Multiple sequence alignment - TraesCS5B01G419400

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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 TraesCS5B01G419400 chr5B 100.000 3235 0 0 1 3235 595011049 595007815 0.000000e+00 5975.0
1 TraesCS5B01G419400 chr5A 90.626 2731 157 43 543 3235 605245988 605243319 0.000000e+00 3533.0
2 TraesCS5B01G419400 chr5A 78.846 260 30 12 181 419 605246286 605246031 5.590000e-33 152.0
3 TraesCS5B01G419400 chr5D 92.595 1796 107 18 1445 3235 483769579 483767805 0.000000e+00 2556.0
4 TraesCS5B01G419400 chr5D 86.695 1180 61 29 1 1143 483770697 483769577 0.000000e+00 1221.0
5 TraesCS5B01G419400 chr5D 93.333 60 4 0 12 71 538566943 538566884 4.450000e-14 89.8
6 TraesCS5B01G419400 chr7D 82.246 1808 257 44 799 2571 500776224 500778002 0.000000e+00 1502.0
7 TraesCS5B01G419400 chr7D 82.161 1564 222 35 799 2336 113583073 113584605 0.000000e+00 1290.0
8 TraesCS5B01G419400 chr7D 92.537 67 4 1 6 71 510397851 510397785 9.550000e-16 95.3
9 TraesCS5B01G419400 chr7B 81.648 1760 255 40 799 2519 528873882 528875612 0.000000e+00 1399.0
10 TraesCS5B01G419400 chr7B 82.313 1617 228 35 800 2380 664398851 664397257 0.000000e+00 1349.0
11 TraesCS5B01G419400 chr7B 81.626 1513 230 30 849 2336 73176689 73178178 0.000000e+00 1210.0
12 TraesCS5B01G419400 chr7B 78.901 1474 260 33 799 2235 529823547 529825006 0.000000e+00 952.0
13 TraesCS5B01G419400 chr7B 81.015 611 86 16 1922 2518 73139884 73140478 2.940000e-125 459.0
14 TraesCS5B01G419400 chr3A 82.447 1618 232 31 801 2380 732404533 732402930 0.000000e+00 1367.0
15 TraesCS5B01G419400 chr7A 81.002 1816 262 51 799 2571 566989681 566991456 0.000000e+00 1365.0
16 TraesCS5B01G419400 chr7A 80.987 1804 250 56 799 2535 566910406 566912183 0.000000e+00 1345.0
17 TraesCS5B01G419400 chr7A 80.572 1817 262 52 799 2568 566790507 566792279 0.000000e+00 1315.0
18 TraesCS5B01G419400 chr7A 82.129 1287 200 21 1060 2336 619305129 619306395 0.000000e+00 1075.0
19 TraesCS5B01G419400 chrUn 80.868 1798 280 41 799 2571 86612162 86613920 0.000000e+00 1356.0
20 TraesCS5B01G419400 chr3D 82.261 1150 158 26 799 1926 598726083 598724958 0.000000e+00 952.0
21 TraesCS5B01G419400 chr3D 84.307 599 78 10 1984 2571 598724947 598724354 3.620000e-159 571.0
22 TraesCS5B01G419400 chr3D 94.828 58 3 0 14 71 390121909 390121966 1.240000e-14 91.6
23 TraesCS5B01G419400 chr3B 82.692 312 39 8 2269 2570 805931910 805931604 2.480000e-66 263.0
24 TraesCS5B01G419400 chr6A 96.610 59 1 1 12 70 502335223 502335166 2.660000e-16 97.1
25 TraesCS5B01G419400 chr1D 96.552 58 2 0 14 71 41987705 41987648 2.660000e-16 97.1
26 TraesCS5B01G419400 chr4D 94.915 59 3 0 13 71 236940126 236940184 3.440000e-15 93.5
27 TraesCS5B01G419400 chr4A 93.443 61 4 0 11 71 143697358 143697418 1.240000e-14 91.6
28 TraesCS5B01G419400 chr1A 94.828 58 3 0 14 71 435377425 435377368 1.240000e-14 91.6


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 TraesCS5B01G419400 chr5B 595007815 595011049 3234 True 5975.0 5975 100.000 1 3235 1 chr5B.!!$R1 3234
1 TraesCS5B01G419400 chr5A 605243319 605246286 2967 True 1842.5 3533 84.736 181 3235 2 chr5A.!!$R1 3054
2 TraesCS5B01G419400 chr5D 483767805 483770697 2892 True 1888.5 2556 89.645 1 3235 2 chr5D.!!$R2 3234
3 TraesCS5B01G419400 chr7D 500776224 500778002 1778 False 1502.0 1502 82.246 799 2571 1 chr7D.!!$F2 1772
4 TraesCS5B01G419400 chr7D 113583073 113584605 1532 False 1290.0 1290 82.161 799 2336 1 chr7D.!!$F1 1537
5 TraesCS5B01G419400 chr7B 528873882 528875612 1730 False 1399.0 1399 81.648 799 2519 1 chr7B.!!$F3 1720
6 TraesCS5B01G419400 chr7B 664397257 664398851 1594 True 1349.0 1349 82.313 800 2380 1 chr7B.!!$R1 1580
7 TraesCS5B01G419400 chr7B 73176689 73178178 1489 False 1210.0 1210 81.626 849 2336 1 chr7B.!!$F2 1487
8 TraesCS5B01G419400 chr7B 529823547 529825006 1459 False 952.0 952 78.901 799 2235 1 chr7B.!!$F4 1436
9 TraesCS5B01G419400 chr7B 73139884 73140478 594 False 459.0 459 81.015 1922 2518 1 chr7B.!!$F1 596
10 TraesCS5B01G419400 chr3A 732402930 732404533 1603 True 1367.0 1367 82.447 801 2380 1 chr3A.!!$R1 1579
11 TraesCS5B01G419400 chr7A 566989681 566991456 1775 False 1365.0 1365 81.002 799 2571 1 chr7A.!!$F3 1772
12 TraesCS5B01G419400 chr7A 566910406 566912183 1777 False 1345.0 1345 80.987 799 2535 1 chr7A.!!$F2 1736
13 TraesCS5B01G419400 chr7A 566790507 566792279 1772 False 1315.0 1315 80.572 799 2568 1 chr7A.!!$F1 1769
14 TraesCS5B01G419400 chr7A 619305129 619306395 1266 False 1075.0 1075 82.129 1060 2336 1 chr7A.!!$F4 1276
15 TraesCS5B01G419400 chrUn 86612162 86613920 1758 False 1356.0 1356 80.868 799 2571 1 chrUn.!!$F1 1772
16 TraesCS5B01G419400 chr3D 598724354 598726083 1729 True 761.5 952 83.284 799 2571 2 chr3D.!!$R1 1772

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
271 290 0.107703 TCAGCCGGTTAAGCATCCTG 60.108 55.0 1.90 7.51 0.00 3.86 F
609 668 0.178767 TCCGACTCCGATCGAGGTAA 59.821 55.0 18.66 1.76 45.13 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2057 0.030235 CTGGCGCATGATCCACAATG 59.970 55.000 10.83 0.0 0.0 2.82 R
2550 2811 1.302431 CAAGGCACCCGTCATCACA 60.302 57.895 0.00 0.0 0.0 3.58 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
24 25 1.199558 GATACGATGTACTCCCTCCGC 59.800 57.143 0.00 0.00 0.00 5.54
25 26 0.820891 TACGATGTACTCCCTCCGCC 60.821 60.000 0.00 0.00 0.00 6.13
26 27 2.857744 CGATGTACTCCCTCCGCCC 61.858 68.421 0.00 0.00 0.00 6.13
36 37 3.112263 CTCCCTCCGCCCCATAATATAA 58.888 50.000 0.00 0.00 0.00 0.98
37 38 3.112263 TCCCTCCGCCCCATAATATAAG 58.888 50.000 0.00 0.00 0.00 1.73
40 41 3.775316 CCTCCGCCCCATAATATAAGAGT 59.225 47.826 0.00 0.00 0.00 3.24
42 43 4.164981 TCCGCCCCATAATATAAGAGTGT 58.835 43.478 0.00 0.00 0.00 3.55
43 44 4.595781 TCCGCCCCATAATATAAGAGTGTT 59.404 41.667 0.00 0.00 0.00 3.32
80 83 2.657372 GTGTCAAAAACGAACGCAACAA 59.343 40.909 0.00 0.00 0.00 2.83
81 84 2.657372 TGTCAAAAACGAACGCAACAAC 59.343 40.909 0.00 0.00 0.00 3.32
82 85 2.912345 GTCAAAAACGAACGCAACAACT 59.088 40.909 0.00 0.00 0.00 3.16
83 86 4.090034 GTCAAAAACGAACGCAACAACTA 58.910 39.130 0.00 0.00 0.00 2.24
84 87 4.554200 GTCAAAAACGAACGCAACAACTAA 59.446 37.500 0.00 0.00 0.00 2.24
85 88 5.228427 GTCAAAAACGAACGCAACAACTAAT 59.772 36.000 0.00 0.00 0.00 1.73
86 89 6.411492 GTCAAAAACGAACGCAACAACTAATA 59.589 34.615 0.00 0.00 0.00 0.98
87 90 6.629649 TCAAAAACGAACGCAACAACTAATAG 59.370 34.615 0.00 0.00 0.00 1.73
88 91 5.910637 AAACGAACGCAACAACTAATAGA 57.089 34.783 0.00 0.00 0.00 1.98
89 92 5.511088 AACGAACGCAACAACTAATAGAG 57.489 39.130 0.00 0.00 0.00 2.43
90 93 4.553323 ACGAACGCAACAACTAATAGAGT 58.447 39.130 0.00 0.00 41.56 3.24
135 138 2.882927 AGTTCAGTACAAGACACGCA 57.117 45.000 0.00 0.00 0.00 5.24
167 170 3.897505 AGAACAAACCAGGAAAATCAGGG 59.102 43.478 0.00 0.00 0.00 4.45
192 195 0.532862 CAAGTGCCCGACAGAACACT 60.533 55.000 0.00 0.00 44.96 3.55
198 217 1.668294 CCGACAGAACACTGAGGCT 59.332 57.895 0.00 0.00 35.80 4.58
199 218 0.668706 CCGACAGAACACTGAGGCTG 60.669 60.000 0.00 0.00 35.80 4.85
200 219 0.668706 CGACAGAACACTGAGGCTGG 60.669 60.000 0.00 0.00 35.80 4.85
201 220 0.952984 GACAGAACACTGAGGCTGGC 60.953 60.000 0.00 0.00 35.80 4.85
202 221 1.071987 CAGAACACTGAGGCTGGCA 59.928 57.895 3.38 0.00 33.94 4.92
203 222 0.535780 CAGAACACTGAGGCTGGCAA 60.536 55.000 3.38 0.00 33.94 4.52
204 223 0.536006 AGAACACTGAGGCTGGCAAC 60.536 55.000 3.38 0.00 0.00 4.17
205 224 1.518903 GAACACTGAGGCTGGCAACC 61.519 60.000 3.38 0.00 0.00 3.77
206 225 1.999634 AACACTGAGGCTGGCAACCT 62.000 55.000 9.69 9.69 41.41 3.50
207 226 1.970114 CACTGAGGCTGGCAACCTG 60.970 63.158 15.46 3.28 37.77 4.00
208 227 2.149383 ACTGAGGCTGGCAACCTGA 61.149 57.895 15.46 4.79 37.77 3.86
209 228 1.673665 CTGAGGCTGGCAACCTGAC 60.674 63.158 15.46 1.06 37.77 3.51
210 229 2.360475 GAGGCTGGCAACCTGACC 60.360 66.667 15.46 0.00 37.77 4.02
211 230 2.856000 AGGCTGGCAACCTGACCT 60.856 61.111 9.03 0.00 35.72 3.85
212 231 2.360475 GGCTGGCAACCTGACCTC 60.360 66.667 0.00 0.00 0.00 3.85
213 232 2.360475 GCTGGCAACCTGACCTCC 60.360 66.667 0.00 0.00 0.00 4.30
214 233 2.046892 CTGGCAACCTGACCTCCG 60.047 66.667 0.00 0.00 0.00 4.63
215 234 2.847234 TGGCAACCTGACCTCCGT 60.847 61.111 0.00 0.00 0.00 4.69
271 290 0.107703 TCAGCCGGTTAAGCATCCTG 60.108 55.000 1.90 7.51 0.00 3.86
419 459 2.696759 GGAACCCACCGGCAAATCG 61.697 63.158 0.00 0.00 0.00 3.34
428 468 1.741145 ACCGGCAAATCGTTTACATCC 59.259 47.619 0.00 0.00 0.00 3.51
508 548 2.473984 CCTCCGTGACGTAACTTTTGAC 59.526 50.000 3.64 0.00 0.00 3.18
513 553 4.442705 CGTGACGTAACTTTTGACATGAC 58.557 43.478 0.00 0.00 0.00 3.06
520 560 0.179215 CTTTTGACATGACGAGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
579 634 3.359523 CGTGTCCGACCTCCGACA 61.360 66.667 0.00 0.00 41.76 4.35
582 637 0.813184 GTGTCCGACCTCCGACAATA 59.187 55.000 0.00 0.00 41.76 1.90
609 668 0.178767 TCCGACTCCGATCGAGGTAA 59.821 55.000 18.66 1.76 45.13 2.85
714 789 3.747193 CGATTTGTGTCCCTGATTTTCG 58.253 45.455 0.00 0.00 0.00 3.46
730 805 3.689224 TCGTCGGCGAAAAGAGTAG 57.311 52.632 10.97 0.00 44.92 2.57
731 806 0.455633 TCGTCGGCGAAAAGAGTAGC 60.456 55.000 10.97 0.00 44.92 3.58
733 808 0.455633 GTCGGCGAAAAGAGTAGCGA 60.456 55.000 12.92 0.00 0.00 4.93
734 809 0.454600 TCGGCGAAAAGAGTAGCGAT 59.545 50.000 7.35 0.00 0.00 4.58
735 810 1.135199 TCGGCGAAAAGAGTAGCGATT 60.135 47.619 7.35 0.00 0.00 3.34
736 811 1.659098 CGGCGAAAAGAGTAGCGATTT 59.341 47.619 0.00 0.00 0.00 2.17
737 812 2.093783 CGGCGAAAAGAGTAGCGATTTT 59.906 45.455 0.00 0.00 0.00 1.82
738 813 3.671256 GGCGAAAAGAGTAGCGATTTTC 58.329 45.455 0.00 0.00 38.80 2.29
739 814 3.371285 GGCGAAAAGAGTAGCGATTTTCT 59.629 43.478 7.72 0.00 39.60 2.52
740 815 4.327024 GCGAAAAGAGTAGCGATTTTCTG 58.673 43.478 7.72 3.80 39.60 3.02
741 816 4.091509 GCGAAAAGAGTAGCGATTTTCTGA 59.908 41.667 7.72 0.00 39.60 3.27
742 817 5.220491 GCGAAAAGAGTAGCGATTTTCTGAT 60.220 40.000 7.72 0.00 39.60 2.90
743 818 6.406820 CGAAAAGAGTAGCGATTTTCTGATC 58.593 40.000 7.72 0.00 39.60 2.92
744 819 6.508721 CGAAAAGAGTAGCGATTTTCTGATCC 60.509 42.308 7.72 0.00 39.60 3.36
745 820 5.606348 AAGAGTAGCGATTTTCTGATCCT 57.394 39.130 0.00 0.00 0.00 3.24
746 821 5.195001 AGAGTAGCGATTTTCTGATCCTC 57.805 43.478 0.00 0.00 0.00 3.71
747 822 3.971150 AGTAGCGATTTTCTGATCCTCG 58.029 45.455 0.00 0.00 0.00 4.63
748 823 2.231215 AGCGATTTTCTGATCCTCGG 57.769 50.000 0.00 0.00 0.00 4.63
749 824 1.202580 AGCGATTTTCTGATCCTCGGG 60.203 52.381 0.00 0.00 0.00 5.14
750 825 1.202533 GCGATTTTCTGATCCTCGGGA 60.203 52.381 0.00 0.00 35.55 5.14
751 826 2.474816 CGATTTTCTGATCCTCGGGAC 58.525 52.381 0.00 0.00 32.98 4.46
752 827 2.159099 CGATTTTCTGATCCTCGGGACA 60.159 50.000 0.00 0.00 32.98 4.02
753 828 3.462021 GATTTTCTGATCCTCGGGACAG 58.538 50.000 12.16 12.16 32.98 3.51
754 829 0.537188 TTTCTGATCCTCGGGACAGC 59.463 55.000 12.93 0.00 32.98 4.40
755 830 1.667154 TTCTGATCCTCGGGACAGCG 61.667 60.000 12.93 0.00 32.98 5.18
756 831 3.144120 CTGATCCTCGGGACAGCGG 62.144 68.421 0.00 0.00 32.98 5.52
776 851 2.111999 TAGCAGCCGCAGAAACCAGT 62.112 55.000 0.00 0.00 42.27 4.00
804 879 0.750546 TACGACCCTCCCACGATGAG 60.751 60.000 0.00 0.00 0.00 2.90
976 1057 2.928396 AACCTCCCACCCACCGAG 60.928 66.667 0.00 0.00 0.00 4.63
1084 1175 4.082733 GGTTCTCCAACTACAAAATCCAGC 60.083 45.833 0.00 0.00 32.50 4.85
1154 1310 8.904099 AGTACTGTTATATTGTAATCCTTGCC 57.096 34.615 0.00 0.00 0.00 4.52
1194 1361 9.396022 ACAATTATCCCTACTCACTGTTTTATG 57.604 33.333 0.00 0.00 0.00 1.90
1331 1498 3.508402 TGCTAGAAAGTACATCACACGGA 59.492 43.478 0.00 0.00 0.00 4.69
1421 1588 0.889306 AGTTGAGTCACTCGGTAGCC 59.111 55.000 0.00 0.00 32.35 3.93
1455 1622 1.401530 CGGCAATGATTATGCAAGCG 58.598 50.000 0.00 0.00 45.60 4.68
1478 1670 3.802948 AGCGTGATTGGTCTAAGTAGG 57.197 47.619 0.00 0.00 0.00 3.18
1529 1726 9.358872 ACGCAGATTGTATATACATCAATACAG 57.641 33.333 16.16 7.15 39.17 2.74
1562 1761 8.947055 AAGAACTAATTTGTTTGTGCATCTTT 57.053 26.923 6.72 0.00 0.00 2.52
1633 1837 1.800586 GTGACAAAAGAGATCGCAGCA 59.199 47.619 0.00 0.00 0.00 4.41
1717 1921 0.248825 GTTGCACGCCATCACAAACA 60.249 50.000 0.00 0.00 0.00 2.83
1737 1941 4.952460 ACACGAACCAATAACTACACTGT 58.048 39.130 0.00 0.00 0.00 3.55
1759 1964 8.085296 ACTGTGTGCGATATTTTTGGAAATTTA 58.915 29.630 0.00 0.00 36.82 1.40
1816 2024 8.562892 CAAGTCATGACAGTAAAGAAGAATGTT 58.437 33.333 27.02 4.47 0.00 2.71
1835 2043 3.242511 TGTTCACATCGTCGACCTATACG 60.243 47.826 10.58 0.00 40.40 3.06
1845 2053 1.665161 CGACCTATACGCCGCCTTTAG 60.665 57.143 0.00 0.00 0.00 1.85
1849 2057 2.593257 CTATACGCCGCCTTTAGTAGC 58.407 52.381 0.00 0.00 0.00 3.58
1885 2102 4.377022 GCGCCAGGTATGTATGTATTTTCG 60.377 45.833 0.00 0.00 0.00 3.46
1967 2192 5.409826 GTGCTTGCACTACTTCTTATGAACT 59.590 40.000 17.36 0.00 0.00 3.01
2155 2383 5.923684 GCAAATTTTTCTATTGGGACGACAA 59.076 36.000 0.00 0.00 34.41 3.18
2473 2723 6.814506 AGTCGAATACTTGCCTATATACGT 57.185 37.500 0.00 0.00 33.35 3.57
2476 2726 5.026462 CGAATACTTGCCTATATACGTCCG 58.974 45.833 0.00 0.00 0.00 4.79
2505 2760 2.351418 TCAACGCAATTCCACATCGATC 59.649 45.455 0.00 0.00 0.00 3.69
2550 2811 1.613255 CCGGGGCAACATGTTCTAAGT 60.613 52.381 8.48 0.00 39.74 2.24
2553 2814 2.228822 GGGGCAACATGTTCTAAGTGTG 59.771 50.000 8.48 0.00 39.74 3.82
2554 2815 3.146066 GGGCAACATGTTCTAAGTGTGA 58.854 45.455 8.48 0.00 39.74 3.58
2555 2816 3.758554 GGGCAACATGTTCTAAGTGTGAT 59.241 43.478 8.48 0.00 39.74 3.06
2586 2850 1.603456 TGTCGACGGTAGTGGTTGTA 58.397 50.000 11.62 0.00 0.00 2.41
2636 2900 9.904198 ATTTATTTTATTTGGGCTGCTTTGTAT 57.096 25.926 0.00 0.00 0.00 2.29
2682 2946 7.549134 AGATCAAAGTCCTTTTTCACCAAAAAC 59.451 33.333 0.00 0.00 36.70 2.43
2755 3022 7.244886 TCTCACAAGATTAGAGGATGTTCAA 57.755 36.000 0.00 0.00 0.00 2.69
2802 3069 8.896744 TGAGGATCTTCAGCATTTAATTAGTTG 58.103 33.333 2.91 0.00 34.92 3.16
2897 3164 4.161333 CCGAGATGCTTGTTTGCTTTTAG 58.839 43.478 0.00 0.00 0.00 1.85
2940 3207 4.380867 CCGCTGCTTTTCCATTAAGAATGT 60.381 41.667 0.00 0.00 37.18 2.71
2941 3208 5.163663 CCGCTGCTTTTCCATTAAGAATGTA 60.164 40.000 0.00 0.00 37.18 2.29
2942 3209 5.967674 CGCTGCTTTTCCATTAAGAATGTAG 59.032 40.000 0.00 0.00 37.18 2.74
3025 3294 5.940470 ACAATAGACTCCACTCCATCAAAAC 59.060 40.000 0.00 0.00 0.00 2.43
3157 3427 7.733501 TGGTGTTGTATTTAATTTTTAGGGGGA 59.266 33.333 0.00 0.00 0.00 4.81
3177 3447 3.557054 GGAGCACAAGTACTTCCATGACA 60.557 47.826 4.77 0.00 0.00 3.58
3183 3453 4.102524 ACAAGTACTTCCATGACAGTCCAA 59.897 41.667 4.77 0.00 0.00 3.53
3190 3460 1.302511 ATGACAGTCCAACCGGCAC 60.303 57.895 0.00 0.00 0.00 5.01
3193 3463 2.377628 GACAGTCCAACCGGCACTCA 62.378 60.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.728817 GGCGGAGGGAGTACATCG 59.271 66.667 0.00 0.00 0.00 3.84
135 138 1.029681 GGTTTGTTCTTCCGGTTGCT 58.970 50.000 0.00 0.00 0.00 3.91
167 170 0.460987 CTGTCGGGCACTTGGATCTC 60.461 60.000 0.00 0.00 0.00 2.75
192 195 2.431683 GTCAGGTTGCCAGCCTCA 59.568 61.111 0.00 0.00 33.31 3.86
198 217 2.847234 ACGGAGGTCAGGTTGCCA 60.847 61.111 0.00 0.00 0.00 4.92
199 218 2.047179 GACGGAGGTCAGGTTGCC 60.047 66.667 0.00 0.00 42.91 4.52
207 226 1.153349 GGCCATCTTGACGGAGGTC 60.153 63.158 0.00 0.00 43.71 3.85
208 227 2.990479 GGCCATCTTGACGGAGGT 59.010 61.111 0.00 0.00 0.00 3.85
209 228 2.202932 CGGCCATCTTGACGGAGG 60.203 66.667 2.24 0.00 0.00 4.30
210 229 0.807667 CTTCGGCCATCTTGACGGAG 60.808 60.000 2.24 0.00 0.00 4.63
211 230 1.218047 CTTCGGCCATCTTGACGGA 59.782 57.895 2.24 0.00 0.00 4.69
212 231 1.815421 CCTTCGGCCATCTTGACGG 60.815 63.158 2.24 0.00 0.00 4.79
213 232 0.807667 CTCCTTCGGCCATCTTGACG 60.808 60.000 2.24 0.00 0.00 4.35
214 233 0.537188 TCTCCTTCGGCCATCTTGAC 59.463 55.000 2.24 0.00 0.00 3.18
215 234 1.208052 CTTCTCCTTCGGCCATCTTGA 59.792 52.381 2.24 0.00 0.00 3.02
403 443 1.110518 AAACGATTTGCCGGTGGGTT 61.111 50.000 1.90 0.00 34.97 4.11
419 459 1.128692 GACGCTGCAGTGGATGTAAAC 59.871 52.381 29.60 7.91 0.00 2.01
428 468 1.889105 ACACCTTGACGCTGCAGTG 60.889 57.895 25.37 25.37 0.00 3.66
541 581 2.345880 ATATGCGTCACGGACCGGAC 62.346 60.000 20.00 19.77 0.00 4.79
542 582 2.067091 GATATGCGTCACGGACCGGA 62.067 60.000 20.00 9.89 0.00 5.14
543 583 1.660575 GATATGCGTCACGGACCGG 60.661 63.158 20.00 0.00 0.00 5.28
544 584 1.660575 GGATATGCGTCACGGACCG 60.661 63.158 13.61 13.61 0.00 4.79
545 585 1.660575 CGGATATGCGTCACGGACC 60.661 63.158 8.66 0.00 0.00 4.46
579 634 1.049289 GGAGTCGGAGCCCCAGTATT 61.049 60.000 0.00 0.00 0.00 1.89
609 668 0.673644 CAAGTCGAAATCGGGCCTGT 60.674 55.000 12.43 0.00 40.29 4.00
670 729 1.446792 CTGCGATGCACGTCCTCTT 60.447 57.895 9.76 0.00 44.60 2.85
694 769 4.669197 CGACGAAAATCAGGGACACAAATC 60.669 45.833 0.00 0.00 0.00 2.17
695 770 3.188460 CGACGAAAATCAGGGACACAAAT 59.812 43.478 0.00 0.00 0.00 2.32
714 789 0.455633 TCGCTACTCTTTTCGCCGAC 60.456 55.000 0.00 0.00 0.00 4.79
724 799 4.261405 CGAGGATCAGAAAATCGCTACTCT 60.261 45.833 0.00 0.00 33.17 3.24
725 800 3.978217 CGAGGATCAGAAAATCGCTACTC 59.022 47.826 0.00 0.00 33.17 2.59
726 801 3.243569 CCGAGGATCAGAAAATCGCTACT 60.244 47.826 0.00 0.00 33.17 2.57
727 802 3.053455 CCGAGGATCAGAAAATCGCTAC 58.947 50.000 0.00 0.00 33.17 3.58
728 803 2.035961 CCCGAGGATCAGAAAATCGCTA 59.964 50.000 0.00 0.00 33.17 4.26
729 804 1.202580 CCCGAGGATCAGAAAATCGCT 60.203 52.381 0.00 0.00 33.17 4.93
730 805 1.202533 TCCCGAGGATCAGAAAATCGC 60.203 52.381 0.00 0.00 33.17 4.58
731 806 2.159099 TGTCCCGAGGATCAGAAAATCG 60.159 50.000 0.00 0.00 32.73 3.34
733 808 2.420687 GCTGTCCCGAGGATCAGAAAAT 60.421 50.000 17.87 0.00 34.88 1.82
734 809 1.066143 GCTGTCCCGAGGATCAGAAAA 60.066 52.381 17.87 0.00 34.88 2.29
735 810 0.537188 GCTGTCCCGAGGATCAGAAA 59.463 55.000 17.87 0.00 34.88 2.52
736 811 1.667154 CGCTGTCCCGAGGATCAGAA 61.667 60.000 17.87 0.00 34.88 3.02
737 812 2.121538 CGCTGTCCCGAGGATCAGA 61.122 63.158 17.87 0.00 34.88 3.27
738 813 2.415010 CGCTGTCCCGAGGATCAG 59.585 66.667 0.00 13.20 35.51 2.90
739 814 2.561467 TACCGCTGTCCCGAGGATCA 62.561 60.000 0.00 0.00 32.73 2.92
740 815 1.797211 CTACCGCTGTCCCGAGGATC 61.797 65.000 0.00 0.00 32.73 3.36
741 816 1.828660 CTACCGCTGTCCCGAGGAT 60.829 63.158 0.00 0.00 32.73 3.24
742 817 2.439701 CTACCGCTGTCCCGAGGA 60.440 66.667 0.00 0.00 0.00 3.71
743 818 4.208686 GCTACCGCTGTCCCGAGG 62.209 72.222 0.00 0.00 0.00 4.63
744 819 3.417275 CTGCTACCGCTGTCCCGAG 62.417 68.421 0.00 0.00 36.97 4.63
745 820 3.449227 CTGCTACCGCTGTCCCGA 61.449 66.667 0.00 0.00 36.97 5.14
747 822 4.840005 GGCTGCTACCGCTGTCCC 62.840 72.222 0.00 0.00 37.41 4.46
755 830 2.399356 GGTTTCTGCGGCTGCTACC 61.399 63.158 20.27 16.05 43.34 3.18
756 831 1.639298 CTGGTTTCTGCGGCTGCTAC 61.639 60.000 20.27 11.08 43.34 3.58
776 851 1.407437 GGGAGGGTCGTACGAGAACTA 60.407 57.143 20.18 0.00 0.00 2.24
976 1057 1.517257 CGACATCTCCGTGACAGGC 60.517 63.158 0.00 0.00 0.00 4.85
1062 1153 4.082733 GGCTGGATTTTGTAGTTGGAGAAC 60.083 45.833 0.00 0.00 0.00 3.01
1084 1175 2.614057 GTGCCTTACCGATGAAATCTGG 59.386 50.000 0.00 0.00 42.58 3.86
1135 1291 5.977489 GGGGGCAAGGATTACAATATAAC 57.023 43.478 0.00 0.00 0.00 1.89
1154 1310 0.615544 AATTGTGATGCACCAGGGGG 60.616 55.000 0.00 0.00 41.29 5.40
1194 1361 5.107375 CCAACATTGTTGCTGCAAGTTATTC 60.107 40.000 21.55 3.32 35.30 1.75
1256 1423 0.179067 ACGGGTCGCAAGTTTTCTCA 60.179 50.000 0.00 0.00 39.48 3.27
1313 1480 4.038763 TGAACTCCGTGTGATGTACTTTCT 59.961 41.667 0.00 0.00 0.00 2.52
1331 1498 1.071471 CTTGCGGAGGGTGTGAACT 59.929 57.895 0.00 0.00 0.00 3.01
1421 1588 4.227134 CCGGAGATGGCCACGAGG 62.227 72.222 8.16 3.53 38.23 4.63
1455 1622 2.076863 ACTTAGACCAATCACGCTTGC 58.923 47.619 0.00 0.00 0.00 4.01
1469 1661 2.766263 CACATCACTGGGCCTACTTAGA 59.234 50.000 4.53 0.00 0.00 2.10
1478 1670 2.988010 TGATACTCACATCACTGGGC 57.012 50.000 0.00 0.00 29.93 5.36
1539 1736 8.579682 AGAAAGATGCACAAACAAATTAGTTC 57.420 30.769 0.00 0.00 0.00 3.01
1576 1780 7.578310 AGCTTTAATCTGCATCACATACATT 57.422 32.000 0.00 0.00 0.00 2.71
1597 1801 7.669722 TCTTTTGTCACCTTTCCAATATAAGCT 59.330 33.333 0.00 0.00 0.00 3.74
1633 1837 4.060205 GCTTCAACAATTGCTCCACATTT 58.940 39.130 5.05 0.00 0.00 2.32
1717 1921 4.748102 CACACAGTGTAGTTATTGGTTCGT 59.252 41.667 5.69 0.00 0.00 3.85
1737 1941 7.543868 CACCTAAATTTCCAAAAATATCGCACA 59.456 33.333 0.00 0.00 33.93 4.57
1759 1964 3.558931 TCGTTATGGATTGATGCACCT 57.441 42.857 0.00 0.00 0.00 4.00
1816 2024 1.262417 GCGTATAGGTCGACGATGTGA 59.738 52.381 9.92 0.00 41.60 3.58
1835 2043 1.064060 CACAATGCTACTAAAGGCGGC 59.936 52.381 0.00 0.00 0.00 6.53
1845 2053 1.334419 GCGCATGATCCACAATGCTAC 60.334 52.381 0.30 3.14 37.84 3.58
1849 2057 0.030235 CTGGCGCATGATCCACAATG 59.970 55.000 10.83 0.00 0.00 2.82
2155 2383 2.282674 CTGCATGTGTGGGGTGCT 60.283 61.111 0.00 0.00 39.52 4.40
2505 2760 3.641648 ACCATGCTGACAACAAAAATCG 58.358 40.909 0.00 0.00 0.00 3.34
2550 2811 1.302431 CAAGGCACCCGTCATCACA 60.302 57.895 0.00 0.00 0.00 3.58
2553 2814 2.100631 CGACAAGGCACCCGTCATC 61.101 63.158 7.42 0.00 0.00 2.92
2554 2815 2.047274 CGACAAGGCACCCGTCAT 60.047 61.111 7.42 0.00 0.00 3.06
2555 2816 3.228017 TCGACAAGGCACCCGTCA 61.228 61.111 7.42 0.00 0.00 4.35
2586 2850 2.039624 AGGGCTCTGGATGACCGT 59.960 61.111 0.00 0.00 39.42 4.83
2802 3069 8.345565 GTGTATTTGGATGGTGTATTTCTGATC 58.654 37.037 0.00 0.00 0.00 2.92
2897 3164 1.597461 CCTTCAGGGAGTTCCGTCC 59.403 63.158 0.00 0.00 41.52 4.79
2918 3185 4.737054 ACATTCTTAATGGAAAAGCAGCG 58.263 39.130 4.78 0.00 43.21 5.18
2940 3207 9.624373 AATTCGGAAGTCTACTGTAACTATCTA 57.376 33.333 0.00 0.00 0.00 1.98
2941 3208 8.522542 AATTCGGAAGTCTACTGTAACTATCT 57.477 34.615 0.00 0.00 0.00 1.98
3025 3294 1.028330 ATGCATGCCCAAGTCGACAG 61.028 55.000 19.50 9.72 0.00 3.51
3157 3427 3.071602 ACTGTCATGGAAGTACTTGTGCT 59.928 43.478 14.14 0.00 0.00 4.40
3177 3447 1.071471 CTTGAGTGCCGGTTGGACT 59.929 57.895 1.90 0.00 37.49 3.85


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

AutoCloner maintained by Alex Coulton.