Multiple sequence alignment - TraesCS4B01G082100

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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 TraesCS4B01G082100 chr4B 100.000 2901 0 0 1 2901 80674443 80671543 0.000000e+00 5358.0
1 TraesCS4B01G082100 chr4D 90.086 2562 157 45 286 2789 54622870 54620348 0.000000e+00 3234.0
2 TraesCS4B01G082100 chr4A 86.285 2428 188 52 1 2356 542498146 542500500 0.000000e+00 2505.0
3 TraesCS4B01G082100 chr4A 87.943 564 37 11 2341 2895 542500703 542501244 1.130000e-178 636.0
4 TraesCS4B01G082100 chr4A 85.216 487 39 13 2231 2706 542523436 542523900 1.220000e-128 470.0
5 TraesCS4B01G082100 chr4A 78.878 303 55 5 1193 1489 658351933 658352232 2.280000e-46 196.0
6 TraesCS4B01G082100 chr4A 78.878 303 55 5 1193 1489 658922414 658922115 2.280000e-46 196.0
7 TraesCS4B01G082100 chr4A 90.217 92 9 0 1810 1901 658352391 658352482 1.410000e-23 121.0
8 TraesCS4B01G082100 chr4A 90.217 92 9 0 1810 1901 658921956 658921865 1.410000e-23 121.0
9 TraesCS4B01G082100 chr4A 90.110 91 9 0 1811 1901 658413266 658413356 5.080000e-23 119.0
10 TraesCS4B01G082100 chrUn 85.793 542 47 18 855 1388 70340009 70340528 5.470000e-152 547.0
11 TraesCS4B01G082100 chr2A 91.282 195 15 2 1195 1388 699381068 699380875 6.160000e-67 265.0
12 TraesCS4B01G082100 chr1B 87.255 204 18 3 1193 1388 29289505 29289708 2.910000e-55 226.0
13 TraesCS4B01G082100 chr7D 79.553 313 55 6 1186 1489 45759935 45760247 6.300000e-52 215.0
14 TraesCS4B01G082100 chr7D 87.500 96 10 2 1807 1901 45760463 45760557 3.060000e-20 110.0
15 TraesCS4B01G082100 chr7D 95.745 47 2 0 335 381 258233483 258233529 3.100000e-10 76.8
16 TraesCS4B01G082100 chr3A 91.729 133 10 1 1255 1387 737993403 737993272 1.780000e-42 183.0
17 TraesCS4B01G082100 chr1A 90.323 124 12 0 1260 1383 45528004 45528127 2.310000e-36 163.0
18 TraesCS4B01G082100 chr7B 80.952 105 20 0 305 409 436827182 436827078 1.850000e-12 84.2


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 TraesCS4B01G082100 chr4B 80671543 80674443 2900 True 5358.0 5358 100.000 1 2901 1 chr4B.!!$R1 2900
1 TraesCS4B01G082100 chr4D 54620348 54622870 2522 True 3234.0 3234 90.086 286 2789 1 chr4D.!!$R1 2503
2 TraesCS4B01G082100 chr4A 542498146 542501244 3098 False 1570.5 2505 87.114 1 2895 2 chr4A.!!$F3 2894
3 TraesCS4B01G082100 chrUn 70340009 70340528 519 False 547.0 547 85.793 855 1388 1 chrUn.!!$F1 533

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
315 316 0.038159 GTCTTATGGGCTCCGATCCG 60.038 60.0 0.00 0.0 0.00 4.18 F
705 745 0.249699 TTACAGCATGGATACGGCGG 60.250 55.0 13.24 0.0 43.62 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1628 0.477597 TCTTCCAGTTGGGGATGGGT 60.478 55.0 0.0 0.0 36.67 4.51 R
2700 3037 0.179089 CGAGCCATCTTGAGGTCTGG 60.179 60.0 0.0 0.0 0.00 3.86 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
62 63 4.764679 TTAGCACACAGTTGCCAATAAG 57.235 40.909 4.63 0.00 44.14 1.73
64 65 3.221771 AGCACACAGTTGCCAATAAGAA 58.778 40.909 4.63 0.00 44.14 2.52
71 72 6.040842 ACACAGTTGCCAATAAGAAAACTCAT 59.959 34.615 0.00 0.00 0.00 2.90
72 73 6.583806 CACAGTTGCCAATAAGAAAACTCATC 59.416 38.462 0.00 0.00 0.00 2.92
73 74 6.095377 CAGTTGCCAATAAGAAAACTCATCC 58.905 40.000 0.00 0.00 0.00 3.51
90 91 9.799106 AAACTCATCCAGATATAAATTAGTGGG 57.201 33.333 0.00 0.00 0.00 4.61
105 106 3.473923 AGTGGGGCAAACATTTTTCAG 57.526 42.857 0.00 0.00 0.00 3.02
133 134 4.023980 TCTTTCAGGAGGCGATTAGAAGA 58.976 43.478 0.00 0.00 0.00 2.87
135 136 2.735151 TCAGGAGGCGATTAGAAGACA 58.265 47.619 0.00 0.00 0.00 3.41
140 141 1.066303 AGGCGATTAGAAGACAGCGAG 59.934 52.381 0.00 0.00 0.00 5.03
157 158 1.801178 CGAGTGCTCCTTTCCTTCAAC 59.199 52.381 0.00 0.00 0.00 3.18
159 160 1.141053 AGTGCTCCTTTCCTTCAACGT 59.859 47.619 0.00 0.00 0.00 3.99
160 161 1.947456 GTGCTCCTTTCCTTCAACGTT 59.053 47.619 0.00 0.00 0.00 3.99
168 169 2.549282 CTTCAACGTTCGGTGCCG 59.451 61.111 0.00 3.94 41.35 5.69
189 190 2.373100 GGGGTTCCCCTAGCCTCT 59.627 66.667 18.94 0.00 44.66 3.69
190 191 1.630442 GGGGTTCCCCTAGCCTCTA 59.370 63.158 18.94 0.00 44.66 2.43
219 220 0.613292 ACAGCGGTGAGAGGATGAGT 60.613 55.000 23.44 0.00 0.00 3.41
221 222 0.323816 AGCGGTGAGAGGATGAGTGA 60.324 55.000 0.00 0.00 0.00 3.41
223 224 1.137872 GCGGTGAGAGGATGAGTGAAT 59.862 52.381 0.00 0.00 0.00 2.57
268 269 5.836024 TGTGGTGAAGGTAGGAATAGTTT 57.164 39.130 0.00 0.00 0.00 2.66
269 270 5.556915 TGTGGTGAAGGTAGGAATAGTTTG 58.443 41.667 0.00 0.00 0.00 2.93
284 285 7.785028 AGGAATAGTTTGAGGGTTTTTCTTCTT 59.215 33.333 0.00 0.00 0.00 2.52
291 292 2.876550 AGGGTTTTTCTTCTTTCGTCGG 59.123 45.455 0.00 0.00 0.00 4.79
315 316 0.038159 GTCTTATGGGCTCCGATCCG 60.038 60.000 0.00 0.00 0.00 4.18
371 372 2.035193 GCTCCAGCGTAGATTCTCATCA 59.965 50.000 0.00 0.00 0.00 3.07
402 403 4.502777 GGAACGACAAGGTTAGGACTTCTT 60.503 45.833 0.00 0.00 0.00 2.52
421 422 0.953471 TGTCAGGCGTACACAATGGC 60.953 55.000 0.00 0.00 39.96 4.40
422 423 0.953471 GTCAGGCGTACACAATGGCA 60.953 55.000 0.00 0.00 42.10 4.92
443 444 4.685924 CAAATTCTGGTGTCAAGTGCTTT 58.314 39.130 0.00 0.00 0.00 3.51
446 447 3.126001 TCTGGTGTCAAGTGCTTTAGG 57.874 47.619 0.00 0.00 0.00 2.69
449 450 2.438021 TGGTGTCAAGTGCTTTAGGTCT 59.562 45.455 0.00 0.00 0.00 3.85
457 458 6.535508 GTCAAGTGCTTTAGGTCTATTCGAAT 59.464 38.462 16.15 16.15 0.00 3.34
461 462 6.879458 AGTGCTTTAGGTCTATTCGAATGTTT 59.121 34.615 20.87 0.00 0.00 2.83
485 486 1.532604 ATGACAACTGCGACTCCGGA 61.533 55.000 2.93 2.93 36.06 5.14
519 547 4.052229 CGTCGACAAGGTCCGGCT 62.052 66.667 17.16 0.00 0.00 5.52
534 562 2.713894 GGCTACAACGACGCGTCAC 61.714 63.158 35.71 14.00 39.99 3.67
569 597 2.259511 GGTAGCGGTCGTTCGGTT 59.740 61.111 9.60 0.00 41.30 4.44
571 599 2.431260 TAGCGGTCGTTCGGTTGC 60.431 61.111 9.60 0.00 41.30 4.17
596 624 6.018262 CGTAGGGATCTCGATGCAATTTTTAA 60.018 38.462 0.00 0.00 0.00 1.52
633 661 6.430000 TGCTTTGTAGATTCTGTAAACCCTTC 59.570 38.462 0.00 0.00 0.00 3.46
634 662 6.402226 GCTTTGTAGATTCTGTAAACCCTTCG 60.402 42.308 0.00 0.00 0.00 3.79
656 690 8.964420 TTCGTAATTGATTCAAGTCATTTTCC 57.036 30.769 2.11 0.00 0.00 3.13
705 745 0.249699 TTACAGCATGGATACGGCGG 60.250 55.000 13.24 0.00 43.62 6.13
749 789 1.154169 GCCACATGTGACATGTGCG 60.154 57.895 39.39 33.01 45.81 5.34
794 835 4.215908 AGACTCATACCACGATACACCAT 58.784 43.478 0.00 0.00 0.00 3.55
830 871 1.386550 GGCAACAACCCATACCCCT 59.613 57.895 0.00 0.00 0.00 4.79
864 905 2.484947 GCTGTACTTATAGGCCCACACC 60.485 54.545 0.00 0.00 0.00 4.16
866 907 2.293318 TGTACTTATAGGCCCACACCCT 60.293 50.000 0.00 0.00 36.47 4.34
880 926 1.133809 CACCCTCTCCCACCCAGAAA 61.134 60.000 0.00 0.00 0.00 2.52
902 958 0.603707 TCCAGCAAAGCAACCGAGAG 60.604 55.000 0.00 0.00 0.00 3.20
903 959 0.603707 CCAGCAAAGCAACCGAGAGA 60.604 55.000 0.00 0.00 0.00 3.10
904 960 0.795085 CAGCAAAGCAACCGAGAGAG 59.205 55.000 0.00 0.00 0.00 3.20
905 961 0.681733 AGCAAAGCAACCGAGAGAGA 59.318 50.000 0.00 0.00 0.00 3.10
906 962 1.070758 AGCAAAGCAACCGAGAGAGAA 59.929 47.619 0.00 0.00 0.00 2.87
907 963 1.873591 GCAAAGCAACCGAGAGAGAAA 59.126 47.619 0.00 0.00 0.00 2.52
908 964 2.096019 GCAAAGCAACCGAGAGAGAAAG 60.096 50.000 0.00 0.00 0.00 2.62
909 965 3.393800 CAAAGCAACCGAGAGAGAAAGA 58.606 45.455 0.00 0.00 0.00 2.52
910 966 3.311486 AAGCAACCGAGAGAGAAAGAG 57.689 47.619 0.00 0.00 0.00 2.85
911 967 2.520069 AGCAACCGAGAGAGAAAGAGA 58.480 47.619 0.00 0.00 0.00 3.10
1503 1583 4.148825 CCGTCCAAGGCCGAGGAG 62.149 72.222 18.17 12.33 33.85 3.69
1601 1681 1.168714 AAGCTCAAATTGCTCGACCC 58.831 50.000 0.00 0.00 40.22 4.46
1620 1701 2.173519 CCATGTTGGTTGGATCTTGCT 58.826 47.619 0.00 0.00 36.26 3.91
1621 1702 2.564062 CCATGTTGGTTGGATCTTGCTT 59.436 45.455 0.00 0.00 36.26 3.91
1644 1725 6.780706 TTCCGATGTGAAAAACTAAGTCTC 57.219 37.500 0.00 0.00 0.00 3.36
1725 1814 6.403866 TGGAACAATTTAAGCACTGTTGAT 57.596 33.333 0.00 0.00 32.31 2.57
1726 1815 6.815089 TGGAACAATTTAAGCACTGTTGATT 58.185 32.000 0.00 0.00 32.21 2.57
1727 1816 7.271511 TGGAACAATTTAAGCACTGTTGATTT 58.728 30.769 0.00 0.00 30.29 2.17
1728 1817 7.437862 TGGAACAATTTAAGCACTGTTGATTTC 59.562 33.333 0.00 0.00 30.29 2.17
1754 1843 2.287427 CGCTTCATGCTTGGATTGGATC 60.287 50.000 0.00 0.00 40.11 3.36
1756 1845 2.715749 TCATGCTTGGATTGGATCGT 57.284 45.000 0.00 0.00 0.00 3.73
1757 1846 3.836365 TCATGCTTGGATTGGATCGTA 57.164 42.857 0.00 0.00 0.00 3.43
1758 1847 3.466836 TCATGCTTGGATTGGATCGTAC 58.533 45.455 0.00 0.00 0.00 3.67
1759 1848 1.934589 TGCTTGGATTGGATCGTACG 58.065 50.000 9.53 9.53 0.00 3.67
1760 1849 1.206132 TGCTTGGATTGGATCGTACGT 59.794 47.619 16.05 2.33 0.00 3.57
1761 1850 2.427812 TGCTTGGATTGGATCGTACGTA 59.572 45.455 16.05 2.34 0.00 3.57
1762 1851 3.069016 TGCTTGGATTGGATCGTACGTAT 59.931 43.478 16.05 7.52 0.00 3.06
1763 1852 4.056050 GCTTGGATTGGATCGTACGTATT 58.944 43.478 16.05 1.28 0.00 1.89
1764 1853 4.510340 GCTTGGATTGGATCGTACGTATTT 59.490 41.667 16.05 0.00 0.00 1.40
1765 1854 5.558273 GCTTGGATTGGATCGTACGTATTTG 60.558 44.000 16.05 0.00 0.00 2.32
1766 1855 5.265350 TGGATTGGATCGTACGTATTTGA 57.735 39.130 16.05 0.00 0.00 2.69
1772 1861 4.506288 TGGATCGTACGTATTTGATTGCTG 59.494 41.667 16.05 0.00 0.00 4.41
1814 1903 6.609237 TTGTTCTTCTCTCTTGATGTGTTG 57.391 37.500 0.00 0.00 0.00 3.33
1815 1904 5.674525 TGTTCTTCTCTCTTGATGTGTTGT 58.325 37.500 0.00 0.00 0.00 3.32
2001 2098 1.138883 GCGACCTATGTGCACGAGA 59.861 57.895 17.73 0.00 0.00 4.04
2038 2135 3.718864 CGAATCGCGTGGAAATTACATTG 59.281 43.478 5.77 0.00 34.64 2.82
2075 2172 0.097674 GCCATCATCACGACAAGCAC 59.902 55.000 0.00 0.00 0.00 4.40
2112 2213 4.586001 GCATCATATTGTGGACTTGGGATT 59.414 41.667 0.00 0.00 0.00 3.01
2136 2239 1.205655 CCTCTGATGACAGGAAGCGAA 59.794 52.381 0.00 0.00 43.60 4.70
2175 2279 0.029300 CACCGGCCATTTCTAATGCG 59.971 55.000 0.00 0.00 0.00 4.73
2197 2301 5.741425 CGGCACTCACACATTATGATTTAG 58.259 41.667 0.00 0.00 0.00 1.85
2198 2302 5.294306 CGGCACTCACACATTATGATTTAGT 59.706 40.000 0.00 0.00 0.00 2.24
2199 2303 6.478673 CGGCACTCACACATTATGATTTAGTA 59.521 38.462 0.00 0.00 0.00 1.82
2222 2326 9.300681 AGTATGAATCACTGAATTTCCTTTCAA 57.699 29.630 0.00 0.00 35.31 2.69
2245 2354 9.519191 TCAAAAGAAAGTATGAATCCTTGATCA 57.481 29.630 0.00 0.00 0.00 2.92
2291 2400 8.652463 TCATGTAAACAGACAACGTATAATGTG 58.348 33.333 0.00 0.00 31.83 3.21
2383 2712 1.063942 TGTCTCTTCTCGGGCATCCTA 60.064 52.381 0.00 0.00 0.00 2.94
2407 2736 1.070615 TGCCAGCTACGTTGCTTGA 59.929 52.632 23.42 8.43 41.98 3.02
2470 2799 6.340537 CGCGAGGTGTTAAAATAACATACT 57.659 37.500 0.00 7.82 32.23 2.12
2471 2800 6.408428 CGCGAGGTGTTAAAATAACATACTC 58.592 40.000 0.00 18.18 35.53 2.59
2472 2801 6.255020 CGCGAGGTGTTAAAATAACATACTCT 59.745 38.462 21.77 12.61 36.12 3.24
2473 2802 7.399523 GCGAGGTGTTAAAATAACATACTCTG 58.600 38.462 21.77 18.27 36.12 3.35
2476 2805 8.494016 AGGTGTTAAAATAACATACTCTGCTC 57.506 34.615 6.26 0.00 32.23 4.26
2478 2807 6.900299 GTGTTAAAATAACATACTCTGCTCGC 59.100 38.462 6.26 0.00 32.23 5.03
2502 2835 3.195610 ACTCTGTTCCTAATCATCACGCA 59.804 43.478 0.00 0.00 0.00 5.24
2507 2840 4.940654 TGTTCCTAATCATCACGCAATTGA 59.059 37.500 10.34 0.00 0.00 2.57
2673 3010 6.053005 CCTACTCCTACTAGTCTGTTCAGAG 58.947 48.000 0.00 0.00 0.00 3.35
2681 3018 0.787183 GTCTGTTCAGAGCTTCGCAC 59.213 55.000 2.53 0.00 0.00 5.34
2706 3043 1.670791 TTTGTCCGTTTGTCCAGACC 58.329 50.000 0.00 0.00 0.00 3.85
2780 3117 0.975556 TCCAGAGTATTCGCCAGCCA 60.976 55.000 0.00 0.00 0.00 4.75
2801 3138 1.852309 TGGACCATGGCACCATAGAAT 59.148 47.619 22.36 0.00 34.91 2.40
2850 3187 3.533606 TGAGGAGCTCAAATCTACTGC 57.466 47.619 17.19 0.00 37.57 4.40
2874 3211 2.857483 TCAAATTTGAGGAGCCGAACA 58.143 42.857 16.91 0.00 32.50 3.18
2895 3232 3.993081 CACAACTCTCAGCGAAAGATTCT 59.007 43.478 0.00 0.00 0.00 2.40
2896 3233 4.450419 CACAACTCTCAGCGAAAGATTCTT 59.550 41.667 0.00 0.00 0.00 2.52
2897 3234 5.049818 CACAACTCTCAGCGAAAGATTCTTT 60.050 40.000 11.40 11.40 0.00 2.52
2898 3235 5.529060 ACAACTCTCAGCGAAAGATTCTTTT 59.471 36.000 12.73 0.00 0.00 2.27
2899 3236 5.854431 ACTCTCAGCGAAAGATTCTTTTC 57.146 39.130 12.73 8.27 34.48 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 6.072563 GCAACCCAAAAAGCATGTTTTCATAT 60.073 34.615 8.06 0.00 38.64 1.78
16 17 4.036616 GCAACCCAAAAAGCATGTTTTCAT 59.963 37.500 8.06 0.00 41.78 2.57
17 18 3.376546 GCAACCCAAAAAGCATGTTTTCA 59.623 39.130 8.06 0.00 0.00 2.69
24 25 3.402110 GCTAAAGCAACCCAAAAAGCAT 58.598 40.909 0.00 0.00 41.59 3.79
50 51 5.774690 TGGATGAGTTTTCTTATTGGCAACT 59.225 36.000 0.00 0.00 37.61 3.16
64 65 9.799106 CCCACTAATTTATATCTGGATGAGTTT 57.201 33.333 0.00 0.00 0.00 2.66
71 72 6.523035 TTGCCCCACTAATTTATATCTGGA 57.477 37.500 0.00 0.00 0.00 3.86
72 73 6.549364 TGTTTGCCCCACTAATTTATATCTGG 59.451 38.462 0.00 0.00 0.00 3.86
73 74 7.581213 TGTTTGCCCCACTAATTTATATCTG 57.419 36.000 0.00 0.00 0.00 2.90
90 91 3.751479 ACCCTCTGAAAAATGTTTGCC 57.249 42.857 0.00 0.00 0.00 4.52
105 106 0.391793 CGCCTCCTGAAAGAACCCTC 60.392 60.000 0.00 0.00 34.07 4.30
140 141 1.594331 ACGTTGAAGGAAAGGAGCAC 58.406 50.000 0.00 0.00 0.00 4.40
149 150 1.595929 GGCACCGAACGTTGAAGGA 60.596 57.895 5.00 0.00 0.00 3.36
200 201 0.613292 ACTCATCCTCTCACCGCTGT 60.613 55.000 0.00 0.00 0.00 4.40
205 206 4.320608 GAGATTCACTCATCCTCTCACC 57.679 50.000 0.00 0.00 44.36 4.02
219 220 4.022503 CCAGACGCTCAGATATGAGATTCA 60.023 45.833 21.35 0.00 38.13 2.57
221 222 3.894427 ACCAGACGCTCAGATATGAGATT 59.106 43.478 21.35 6.20 38.13 2.40
223 224 2.937519 ACCAGACGCTCAGATATGAGA 58.062 47.619 21.35 0.00 38.13 3.27
243 244 6.195600 ACTATTCCTACCTTCACCACAAAA 57.804 37.500 0.00 0.00 0.00 2.44
268 269 3.558418 CGACGAAAGAAGAAAAACCCTCA 59.442 43.478 0.00 0.00 0.00 3.86
269 270 3.059120 CCGACGAAAGAAGAAAAACCCTC 60.059 47.826 0.00 0.00 0.00 4.30
284 285 1.411246 CCATAAGACCATCCCGACGAA 59.589 52.381 0.00 0.00 0.00 3.85
291 292 0.035458 CGGAGCCCATAAGACCATCC 59.965 60.000 0.00 0.00 0.00 3.51
355 356 4.406456 AGGAGATGATGAGAATCTACGCT 58.594 43.478 0.00 0.00 39.60 5.07
367 368 1.405463 TGTCGTTCCGAGGAGATGATG 59.595 52.381 0.00 0.00 36.23 3.07
368 369 1.763968 TGTCGTTCCGAGGAGATGAT 58.236 50.000 0.00 0.00 36.23 2.45
371 372 0.818296 CCTTGTCGTTCCGAGGAGAT 59.182 55.000 0.00 0.00 36.23 2.75
396 397 1.411246 TGTGTACGCCTGACAAGAAGT 59.589 47.619 3.51 0.00 0.00 3.01
402 403 0.953471 GCCATTGTGTACGCCTGACA 60.953 55.000 3.51 0.00 0.00 3.58
404 405 0.250510 TTGCCATTGTGTACGCCTGA 60.251 50.000 3.51 0.00 0.00 3.86
421 422 3.996150 AGCACTTGACACCAGAATTTG 57.004 42.857 0.00 0.00 0.00 2.32
422 423 5.010012 CCTAAAGCACTTGACACCAGAATTT 59.990 40.000 0.00 0.00 0.00 1.82
449 450 9.986833 CAGTTGTCATCATTAAACATTCGAATA 57.013 29.630 10.97 0.00 0.00 1.75
457 458 4.754618 AGTCGCAGTTGTCATCATTAAACA 59.245 37.500 0.00 0.00 0.00 2.83
461 462 3.521560 GGAGTCGCAGTTGTCATCATTA 58.478 45.455 0.00 0.00 0.00 1.90
485 486 1.006102 CGACAGCTGAGGAACCGTT 60.006 57.895 23.35 0.00 0.00 4.44
489 490 0.729816 GTCGACGACAGCTGAGGAAC 60.730 60.000 23.35 6.83 32.09 3.62
491 492 1.170290 TTGTCGACGACAGCTGAGGA 61.170 55.000 27.75 11.12 43.69 3.71
492 493 0.730834 CTTGTCGACGACAGCTGAGG 60.731 60.000 27.75 13.87 43.69 3.86
569 597 1.106944 TGCATCGAGATCCCTACGCA 61.107 55.000 0.00 0.00 0.00 5.24
571 599 2.732412 ATTGCATCGAGATCCCTACG 57.268 50.000 0.00 0.00 0.00 3.51
596 624 7.781693 AGAATCTACAAAGCATCCCAAACATAT 59.218 33.333 0.00 0.00 0.00 1.78
705 745 1.614241 ATGTGTCCGGCCTAGTCACC 61.614 60.000 14.32 2.06 0.00 4.02
794 835 3.334891 ATGTGGGGCCCGCTTGTA 61.335 61.111 34.46 16.87 34.70 2.41
864 905 0.995024 ATGTTTCTGGGTGGGAGAGG 59.005 55.000 0.00 0.00 0.00 3.69
866 907 0.991920 GGATGTTTCTGGGTGGGAGA 59.008 55.000 0.00 0.00 0.00 3.71
880 926 0.537143 TCGGTTGCTTTGCTGGATGT 60.537 50.000 0.00 0.00 0.00 3.06
902 958 2.477189 CGTCTTCCGCTCTCTCTTTCTC 60.477 54.545 0.00 0.00 0.00 2.87
903 959 1.470890 CGTCTTCCGCTCTCTCTTTCT 59.529 52.381 0.00 0.00 0.00 2.52
904 960 1.902840 CGTCTTCCGCTCTCTCTTTC 58.097 55.000 0.00 0.00 0.00 2.62
970 1026 2.258591 GGTCGTTGAGCTCGCTGA 59.741 61.111 9.64 3.27 0.00 4.26
993 1061 3.188786 GTGCTCCACATCGTCGCC 61.189 66.667 0.00 0.00 34.08 5.54
994 1062 3.188786 GGTGCTCCACATCGTCGC 61.189 66.667 0.00 0.00 35.86 5.19
1063 1131 0.690411 AGGGAGCATGAGGAGGACAG 60.690 60.000 0.00 0.00 0.00 3.51
1191 1268 4.135153 CACACCTCCTCCGCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
1192 1269 3.775654 CCACACCTCCTCCGCCTC 61.776 72.222 0.00 0.00 0.00 4.70
1193 1270 4.640690 ACCACACCTCCTCCGCCT 62.641 66.667 0.00 0.00 0.00 5.52
1194 1271 4.394712 CACCACACCTCCTCCGCC 62.395 72.222 0.00 0.00 0.00 6.13
1196 1273 4.742201 CGCACCACACCTCCTCCG 62.742 72.222 0.00 0.00 0.00 4.63
1548 1628 0.477597 TCTTCCAGTTGGGGATGGGT 60.478 55.000 0.00 0.00 36.67 4.51
1601 1681 3.947910 AAGCAAGATCCAACCAACATG 57.052 42.857 0.00 0.00 0.00 3.21
1620 1701 6.990349 AGAGACTTAGTTTTTCACATCGGAAA 59.010 34.615 0.00 0.00 35.11 3.13
1621 1702 6.522054 AGAGACTTAGTTTTTCACATCGGAA 58.478 36.000 0.00 0.00 0.00 4.30
1644 1725 5.515548 TCAAGAATCGATGTTGAACGAAG 57.484 39.130 17.09 0.00 41.65 3.79
1754 1843 5.198116 TCAACAGCAATCAAATACGTACG 57.802 39.130 15.01 15.01 0.00 3.67
1756 1845 5.216566 GCTCAACAGCAATCAAATACGTA 57.783 39.130 0.00 0.00 46.06 3.57
1757 1846 4.083581 GCTCAACAGCAATCAAATACGT 57.916 40.909 0.00 0.00 46.06 3.57
1906 1999 1.452110 CAGGATTGATTGACCGTGCA 58.548 50.000 0.00 0.00 0.00 4.57
2038 2135 1.790623 GGCGATGAATTGATGCAATGC 59.209 47.619 0.00 0.00 34.04 3.56
2075 2172 2.360350 ATGCGTGCACCCTTCCTG 60.360 61.111 12.15 0.00 0.00 3.86
2112 2213 1.543944 TTCCTGTCATCAGAGGCGCA 61.544 55.000 10.83 0.00 43.76 6.09
2136 2239 1.034838 ACATCTCCTCGCTCGCTTCT 61.035 55.000 0.00 0.00 0.00 2.85
2175 2279 6.683974 ACTAAATCATAATGTGTGAGTGCC 57.316 37.500 0.00 0.00 0.00 5.01
2197 2301 9.912634 TTTGAAAGGAAATTCAGTGATTCATAC 57.087 29.630 8.38 1.85 40.21 2.39
2199 2303 9.485206 CTTTTGAAAGGAAATTCAGTGATTCAT 57.515 29.630 8.38 0.00 40.21 2.57
2222 2326 7.613022 TGCTGATCAAGGATTCATACTTTCTTT 59.387 33.333 0.00 0.00 0.00 2.52
2383 2712 3.159858 AACGTAGCTGGCACACGGT 62.160 57.895 18.56 12.45 39.91 4.83
2407 2736 0.974010 TCGTCCGCTTCCCACCTAAT 60.974 55.000 0.00 0.00 0.00 1.73
2468 2797 1.470890 GAACAGAGTAGCGAGCAGAGT 59.529 52.381 0.00 0.00 0.00 3.24
2469 2798 1.202245 GGAACAGAGTAGCGAGCAGAG 60.202 57.143 0.00 0.00 0.00 3.35
2470 2799 0.811915 GGAACAGAGTAGCGAGCAGA 59.188 55.000 0.00 0.00 0.00 4.26
2471 2800 0.814457 AGGAACAGAGTAGCGAGCAG 59.186 55.000 0.00 0.00 0.00 4.24
2472 2801 2.124277 TAGGAACAGAGTAGCGAGCA 57.876 50.000 0.00 0.00 0.00 4.26
2473 2802 3.066900 TGATTAGGAACAGAGTAGCGAGC 59.933 47.826 0.00 0.00 0.00 5.03
2476 2805 4.979197 GTGATGATTAGGAACAGAGTAGCG 59.021 45.833 0.00 0.00 0.00 4.26
2478 2807 4.979197 GCGTGATGATTAGGAACAGAGTAG 59.021 45.833 0.00 0.00 0.00 2.57
2502 2835 7.222611 GCGCTTCCACACATAAATAAATCAATT 59.777 33.333 0.00 0.00 0.00 2.32
2507 2840 4.497340 CGGCGCTTCCACACATAAATAAAT 60.497 41.667 7.64 0.00 34.01 1.40
2516 2849 2.449031 ATCTTCGGCGCTTCCACACA 62.449 55.000 7.64 0.00 34.01 3.72
2517 2850 1.696832 GATCTTCGGCGCTTCCACAC 61.697 60.000 7.64 0.00 34.01 3.82
2586 2919 2.680913 GCCAACTAGCCACAGCACG 61.681 63.158 0.00 0.00 43.56 5.34
2700 3037 0.179089 CGAGCCATCTTGAGGTCTGG 60.179 60.000 0.00 0.00 0.00 3.86
2706 3043 2.376808 ACTTGTCGAGCCATCTTGAG 57.623 50.000 0.00 0.00 33.51 3.02
2780 3117 1.521764 TCTATGGTGCCATGGTCCAT 58.478 50.000 31.19 31.19 43.30 3.41
2783 3120 2.233271 CCATTCTATGGTGCCATGGTC 58.767 52.381 14.67 6.41 45.54 4.02
2837 3174 2.299993 TGAGCCGCAGTAGATTTGAG 57.700 50.000 0.00 0.00 0.00 3.02
2844 3181 3.395858 CTCAAATTTGAGCCGCAGTAG 57.604 47.619 29.90 9.15 46.97 2.57
2873 3210 3.993081 AGAATCTTTCGCTGAGAGTTGTG 59.007 43.478 0.00 0.00 34.02 3.33
2874 3211 4.264460 AGAATCTTTCGCTGAGAGTTGT 57.736 40.909 0.00 0.00 34.02 3.32


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

AutoCloner maintained by Alex Coulton.