCTTTGTTCGTGAT 58.596 47.619 0.00 0.00 0.00 3.06
1431 3041 2.408704 CACTCCGTCTTTGTTCGTGATC 59.591 50.000 0.00 0.00 0.00 2.92
1432 3042 2.035449 ACTCCGTCTTTGTTCGTGATCA 59.965 45.455 0.00 0.00 0.00 2.92
1433 3043 3.254060 CTCCGTCTTTGTTCGTGATCAT 58.746 45.455 0.00 0.00 0.00 2.45
1434 3044 3.659786 TCCGTCTTTGTTCGTGATCATT 58.340 40.909 0.00 0.00 0.00 2.57
1435 3045 4.062293 TCCGTCTTTGTTCGTGATCATTT 58.938 39.130 0.00 0.00 0.00 2.32
1436 3046 4.513692 TCCGTCTTTGTTCGTGATCATTTT 59.486 37.500 0.00 0.00 0.00 1.82
1437 3047 4.846137 CCGTCTTTGTTCGTGATCATTTTC 59.154 41.667 0.00 0.00 0.00 2.29
1438 3048 5.439828 CGTCTTTGTTCGTGATCATTTTCA 58.560 37.500 0.00 0.00 0.00 2.69
1439 3049 5.561499 CGTCTTTGTTCGTGATCATTTTCAG 59.439 40.000 0.00 0.00 0.00 3.02
1440 3050 6.430451 GTCTTTGTTCGTGATCATTTTCAGT 58.570 36.000 0.00 0.00 0.00 3.41
1441 3051 6.575201 GTCTTTGTTCGTGATCATTTTCAGTC 59.425 38.462 0.00 0.00 0.00 3.51
1442 3052 4.645667 TGTTCGTGATCATTTTCAGTCG 57.354 40.909 0.00 0.00 0.00 4.18
1443 3053 3.431912 TGTTCGTGATCATTTTCAGTCGG 59.568 43.478 0.00 0.00 0.00 4.79
1444 3054 3.313012 TCGTGATCATTTTCAGTCGGT 57.687 42.857 0.00 0.00 0.00 4.69
1445 3055 3.659786 TCGTGATCATTTTCAGTCGGTT 58.340 40.909 0.00 0.00 0.00 4.44
1446 3056 4.062293 TCGTGATCATTTTCAGTCGGTTT 58.938 39.130 0.00 0.00 0.00 3.27
1447 3057 5.231702 TCGTGATCATTTTCAGTCGGTTTA 58.768 37.500 0.00 0.00 0.00 2.01
1448 3058 5.347635 TCGTGATCATTTTCAGTCGGTTTAG 59.652 40.000 0.00 0.00 0.00 1.85
1449 3059 5.324697 GTGATCATTTTCAGTCGGTTTAGC 58.675 41.667 0.00 0.00 0.00 3.09
1450 3060 5.000591 TGATCATTTTCAGTCGGTTTAGCA 58.999 37.500 0.00 0.00 0.00 3.49
1451 3061 5.647658 TGATCATTTTCAGTCGGTTTAGCAT 59.352 36.000 0.00 0.00 0.00 3.79
1452 3062 5.545658 TCATTTTCAGTCGGTTTAGCATC 57.454 39.130 0.00 0.00 0.00 3.91
1474 3084 4.335315 TCTGTTTGTCATTGCTTCGTCTTT 59.665 37.500 0.00 0.00 0.00 2.52
1518 3128 4.443621 GACTAGTCCAAATAAGCAGTCCC 58.556 47.826 12.13 0.00 0.00 4.46
1558 3168 6.721668 TGTACATATGTAAGATCTCTCCCTGG 59.278 42.308 17.07 0.00 31.52 4.45
1559 3169 4.530161 ACATATGTAAGATCTCTCCCTGGC 59.470 45.833 6.56 0.00 0.00 4.85
1560 3170 2.856760 TGTAAGATCTCTCCCTGGCT 57.143 50.000 0.00 0.00 0.00 4.75
1561 3171 2.672098 TGTAAGATCTCTCCCTGGCTC 58.328 52.381 0.00 0.00 0.00 4.70
1562 3172 1.967779 GTAAGATCTCTCCCTGGCTCC 59.032 57.143 0.00 0.00 0.00 4.70
1563 3173 0.399806 AAGATCTCTCCCTGGCTCCC 60.400 60.000 0.00 0.00 0.00 4.30
1564 3174 1.235696 GATCTCTCCCTGGCTCCCT 59.764 63.158 0.00 0.00 0.00 4.20
1565 3175 1.074623 ATCTCTCCCTGGCTCCCTG 60.075 63.158 0.00 0.00 0.00 4.45
1614 3224 9.098355 CATATTATCCTTTCGTCTTTGTGAAGA 57.902 33.333 0.00 0.00 39.54 2.87
1634 3244 6.750501 TGAAGAATATTGTGTACGTACTCTGC 59.249 38.462 25.12 16.27 0.00 4.26
1713 3323 0.247185 AAATGGCGCATGGGAAACAG 59.753 50.000 14.90 0.00 0.00 3.16
1791 3401 6.389830 AACTTGCATCACATGTTCAGTTTA 57.610 33.333 0.00 0.00 41.44 2.01
1798 3408 7.028962 GCATCACATGTTCAGTTTAATGCTAA 58.971 34.615 0.00 0.00 0.00 3.09
1819 3429 8.612619 TGCTAAAATTTTGAAAATGCGGTTTTA 58.387 25.926 13.76 5.23 40.04 1.52
1833 3443 6.671614 TGCGGTTTTATGGTCACTTAATAG 57.328 37.500 0.00 0.00 0.00 1.73
1860 3470 4.827692 ACTCAAGCGTGTAAATATGGTCA 58.172 39.130 0.00 0.00 0.00 4.02
1861 3471 4.630069 ACTCAAGCGTGTAAATATGGTCAC 59.370 41.667 0.00 0.00 0.00 3.67
1867 3477 3.919827 GTGTAAATATGGTCACGAACGC 58.080 45.455 0.00 0.00 0.00 4.84
1916 3533 1.339438 CCACCTGTCATTGAGTGAGGG 60.339 57.143 6.19 0.00 37.56 4.30
1986 3603 2.762535 TTCGAGAAATCTGACCACCC 57.237 50.000 0.00 0.00 0.00 4.61
1991 3608 1.780309 AGAAATCTGACCACCCCAACA 59.220 47.619 0.00 0.00 0.00 3.33
2009 3626 4.484236 CAACACACTTTTGCACAGAAAGA 58.516 39.130 14.71 0.00 37.50 2.52
2010 3627 4.782019 ACACACTTTTGCACAGAAAGAA 57.218 36.364 14.71 0.00 37.50 2.52
2016 3633 6.038356 CACTTTTGCACAGAAAGAACTTGAT 58.962 36.000 14.71 0.00 37.50 2.57
2085 3702 5.629020 GCTCATGATGCGAAAAGTAAAACAA 59.371 36.000 0.00 0.00 0.00 2.83
2131 3749 6.126863 ACAAGAGACCCAATGTTAGATCAA 57.873 37.500 0.00 0.00 0.00 2.57
2166 3784 3.125829 CCACTCCACGATTCACATTTGAG 59.874 47.826 0.00 0.00 31.71 3.02
2167 3785 2.744202 ACTCCACGATTCACATTTGAGC 59.256 45.455 0.00 0.00 31.71 4.26
2168 3786 3.005554 CTCCACGATTCACATTTGAGCT 58.994 45.455 0.00 0.00 31.71 4.09
2169 3787 4.183865 CTCCACGATTCACATTTGAGCTA 58.816 43.478 0.00 0.00 31.71 3.32
2170 3788 4.769688 TCCACGATTCACATTTGAGCTAT 58.230 39.130 0.00 0.00 31.71 2.97
2174 3792 7.598869 TCCACGATTCACATTTGAGCTATATAC 59.401 37.037 0.00 0.00 31.71 1.47
2177 3795 7.815068 ACGATTCACATTTGAGCTATATACTCC 59.185 37.037 0.00 0.00 32.98 3.85
2178 3796 7.276658 CGATTCACATTTGAGCTATATACTCCC 59.723 40.741 0.00 0.00 32.98 4.30
2179 3797 7.618019 TTCACATTTGAGCTATATACTCCCT 57.382 36.000 0.00 0.00 32.98 4.20
2180 3798 7.233389 TCACATTTGAGCTATATACTCCCTC 57.767 40.000 0.00 0.00 32.98 4.30
2183 3801 4.383931 TTGAGCTATATACTCCCTCCGT 57.616 45.455 0.00 0.00 32.98 4.69
2184 3802 4.383931 TGAGCTATATACTCCCTCCGTT 57.616 45.455 0.00 0.00 32.98 4.44
2185 3803 4.333690 TGAGCTATATACTCCCTCCGTTC 58.666 47.826 0.00 0.00 32.98 3.95
2188 3806 3.816842 GCTATATACTCCCTCCGTTCCCA 60.817 52.174 0.00 0.00 0.00 4.37
2189 3807 2.852714 TATACTCCCTCCGTTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2191 5024 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
2195 5028 3.268595 ACTCCCTCCGTTCCCAAATATTT 59.731 43.478 0.00 0.00 0.00 1.40
2201 5034 6.227522 CCTCCGTTCCCAAATATTTGTTTTT 58.772 36.000 23.24 0.00 36.45 1.94
2226 5059 9.959749 TTTTAGACATTTCAAATGGACTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
2227 5060 8.684386 TTAGACATTTCAAATGGACTACAACA 57.316 30.769 14.70 1.25 0.00 3.33
2228 5061 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
2229 5062 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
2230 5063 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
2231 5064 7.526608 ACATTTCAAATGGACTACAACATACG 58.473 34.615 14.70 0.00 0.00 3.06
2232 5065 7.389330 ACATTTCAAATGGACTACAACATACGA 59.611 33.333 14.70 0.00 0.00 3.43
2234 5067 7.915293 TTCAAATGGACTACAACATACGAAT 57.085 32.000 0.00 0.00 0.00 3.34
2235 5068 7.302350 TCAAATGGACTACAACATACGAATG 57.698 36.000 0.00 0.00 39.17 2.67
2237 5070 8.035984 TCAAATGGACTACAACATACGAATGTA 58.964 33.333 0.00 0.00 45.79 2.29
2238 5071 8.826710 CAAATGGACTACAACATACGAATGTAT 58.173 33.333 0.00 0.00 45.79 2.29
2277 5110 6.276832 AGTGCATACTCATTCATTTTGCTT 57.723 33.333 0.00 0.00 28.79 3.91
2278 5111 6.327934 AGTGCATACTCATTCATTTTGCTTC 58.672 36.000 0.00 0.00 28.79 3.86
2279 5112 5.228635 GTGCATACTCATTCATTTTGCTTCG 59.771 40.000 0.00 0.00 0.00 3.79
2282 5115 7.134815 GCATACTCATTCATTTTGCTTCGTAT 58.865 34.615 0.00 0.00 0.00 3.06
2283 5116 7.112565 GCATACTCATTCATTTTGCTTCGTATG 59.887 37.037 0.00 0.00 35.72 2.39
2284 5117 6.500684 ACTCATTCATTTTGCTTCGTATGT 57.499 33.333 0.00 0.00 0.00 2.29
2286 5119 7.688372 ACTCATTCATTTTGCTTCGTATGTAG 58.312 34.615 0.00 0.00 0.00 2.74
2287 5120 7.334421 ACTCATTCATTTTGCTTCGTATGTAGT 59.666 33.333 0.00 0.00 0.00 2.73
2290 5144 7.609760 TTCATTTTGCTTCGTATGTAGTCAT 57.390 32.000 0.00 0.00 38.00 3.06
2293 5147 7.962373 TCATTTTGCTTCGTATGTAGTCATTTG 59.038 33.333 0.00 0.00 35.70 2.32
2299 5153 7.041712 TGCTTCGTATGTAGTCATTTGTTGAAA 60.042 33.333 0.00 0.00 35.70 2.69
2300 5154 7.962918 GCTTCGTATGTAGTCATTTGTTGAAAT 59.037 33.333 0.00 0.00 35.70 2.17
2303 5157 9.214957 TCGTATGTAGTCATTTGTTGAAATCTT 57.785 29.630 0.00 0.00 35.70 2.40
2334 5562 8.115490 AGACAAATATTTGGAAACTGAGGAAG 57.885 34.615 27.43 2.64 42.34 3.46
2365 7713 1.579698 CGAGGATCATGTGGAGCTTG 58.420 55.000 0.00 0.00 33.17 4.01
2368 7716 1.911357 AGGATCATGTGGAGCTTGTCA 59.089 47.619 0.00 0.00 30.93 3.58
2369 7717 2.508716 AGGATCATGTGGAGCTTGTCAT 59.491 45.455 0.00 0.00 30.93 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 181 6.825721 GTGAGGATTGAACATTGGTAGATTCT 59.174 38.462 0.00 0.00 0.00 2.40
178 199 5.819991 TCTTGGCTTGAATTTAGTGAGGAT 58.180 37.500 0.00 0.00 0.00 3.24
215 265 3.641437 TTGCTTTCATCCTTTTCACCG 57.359 42.857 0.00 0.00 0.00 4.94
284 335 7.639113 TTCCTTTCAAGAGAAACTGCTTTTA 57.361 32.000 0.00 0.00 38.76 1.52
313 1034 0.829990 TGGCCGAGCTTGATGTGATA 59.170 50.000 1.22 0.00 0.00 2.15
350 1071 4.474226 GTCACAAGGACAAAGATGTGTC 57.526 45.455 4.86 0.00 46.19 3.67
389 1110 6.963083 AGCTCGTATAGGAGTACATTTCTT 57.037 37.500 20.49 0.00 36.41 2.52
565 1288 5.276440 TCATATGTGCCCACCCTTTTTAAT 58.724 37.500 1.90 0.00 0.00 1.40
597 1320 3.312146 GCAACAACAAAATCTTTGTGGGG 59.688 43.478 10.58 4.59 36.08 4.96
598 1321 4.034279 CAGCAACAACAAAATCTTTGTGGG 59.966 41.667 10.58 6.99 36.08 4.61
637 1360 5.195146 TCCTTACAAGAGGACTAGACCCATA 59.805 44.000 7.68 0.00 40.87 2.74
638 1361 4.016479 TCCTTACAAGAGGACTAGACCCAT 60.016 45.833 7.68 0.00 40.87 4.00
639 1362 3.335786 TCCTTACAAGAGGACTAGACCCA 59.664 47.826 7.68 0.00 40.87 4.51
662 1385 3.225104 ACATGCCTTGTCAAGTTCACAT 58.775 40.909 11.61 6.78 30.89 3.21
707 1430 6.659776 ACAAGAAACAGTAAAGAAAGATCGC 58.340 36.000 0.00 0.00 0.00 4.58
776 1500 8.637986 TGTACTAAGCCAAACTGAAATTTTGAT 58.362 29.630 0.00 0.00 36.24 2.57
778 1502 7.920682 AGTGTACTAAGCCAAACTGAAATTTTG 59.079 33.333 0.00 0.00 34.31 2.44
779 1503 8.007405 AGTGTACTAAGCCAAACTGAAATTTT 57.993 30.769 0.00 0.00 0.00 1.82
811 2371 8.576442 CCTCTACAAAAGTAAAACCACATTGAT 58.424 33.333 0.00 0.00 0.00 2.57
814 2374 6.837048 ACCCTCTACAAAAGTAAAACCACATT 59.163 34.615 0.00 0.00 0.00 2.71
874 2444 0.036164 CCGGTCACAGGACATTTGGA 59.964 55.000 0.00 0.00 46.17 3.53
881 2451 2.668550 GTTGGCCGGTCACAGGAC 60.669 66.667 9.15 0.00 43.55 3.85
999 2571 4.157958 GCGCGTACGTCGGAGAGT 62.158 66.667 25.35 0.00 42.83 3.24
1324 2902 3.418913 CAAACATGGTCGCCGCGA 61.419 61.111 12.39 12.39 0.00 5.87
1412 3022 2.672714 TGATCACGAACAAAGACGGAG 58.327 47.619 0.00 0.00 0.00 4.63
1413 3023 2.804697 TGATCACGAACAAAGACGGA 57.195 45.000 0.00 0.00 0.00 4.69
1414 3024 4.404507 AAATGATCACGAACAAAGACGG 57.595 40.909 0.00 0.00 0.00 4.79
1415 3025 5.439828 TGAAAATGATCACGAACAAAGACG 58.560 37.500 0.00 0.00 0.00 4.18
1416 3026 6.430451 ACTGAAAATGATCACGAACAAAGAC 58.570 36.000 0.00 0.00 0.00 3.01
1417 3027 6.563939 CGACTGAAAATGATCACGAACAAAGA 60.564 38.462 0.00 0.00 0.00 2.52
1418 3028 5.561499 CGACTGAAAATGATCACGAACAAAG 59.439 40.000 0.00 0.00 0.00 2.77
1419 3029 5.439828 CGACTGAAAATGATCACGAACAAA 58.560 37.500 0.00 0.00 0.00 2.83
1420 3030 4.084066 CCGACTGAAAATGATCACGAACAA 60.084 41.667 0.00 0.00 0.00 2.83
1421 3031 3.431912 CCGACTGAAAATGATCACGAACA 59.568 43.478 0.00 0.00 0.00 3.18
1422 3032 3.432252 ACCGACTGAAAATGATCACGAAC 59.568 43.478 0.00 0.00 0.00 3.95
1423 3033 3.659786 ACCGACTGAAAATGATCACGAA 58.340 40.909 0.00 0.00 0.00 3.85
1424 3034 3.313012 ACCGACTGAAAATGATCACGA 57.687 42.857 0.00 0.00 0.00 4.35
1425 3035 4.404507 AAACCGACTGAAAATGATCACG 57.595 40.909 0.00 0.00 0.00 4.35
1426 3036 5.106712 TGCTAAACCGACTGAAAATGATCAC 60.107 40.000 0.00 0.00 0.00 3.06
1427 3037 5.000591 TGCTAAACCGACTGAAAATGATCA 58.999 37.500 0.00 0.00 0.00 2.92
1428 3038 5.545658 TGCTAAACCGACTGAAAATGATC 57.454 39.130 0.00 0.00 0.00 2.92
1429 3039 5.882557 AGATGCTAAACCGACTGAAAATGAT 59.117 36.000 0.00 0.00 0.00 2.45
1430 3040 5.122239 CAGATGCTAAACCGACTGAAAATGA 59.878 40.000 0.00 0.00 0.00 2.57
1431 3041 5.106555 ACAGATGCTAAACCGACTGAAAATG 60.107 40.000 0.00 0.00 0.00 2.32
1432 3042 5.003804 ACAGATGCTAAACCGACTGAAAAT 58.996 37.500 0.00 0.00 0.00 1.82
1433 3043 4.385825 ACAGATGCTAAACCGACTGAAAA 58.614 39.130 0.00 0.00 0.00 2.29
1434 3044 4.002906 ACAGATGCTAAACCGACTGAAA 57.997 40.909 0.00 0.00 0.00 2.69
1435 3045 3.678056 ACAGATGCTAAACCGACTGAA 57.322 42.857 0.00 0.00 0.00 3.02
1436 3046 3.678056 AACAGATGCTAAACCGACTGA 57.322 42.857 0.00 0.00 0.00 3.41
1437 3047 3.498397 ACAAACAGATGCTAAACCGACTG 59.502 43.478 0.00 0.00 0.00 3.51
1438 3048 3.740115 ACAAACAGATGCTAAACCGACT 58.260 40.909 0.00 0.00 0.00 4.18
1439 3049 3.496884 TGACAAACAGATGCTAAACCGAC 59.503 43.478 0.00 0.00 0.00 4.79
1440 3050 3.734463 TGACAAACAGATGCTAAACCGA 58.266 40.909 0.00 0.00 0.00 4.69
1441 3051 4.685169 ATGACAAACAGATGCTAAACCG 57.315 40.909 0.00 0.00 0.00 4.44
1442 3052 4.622740 GCAATGACAAACAGATGCTAAACC 59.377 41.667 0.00 0.00 40.08 3.27
1443 3053 5.464168 AGCAATGACAAACAGATGCTAAAC 58.536 37.500 0.00 0.00 46.39 2.01
1444 3054 5.710513 AGCAATGACAAACAGATGCTAAA 57.289 34.783 0.00 0.00 46.39 1.85
1448 3058 2.912967 CGAAGCAATGACAAACAGATGC 59.087 45.455 0.00 0.00 42.04 3.91
1449 3059 4.083643 AGACGAAGCAATGACAAACAGATG 60.084 41.667 0.00 0.00 0.00 2.90
1450 3060 4.067896 AGACGAAGCAATGACAAACAGAT 58.932 39.130 0.00 0.00 0.00 2.90
1451 3061 3.466836 AGACGAAGCAATGACAAACAGA 58.533 40.909 0.00 0.00 0.00 3.41
1452 3062 3.885484 AGACGAAGCAATGACAAACAG 57.115 42.857 0.00 0.00 0.00 3.16
1474 3084 4.878971 TCCACGATGAAAACACAAGAGAAA 59.121 37.500 0.00 0.00 0.00 2.52
1518 3128 3.678056 TGTACAGGCAGTTCAGTTAGG 57.322 47.619 0.00 0.00 0.00 2.69
1558 3168 2.346541 GGAAAAGGCAGCAGGGAGC 61.347 63.158 0.00 0.00 46.19 4.70
1559 3169 1.680314 GGGAAAAGGCAGCAGGGAG 60.680 63.158 0.00 0.00 0.00 4.30
1560 3170 2.440599 GGGAAAAGGCAGCAGGGA 59.559 61.111 0.00 0.00 0.00 4.20
1561 3171 2.681421 GGGGAAAAGGCAGCAGGG 60.681 66.667 0.00 0.00 0.00 4.45
1562 3172 2.681421 GGGGGAAAAGGCAGCAGG 60.681 66.667 0.00 0.00 0.00 4.85
1563 3173 1.680314 GAGGGGGAAAAGGCAGCAG 60.680 63.158 0.00 0.00 0.00 4.24
1564 3174 1.729267 AAGAGGGGGAAAAGGCAGCA 61.729 55.000 0.00 0.00 0.00 4.41
1565 3175 0.967887 GAAGAGGGGGAAAAGGCAGC 60.968 60.000 0.00 0.00 0.00 5.25
1608 3218 7.253684 GCAGAGTACGTACACAATATTCTTCAC 60.254 40.741 26.55 7.71 0.00 3.18
1614 3224 6.864342 AGAAGCAGAGTACGTACACAATATT 58.136 36.000 26.55 13.69 0.00 1.28
1634 3244 1.138859 TCCCGTGCCATGTGATAGAAG 59.861 52.381 0.00 0.00 0.00 2.85
1679 3289 7.094508 TGCGCCATTTTATTCTGAAGAAATA 57.905 32.000 10.61 3.69 37.61 1.40
1755 3365 5.409520 GTGATGCAAGTTATGTGACTCTCAA 59.590 40.000 0.00 0.00 0.00 3.02
1791 3401 7.200778 ACCGCATTTTCAAAATTTTAGCATT 57.799 28.000 2.44 0.00 0.00 3.56
1798 3408 7.935520 ACCATAAAACCGCATTTTCAAAATTT 58.064 26.923 0.00 0.00 40.99 1.82
1801 3411 6.018669 GTGACCATAAAACCGCATTTTCAAAA 60.019 34.615 0.00 0.00 40.99 2.44
1811 3421 5.296035 AGCTATTAAGTGACCATAAAACCGC 59.704 40.000 0.00 0.00 0.00 5.68
1819 3429 6.299805 TGAGTCAAGCTATTAAGTGACCAT 57.700 37.500 9.76 0.00 41.05 3.55
1860 3470 2.171079 CGCCCACATATGCGTTCGT 61.171 57.895 1.58 0.00 45.43 3.85
1861 3471 2.625906 CGCCCACATATGCGTTCG 59.374 61.111 1.58 0.00 45.43 3.95
1866 3476 1.739466 CATGGATACGCCCACATATGC 59.261 52.381 1.58 0.00 39.34 3.14
1867 3477 2.743664 CACATGGATACGCCCACATATG 59.256 50.000 0.00 0.00 39.34 1.78
1916 3533 0.740737 AAAATGCATAGCCCGAGTGC 59.259 50.000 0.00 0.00 39.26 4.40
1963 3580 4.459337 GGGTGGTCAGATTTCTCGAAAATT 59.541 41.667 6.91 0.00 33.56 1.82
1972 3589 1.886542 GTGTTGGGGTGGTCAGATTTC 59.113 52.381 0.00 0.00 0.00 2.17
1986 3603 2.937469 TCTGTGCAAAAGTGTGTTGG 57.063 45.000 0.00 0.00 0.00 3.77
1991 3608 5.048083 TCAAGTTCTTTCTGTGCAAAAGTGT 60.048 36.000 8.76 0.00 35.64 3.55
2023 3640 3.190535 GGGCGACTTTTCTGCAAATAGAA 59.809 43.478 0.00 0.00 35.02 2.10
2024 3641 2.747446 GGGCGACTTTTCTGCAAATAGA 59.253 45.455 0.00 0.00 0.00 1.98
2025 3642 2.487762 TGGGCGACTTTTCTGCAAATAG 59.512 45.455 0.00 0.00 0.00 1.73
2085 3702 3.547746 TGAGTTTTGACGTAGCCCTTTT 58.452 40.909 0.00 0.00 0.00 2.27
2166 3784 2.759535 GGGAACGGAGGGAGTATATAGC 59.240 54.545 0.00 0.00 0.00 2.97
2167 3785 4.043608 TGGGAACGGAGGGAGTATATAG 57.956 50.000 0.00 0.00 0.00 1.31
2168 3786 4.474303 TTGGGAACGGAGGGAGTATATA 57.526 45.455 0.00 0.00 0.00 0.86
2169 3787 3.339713 TTGGGAACGGAGGGAGTATAT 57.660 47.619 0.00 0.00 0.00 0.86
2170 3788 2.852714 TTGGGAACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
2174 3792 3.577805 AATATTTGGGAACGGAGGGAG 57.422 47.619 0.00 0.00 0.00 4.30
2177 3795 5.400066 AAACAAATATTTGGGAACGGAGG 57.600 39.130 27.43 3.68 42.34 4.30
2201 5034 9.126151 TGTTGTAGTCCATTTGAAATGTCTAAA 57.874 29.630 15.93 10.39 0.00 1.85
2206 5039 7.389330 TCGTATGTTGTAGTCCATTTGAAATGT 59.611 33.333 15.93 1.43 0.00 2.71
2207 5040 7.747888 TCGTATGTTGTAGTCCATTTGAAATG 58.252 34.615 10.84 10.84 0.00 2.32
2209 5042 7.731882 TTCGTATGTTGTAGTCCATTTGAAA 57.268 32.000 0.00 0.00 0.00 2.69
2254 5087 5.909621 AGCAAAATGAATGAGTATGCACT 57.090 34.783 0.00 0.00 37.87 4.40
2255 5088 5.228635 CGAAGCAAAATGAATGAGTATGCAC 59.771 40.000 0.00 0.00 34.89 4.57
2256 5089 5.106197 ACGAAGCAAAATGAATGAGTATGCA 60.106 36.000 0.00 0.00 34.89 3.96
2257 5090 5.335127 ACGAAGCAAAATGAATGAGTATGC 58.665 37.500 0.00 0.00 0.00 3.14
2258 5091 8.124823 ACATACGAAGCAAAATGAATGAGTATG 58.875 33.333 0.00 0.00 41.70 2.39
2259 5092 8.213518 ACATACGAAGCAAAATGAATGAGTAT 57.786 30.769 0.00 0.00 0.00 2.12
2260 5093 7.609760 ACATACGAAGCAAAATGAATGAGTA 57.390 32.000 0.00 0.00 0.00 2.59
2262 5095 7.688372 ACTACATACGAAGCAAAATGAATGAG 58.312 34.615 0.00 0.00 0.00 2.90
2263 5096 7.333174 TGACTACATACGAAGCAAAATGAATGA 59.667 33.333 0.00 0.00 0.00 2.57
2264 5097 7.463544 TGACTACATACGAAGCAAAATGAATG 58.536 34.615 0.00 0.00 0.00 2.67
2265 5098 7.609760 TGACTACATACGAAGCAAAATGAAT 57.390 32.000 0.00 0.00 0.00 2.57
2266 5099 7.609760 ATGACTACATACGAAGCAAAATGAA 57.390 32.000 0.00 0.00 34.71 2.57
2270 5103 7.197071 ACAAATGACTACATACGAAGCAAAA 57.803 32.000 0.00 0.00 35.50 2.44
2272 5105 6.425417 TCAACAAATGACTACATACGAAGCAA 59.575 34.615 0.00 0.00 35.50 3.91
2273 5106 5.929415 TCAACAAATGACTACATACGAAGCA 59.071 36.000 0.00 0.00 35.50 3.91
2274 5107 6.403333 TCAACAAATGACTACATACGAAGC 57.597 37.500 0.00 0.00 35.50 3.86
2275 5108 9.478019 GATTTCAACAAATGACTACATACGAAG 57.522 33.333 0.00 0.00 37.92 3.79
2277 5110 8.771920 AGATTTCAACAAATGACTACATACGA 57.228 30.769 0.00 0.00 37.92 3.43
2278 5111 9.825972 AAAGATTTCAACAAATGACTACATACG 57.174 29.630 0.00 0.00 37.92 3.06
2310 5164 7.886338 ACTTCCTCAGTTTCCAAATATTTGTC 58.114 34.615 23.24 12.42 31.70 3.18
2320 5548 9.998106 GCTTAATATATACTTCCTCAGTTTCCA 57.002 33.333 0.00 0.00 36.88 3.53
2326 5554 8.282455 TCCTCGCTTAATATATACTTCCTCAG 57.718 38.462 0.00 0.00 0.00 3.35
2334 5562 8.414003 TCCACATGATCCTCGCTTAATATATAC 58.586 37.037 0.00 0.00 0.00 1.47
2357 7705 1.676635 GCAGCCATGACAAGCTCCA 60.677 57.895 0.00 0.00 37.18 3.86


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

AutoCloner maintained by Alex Coulton.