Multiple sequence alignment - TraesCS4B01G160700

Loading Multiple Alignment...

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 TraesCS4B01G160700 chr4B 100.000 2912 0 0 1 2912 315712780 315709869 0.000000e+00 5378
1 TraesCS4B01G160700 chr4B 81.223 916 139 11 49 963 252633923 252634806 0.000000e+00 708
2 TraesCS4B01G160700 chr4B 76.170 470 102 9 2446 2910 252636282 252636746 3.750000e-59 239
3 TraesCS4B01G160700 chr3B 87.453 2678 267 29 271 2912 309761968 309764612 0.000000e+00 3020
4 TraesCS4B01G160700 chr3B 90.149 335 26 4 2583 2912 309804433 309804765 2.070000e-116 429
5 TraesCS4B01G160700 chr3B 75.802 405 90 8 80 480 206425915 206425515 6.370000e-47 198
6 TraesCS4B01G160700 chr5B 88.724 2226 204 23 726 2912 293491310 293493527 0.000000e+00 2676
7 TraesCS4B01G160700 chr5B 90.313 671 59 4 44 714 293483043 293483707 0.000000e+00 874
8 TraesCS4B01G160700 chr6A 84.854 2093 247 37 36 2083 298461547 298463614 0.000000e+00 2045
9 TraesCS4B01G160700 chr6B 81.910 2388 363 32 50 2403 461591236 461593588 0.000000e+00 1953
10 TraesCS4B01G160700 chr6B 77.282 471 96 9 2446 2909 461593604 461594070 1.720000e-67 267
11 TraesCS4B01G160700 chr7B 80.669 1464 257 19 1074 2527 151020099 151021546 0.000000e+00 1112
12 TraesCS4B01G160700 chr7B 83.673 784 105 8 57 838 150929828 150930590 0.000000e+00 717
13 TraesCS4B01G160700 chr7B 82.407 324 53 1 2593 2912 151052611 151052934 2.210000e-71 279
14 TraesCS4B01G160700 chr7D 83.030 1155 179 10 1194 2344 182537781 182538922 0.000000e+00 1031
15 TraesCS4B01G160700 chr7D 85.558 547 74 4 57 602 182513062 182513604 4.210000e-158 568
16 TraesCS4B01G160700 chr6D 80.914 1116 162 15 1825 2912 219106237 219105145 0.000000e+00 833
17 TraesCS4B01G160700 chrUn 81.000 300 51 3 2616 2910 85698830 85698532 1.740000e-57 233
18 TraesCS4B01G160700 chrUn 80.333 300 53 3 2616 2910 235704852 235705150 3.780000e-54 222


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 TraesCS4B01G160700 chr4B 315709869 315712780 2911 True 5378.0 5378 100.0000 1 2912 1 chr4B.!!$R1 2911
1 TraesCS4B01G160700 chr4B 252633923 252636746 2823 False 473.5 708 78.6965 49 2910 2 chr4B.!!$F1 2861
2 TraesCS4B01G160700 chr3B 309761968 309764612 2644 False 3020.0 3020 87.4530 271 2912 1 chr3B.!!$F1 2641
3 TraesCS4B01G160700 chr5B 293491310 293493527 2217 False 2676.0 2676 88.7240 726 2912 1 chr5B.!!$F2 2186
4 TraesCS4B01G160700 chr5B 293483043 293483707 664 False 874.0 874 90.3130 44 714 1 chr5B.!!$F1 670
5 TraesCS4B01G160700 chr6A 298461547 298463614 2067 False 2045.0 2045 84.8540 36 2083 1 chr6A.!!$F1 2047
6 TraesCS4B01G160700 chr6B 461591236 461594070 2834 False 1110.0 1953 79.5960 50 2909 2 chr6B.!!$F1 2859
7 TraesCS4B01G160700 chr7B 151020099 151021546 1447 False 1112.0 1112 80.6690 1074 2527 1 chr7B.!!$F2 1453
8 TraesCS4B01G160700 chr7B 150929828 150930590 762 False 717.0 717 83.6730 57 838 1 chr7B.!!$F1 781
9 TraesCS4B01G160700 chr7D 182537781 182538922 1141 False 1031.0 1031 83.0300 1194 2344 1 chr7D.!!$F2 1150
10 TraesCS4B01G160700 chr7D 182513062 182513604 542 False 568.0 568 85.5580 57 602 1 chr7D.!!$F1 545
11 TraesCS4B01G160700 chr6D 219105145 219106237 1092 True 833.0 833 80.9140 1825 2912 1 chr6D.!!$R1 1087

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
201 203 0.249120 AGGAATTCGTCATGGTCGCA 59.751 50.0 0.00 0.00 0.0 5.10 F
1014 1046 0.038251 TCAACATGACTCGCGAGCTT 60.038 50.0 34.83 21.37 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1893 0.252761 TGATGGAATTGCTCCTGCGA 59.747 50.0 0.00 0.0 45.64 5.10 R
2493 2546 0.250727 GTAGGCTTTGGAGGTGCACA 60.251 55.0 20.43 0.0 0.00 4.57 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
22 23 5.452078 CATCTCCTGTGTTTGCCTTTTAA 57.548 39.130 0.00 0.00 0.00 1.52
23 24 5.464168 CATCTCCTGTGTTTGCCTTTTAAG 58.536 41.667 0.00 0.00 0.00 1.85
24 25 4.532834 TCTCCTGTGTTTGCCTTTTAAGT 58.467 39.130 0.00 0.00 0.00 2.24
25 26 4.578928 TCTCCTGTGTTTGCCTTTTAAGTC 59.421 41.667 0.00 0.00 0.00 3.01
26 27 4.274147 TCCTGTGTTTGCCTTTTAAGTCA 58.726 39.130 0.00 0.00 0.00 3.41
27 28 4.892934 TCCTGTGTTTGCCTTTTAAGTCAT 59.107 37.500 0.00 0.00 0.00 3.06
28 29 5.362430 TCCTGTGTTTGCCTTTTAAGTCATT 59.638 36.000 0.00 0.00 0.00 2.57
29 30 5.463061 CCTGTGTTTGCCTTTTAAGTCATTG 59.537 40.000 0.00 0.00 0.00 2.82
30 31 6.214191 TGTGTTTGCCTTTTAAGTCATTGA 57.786 33.333 0.00 0.00 0.00 2.57
31 32 6.039616 TGTGTTTGCCTTTTAAGTCATTGAC 58.960 36.000 8.82 8.82 0.00 3.18
32 33 6.127479 TGTGTTTGCCTTTTAAGTCATTGACT 60.127 34.615 13.61 13.61 45.64 3.41
33 34 7.067615 TGTGTTTGCCTTTTAAGTCATTGACTA 59.932 33.333 19.27 2.44 42.59 2.59
34 35 7.378728 GTGTTTGCCTTTTAAGTCATTGACTAC 59.621 37.037 19.27 10.20 42.59 2.73
35 36 6.569179 TTGCCTTTTAAGTCATTGACTACC 57.431 37.500 19.27 4.55 42.59 3.18
36 37 5.876357 TGCCTTTTAAGTCATTGACTACCT 58.124 37.500 19.27 7.18 42.59 3.08
37 38 6.303839 TGCCTTTTAAGTCATTGACTACCTT 58.696 36.000 19.27 6.83 42.59 3.50
38 39 6.430000 TGCCTTTTAAGTCATTGACTACCTTC 59.570 38.462 19.27 7.00 42.59 3.46
39 40 6.127980 GCCTTTTAAGTCATTGACTACCTTCC 60.128 42.308 19.27 3.23 42.59 3.46
46 47 3.907474 TCATTGACTACCTTCCCACTCAA 59.093 43.478 0.00 0.00 0.00 3.02
201 203 0.249120 AGGAATTCGTCATGGTCGCA 59.751 50.000 0.00 0.00 0.00 5.10
222 224 3.999663 CAGAATTCTCTCGTTCAAGGCTT 59.000 43.478 4.57 0.00 0.00 4.35
235 237 5.324697 GTTCAAGGCTTCGTATCAACATTC 58.675 41.667 0.00 0.00 0.00 2.67
244 246 2.738643 CGTATCAACATTCACTCGGCCT 60.739 50.000 0.00 0.00 0.00 5.19
332 334 4.196193 TGGTCTTTCAAATTCAGTGTCGT 58.804 39.130 0.00 0.00 0.00 4.34
359 361 3.197766 AGAGATGTGGGTTTCGCTATCAA 59.802 43.478 0.00 0.00 0.00 2.57
377 379 5.628797 ATCAACAAAGGTGGGAATTGTTT 57.371 34.783 0.72 0.00 42.82 2.83
407 409 4.515191 TCTCTTCAATGTGGGTTTCTTTCG 59.485 41.667 0.00 0.00 0.00 3.46
470 472 5.625150 ACTCTACCAACAAGAAATTGAGCT 58.375 37.500 0.00 0.00 0.00 4.09
511 513 5.171147 TCGTTCCAAAGATCGTAGATCTC 57.829 43.478 12.31 0.00 45.12 2.75
536 538 1.881925 CGAAGCAGTTCAATCCCCACA 60.882 52.381 0.00 0.00 32.36 4.17
574 576 6.666546 AGGTGAATTGAATGTTCATCCTTCAT 59.333 34.615 13.88 3.47 37.40 2.57
579 581 9.859427 GAATTGAATGTTCATCCTTCATGTTTA 57.141 29.630 0.00 0.00 37.00 2.01
603 605 9.778741 TTACATGACTTTTGATAGTTTCTCAGT 57.221 29.630 0.00 0.00 0.00 3.41
679 681 2.492019 GCTATTGTTGGGGCGAAATC 57.508 50.000 0.00 0.00 0.00 2.17
680 682 2.024414 GCTATTGTTGGGGCGAAATCT 58.976 47.619 0.00 0.00 0.00 2.40
681 683 3.211045 GCTATTGTTGGGGCGAAATCTA 58.789 45.455 0.00 0.00 0.00 1.98
682 684 3.821033 GCTATTGTTGGGGCGAAATCTAT 59.179 43.478 0.00 0.00 0.00 1.98
683 685 4.320494 GCTATTGTTGGGGCGAAATCTATG 60.320 45.833 0.00 0.00 0.00 2.23
684 686 2.051334 TGTTGGGGCGAAATCTATGG 57.949 50.000 0.00 0.00 0.00 2.74
685 687 1.318576 GTTGGGGCGAAATCTATGGG 58.681 55.000 0.00 0.00 0.00 4.00
686 688 0.923358 TTGGGGCGAAATCTATGGGT 59.077 50.000 0.00 0.00 0.00 4.51
687 689 1.809133 TGGGGCGAAATCTATGGGTA 58.191 50.000 0.00 0.00 0.00 3.69
688 690 2.344592 TGGGGCGAAATCTATGGGTAT 58.655 47.619 0.00 0.00 0.00 2.73
689 691 2.039746 TGGGGCGAAATCTATGGGTATG 59.960 50.000 0.00 0.00 0.00 2.39
690 692 2.084546 GGGCGAAATCTATGGGTATGC 58.915 52.381 0.00 0.00 0.00 3.14
691 693 1.732259 GGCGAAATCTATGGGTATGCG 59.268 52.381 0.00 0.00 0.00 4.73
692 694 2.611971 GGCGAAATCTATGGGTATGCGA 60.612 50.000 0.00 0.00 0.00 5.10
693 695 3.064207 GCGAAATCTATGGGTATGCGAA 58.936 45.455 0.00 0.00 0.00 4.70
853 855 1.251251 GATGCAATAGGATGGGCCAC 58.749 55.000 9.28 2.43 40.02 5.01
860 862 1.868713 TAGGATGGGCCACGTTAAGA 58.131 50.000 9.28 0.00 40.02 2.10
861 863 1.213296 AGGATGGGCCACGTTAAGAT 58.787 50.000 9.28 0.00 40.02 2.40
1014 1046 0.038251 TCAACATGACTCGCGAGCTT 60.038 50.000 34.83 21.37 0.00 3.74
1086 1119 2.182842 GCATAGTTGCTCCCCTGCG 61.183 63.158 0.00 0.00 45.77 5.18
1161 1203 2.733517 GTTGCTAGAGATGGCTACGTC 58.266 52.381 0.00 0.00 0.00 4.34
1180 1222 2.111043 CCATTCGATCCCACCCCG 59.889 66.667 0.00 0.00 0.00 5.73
1187 1230 1.119574 CGATCCCACCCCGTTATCCT 61.120 60.000 0.00 0.00 0.00 3.24
1191 1234 0.330267 CCCACCCCGTTATCCTTGTT 59.670 55.000 0.00 0.00 0.00 2.83
1222 1265 1.982395 ATTGAGGTCGACGGCAGGA 60.982 57.895 9.92 0.00 0.00 3.86
1276 1319 1.118965 TCCTGCCAACGAAGACCTCA 61.119 55.000 0.00 0.00 0.00 3.86
1499 1543 4.448537 TCCATATTGTTTTCCAAAGGCG 57.551 40.909 0.00 0.00 36.44 5.52
1515 1559 1.450531 GGCGCAATGAGGGGATGAAG 61.451 60.000 10.83 0.00 0.00 3.02
1604 1651 6.392354 GCTTGTTCCATGAAATCTCAAATGA 58.608 36.000 0.00 0.00 34.49 2.57
1606 1653 5.941733 TGTTCCATGAAATCTCAAATGACG 58.058 37.500 0.00 0.00 34.49 4.35
1624 1671 2.424246 GACGTTCCTGGTTTTGGACAAA 59.576 45.455 0.00 0.00 32.65 2.83
1664 1711 8.193250 AGATTTAAATCATTTGATGCAGCAAC 57.807 30.769 26.02 0.93 37.89 4.17
1717 1764 1.271856 TGTTCCGGCCAGTATCTTGA 58.728 50.000 2.24 0.00 0.00 3.02
1759 1806 1.352622 TGGGCAGTCTTGGACCTGTT 61.353 55.000 0.00 0.00 32.18 3.16
1819 1869 1.134280 CAGATGAAGATCCGGTGCCTT 60.134 52.381 0.00 3.22 0.00 4.35
1843 1893 1.985622 TGGAAATCCTCACCCCAGAT 58.014 50.000 0.44 0.00 36.82 2.90
1870 1920 0.179129 GCAATTCCATCAGCCCAACG 60.179 55.000 0.00 0.00 0.00 4.10
1908 1958 4.096984 GGACCTGTTGGCTTTCATCTTATG 59.903 45.833 0.00 0.00 36.63 1.90
1909 1959 4.666512 ACCTGTTGGCTTTCATCTTATGT 58.333 39.130 0.00 0.00 36.63 2.29
2016 2066 0.908198 AGGAGATCCAAGCTGGTGAC 59.092 55.000 0.92 0.00 39.03 3.67
2127 2177 2.092429 TGGTCTGAATATTGGAGTGCCC 60.092 50.000 0.00 0.00 0.00 5.36
2213 2265 3.678965 TCTAGCTTCTCTGGTCATCCT 57.321 47.619 0.00 0.00 34.23 3.24
2380 2433 3.087031 CAGTTCAACAGGAAGATGCCAT 58.913 45.455 0.00 0.00 35.82 4.40
2404 2457 3.397482 CAGATATGCTGCAAGTAGTCCC 58.603 50.000 6.36 0.00 37.90 4.46
2435 2488 6.253758 TCCTCATTTGACTCTACTTCCACTA 58.746 40.000 0.00 0.00 0.00 2.74
2441 2494 7.962995 TTTGACTCTACTTCCACTAGATGAT 57.037 36.000 0.00 0.00 0.00 2.45
2443 2496 8.684386 TTGACTCTACTTCCACTAGATGATAG 57.316 38.462 0.00 0.00 0.00 2.08
2464 2517 2.683742 GCCCTGGCTCTGCTAATGTTTA 60.684 50.000 0.00 0.00 38.26 2.01
2584 2662 1.517242 GCTCAGGAAGACACAACTGG 58.483 55.000 0.00 0.00 0.00 4.00
2672 2750 0.327000 CCACCTGGATTCCCTCTCCT 60.327 60.000 0.00 0.00 37.39 3.69
2674 2752 1.211457 CACCTGGATTCCCTCTCCTTG 59.789 57.143 0.00 0.00 33.69 3.61
2681 2759 4.013050 GGATTCCCTCTCCTTGTTTTCAG 58.987 47.826 0.00 0.00 0.00 3.02
2706 2784 7.713507 AGTGTTGCAGTTACTGTTTCTAATGTA 59.286 33.333 14.23 0.00 33.43 2.29
2723 2801 3.791973 TGTACAAAACCCAAAGCAGTG 57.208 42.857 0.00 0.00 0.00 3.66
2899 2983 2.061773 CACTGTTGCTCTCCTAACACG 58.938 52.381 0.00 0.00 33.60 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.140454 ACTTAAAAGGCAAACACAGGAGAT 58.860 37.500 0.00 0.00 0.00 2.75
4 5 4.274147 TGACTTAAAAGGCAAACACAGGA 58.726 39.130 0.00 0.00 42.17 3.86
5 6 4.647424 TGACTTAAAAGGCAAACACAGG 57.353 40.909 0.00 0.00 42.17 4.00
14 15 6.127980 GGAAGGTAGTCAATGACTTAAAAGGC 60.128 42.308 21.83 5.67 40.28 4.35
15 16 6.374613 GGGAAGGTAGTCAATGACTTAAAAGG 59.625 42.308 21.83 0.00 40.28 3.11
16 17 6.940298 TGGGAAGGTAGTCAATGACTTAAAAG 59.060 38.462 21.83 0.00 40.28 2.27
17 18 6.713450 GTGGGAAGGTAGTCAATGACTTAAAA 59.287 38.462 21.83 0.00 40.28 1.52
18 19 6.043938 AGTGGGAAGGTAGTCAATGACTTAAA 59.956 38.462 21.83 0.12 40.28 1.52
19 20 5.546499 AGTGGGAAGGTAGTCAATGACTTAA 59.454 40.000 21.83 0.94 40.28 1.85
20 21 5.091552 AGTGGGAAGGTAGTCAATGACTTA 58.908 41.667 21.83 4.95 40.28 2.24
21 22 3.910627 AGTGGGAAGGTAGTCAATGACTT 59.089 43.478 21.83 2.79 40.28 3.01
22 23 3.515901 GAGTGGGAAGGTAGTCAATGACT 59.484 47.826 20.48 20.48 45.54 3.41
23 24 3.260884 TGAGTGGGAAGGTAGTCAATGAC 59.739 47.826 5.02 5.02 0.00 3.06
24 25 3.516586 TGAGTGGGAAGGTAGTCAATGA 58.483 45.455 0.00 0.00 0.00 2.57
25 26 3.981071 TGAGTGGGAAGGTAGTCAATG 57.019 47.619 0.00 0.00 0.00 2.82
26 27 4.785376 AGATTGAGTGGGAAGGTAGTCAAT 59.215 41.667 6.93 6.93 45.05 2.57
27 28 4.168101 AGATTGAGTGGGAAGGTAGTCAA 58.832 43.478 0.00 0.00 39.69 3.18
28 29 3.769844 GAGATTGAGTGGGAAGGTAGTCA 59.230 47.826 0.00 0.00 0.00 3.41
29 30 4.027437 AGAGATTGAGTGGGAAGGTAGTC 58.973 47.826 0.00 0.00 0.00 2.59
30 31 4.027437 GAGAGATTGAGTGGGAAGGTAGT 58.973 47.826 0.00 0.00 0.00 2.73
31 32 3.386402 GGAGAGATTGAGTGGGAAGGTAG 59.614 52.174 0.00 0.00 0.00 3.18
32 33 3.012959 AGGAGAGATTGAGTGGGAAGGTA 59.987 47.826 0.00 0.00 0.00 3.08
33 34 2.192263 GGAGAGATTGAGTGGGAAGGT 58.808 52.381 0.00 0.00 0.00 3.50
34 35 2.476199 AGGAGAGATTGAGTGGGAAGG 58.524 52.381 0.00 0.00 0.00 3.46
35 36 4.566426 AAAGGAGAGATTGAGTGGGAAG 57.434 45.455 0.00 0.00 0.00 3.46
36 37 5.046304 CACTAAAGGAGAGATTGAGTGGGAA 60.046 44.000 0.00 0.00 31.34 3.97
37 38 4.467795 CACTAAAGGAGAGATTGAGTGGGA 59.532 45.833 0.00 0.00 31.34 4.37
38 39 4.764172 CACTAAAGGAGAGATTGAGTGGG 58.236 47.826 0.00 0.00 31.34 4.61
39 40 4.081198 AGCACTAAAGGAGAGATTGAGTGG 60.081 45.833 5.56 0.00 34.70 4.00
46 47 6.372931 AGATCACTAGCACTAAAGGAGAGAT 58.627 40.000 0.00 0.00 0.00 2.75
201 203 3.971245 AGCCTTGAACGAGAGAATTCT 57.029 42.857 7.95 7.95 36.01 2.40
222 224 2.536365 GCCGAGTGAATGTTGATACGA 58.464 47.619 0.00 0.00 0.00 3.43
235 237 0.534412 AGAATGAGACAGGCCGAGTG 59.466 55.000 8.69 0.00 0.00 3.51
244 246 6.210796 CAAAACAAGATTGCAGAATGAGACA 58.789 36.000 0.00 0.00 39.69 3.41
301 303 6.347696 TGAATTTGAAAGACCAGTTTTGCAT 58.652 32.000 0.00 0.00 0.00 3.96
332 334 2.427453 GCGAAACCCACATCTCTAGAGA 59.573 50.000 24.36 24.36 42.37 3.10
359 361 7.130681 TCATTTAAACAATTCCCACCTTTGT 57.869 32.000 0.00 0.00 35.19 2.83
377 379 7.890127 AGAAACCCACATTGAAGAGATCATTTA 59.110 33.333 0.00 0.00 38.03 1.40
470 472 1.284785 GATCAACCAGGGTCCATTCCA 59.715 52.381 0.00 0.00 0.00 3.53
544 546 6.151648 GGATGAACATTCAATTCACCTGAAGA 59.848 38.462 0.00 0.00 41.13 2.87
549 551 6.012113 TGAAGGATGAACATTCAATTCACCT 58.988 36.000 12.55 8.13 44.44 4.00
579 581 7.308229 GCACTGAGAAACTATCAAAAGTCATGT 60.308 37.037 0.00 0.00 0.00 3.21
603 605 2.290260 ACGACCTTGATTGAATCAGGCA 60.290 45.455 17.72 1.83 40.94 4.75
675 677 7.554118 CCATAGATTTCGCATACCCATAGATTT 59.446 37.037 0.00 0.00 0.00 2.17
676 678 7.050377 CCATAGATTTCGCATACCCATAGATT 58.950 38.462 0.00 0.00 0.00 2.40
677 679 6.408548 CCCATAGATTTCGCATACCCATAGAT 60.409 42.308 0.00 0.00 0.00 1.98
678 680 5.104941 CCCATAGATTTCGCATACCCATAGA 60.105 44.000 0.00 0.00 0.00 1.98
679 681 5.118990 CCCATAGATTTCGCATACCCATAG 58.881 45.833 0.00 0.00 0.00 2.23
680 682 4.534500 ACCCATAGATTTCGCATACCCATA 59.466 41.667 0.00 0.00 0.00 2.74
681 683 3.330701 ACCCATAGATTTCGCATACCCAT 59.669 43.478 0.00 0.00 0.00 4.00
682 684 2.708861 ACCCATAGATTTCGCATACCCA 59.291 45.455 0.00 0.00 0.00 4.51
683 685 3.418684 ACCCATAGATTTCGCATACCC 57.581 47.619 0.00 0.00 0.00 3.69
684 686 6.170506 TGAATACCCATAGATTTCGCATACC 58.829 40.000 0.00 0.00 0.00 2.73
685 687 7.667043 TTGAATACCCATAGATTTCGCATAC 57.333 36.000 0.00 0.00 0.00 2.39
686 688 8.684386 TTTTGAATACCCATAGATTTCGCATA 57.316 30.769 0.00 0.00 0.00 3.14
687 689 7.581213 TTTTGAATACCCATAGATTTCGCAT 57.419 32.000 0.00 0.00 0.00 4.73
688 690 7.581213 ATTTTGAATACCCATAGATTTCGCA 57.419 32.000 0.00 0.00 0.00 5.10
689 691 8.352942 AGAATTTTGAATACCCATAGATTTCGC 58.647 33.333 0.00 0.00 0.00 4.70
690 692 9.669353 CAGAATTTTGAATACCCATAGATTTCG 57.331 33.333 0.00 0.00 0.00 3.46
691 693 9.971922 CCAGAATTTTGAATACCCATAGATTTC 57.028 33.333 0.00 0.00 0.00 2.17
692 694 8.927411 CCCAGAATTTTGAATACCCATAGATTT 58.073 33.333 0.00 0.00 0.00 2.17
693 695 7.015584 GCCCAGAATTTTGAATACCCATAGATT 59.984 37.037 0.00 0.00 0.00 2.40
752 754 3.077359 CACAAAAGGGAGGTCTGTCATC 58.923 50.000 0.00 0.00 0.00 2.92
793 795 1.126488 TGCATTTGGGCCAAAAGTGA 58.874 45.000 33.40 17.71 36.90 3.41
853 855 5.965334 ACGCATTCTGCAATTAATCTTAACG 59.035 36.000 0.00 0.00 45.36 3.18
860 862 2.166050 TGCCACGCATTCTGCAATTAAT 59.834 40.909 0.00 0.00 45.36 1.40
861 863 1.543358 TGCCACGCATTCTGCAATTAA 59.457 42.857 0.00 0.00 45.36 1.40
897 903 1.303317 ACGGGCACAGGATTGGAAC 60.303 57.895 0.00 0.00 0.00 3.62
1051 1084 2.354729 CGGTGGGAATTGGAGGCA 59.645 61.111 0.00 0.00 0.00 4.75
1086 1119 1.439353 ATGCGATGAATGCGGGTGTC 61.439 55.000 0.00 0.00 34.24 3.67
1139 1181 1.065701 CGTAGCCATCTCTAGCAACGT 59.934 52.381 0.00 0.00 0.00 3.99
1161 1203 1.451936 GGGGTGGGATCGAATGGAG 59.548 63.158 0.00 0.00 0.00 3.86
1165 1207 1.346722 GATAACGGGGTGGGATCGAAT 59.653 52.381 0.00 0.00 0.00 3.34
1180 1222 3.243201 GCATGGCAGCTAACAAGGATAAC 60.243 47.826 0.00 0.00 0.00 1.89
1187 1230 1.205179 CAATGGCATGGCAGCTAACAA 59.795 47.619 27.02 0.67 34.17 2.83
1191 1234 0.466739 CCTCAATGGCATGGCAGCTA 60.467 55.000 27.02 13.19 34.17 3.32
1276 1319 5.682990 GCATTGGAATGATTGTAGCAATGGT 60.683 40.000 0.00 0.00 38.70 3.55
1499 1543 1.064463 TCCACTTCATCCCCTCATTGC 60.064 52.381 0.00 0.00 0.00 3.56
1515 1559 6.427242 CCCTAGTAAGTTCAAAGTTTCTCCAC 59.573 42.308 0.00 0.00 0.00 4.02
1604 1651 2.131776 TTGTCCAAAACCAGGAACGT 57.868 45.000 0.00 0.00 36.80 3.99
1606 1653 4.664150 TCATTTGTCCAAAACCAGGAAC 57.336 40.909 0.00 0.00 36.80 3.62
1624 1671 9.659135 TGATTTAAATCTATCCCAAACCATCAT 57.341 29.630 24.77 0.00 36.39 2.45
1652 1699 0.310543 GACAACGGTTGCTGCATCAA 59.689 50.000 20.20 0.00 0.00 2.57
1663 1710 5.605034 TCAATCTTGACACGGACAACGGT 62.605 47.826 0.00 0.00 38.55 4.83
1664 1711 3.120521 TCAATCTTGACACGGACAACGG 61.121 50.000 0.00 0.00 38.55 4.44
1717 1764 4.070716 CTGAAGTTCTTTGCACCAGAGAT 58.929 43.478 4.17 0.00 0.00 2.75
1759 1806 2.938451 GCATGTCAAAGATGATCACCGA 59.062 45.455 0.00 0.00 38.01 4.69
1819 1869 1.211949 GGGGTGAGGATTTCCATTCGA 59.788 52.381 0.00 0.00 38.89 3.71
1843 1893 0.252761 TGATGGAATTGCTCCTGCGA 59.747 50.000 0.00 0.00 45.64 5.10
1863 1913 1.951602 ACAAGTAGGTTTTCGTTGGGC 59.048 47.619 0.00 0.00 0.00 5.36
1908 1958 9.481340 TGCTCTAGAACATTATCATCATGTTAC 57.519 33.333 0.00 0.00 43.47 2.50
2016 2066 5.235516 AGCAAATCATTCAGCTCCAAAAAG 58.764 37.500 0.00 0.00 30.05 2.27
2127 2177 3.732849 GGGTGAGCTTCCCCAGGG 61.733 72.222 15.02 0.00 40.88 4.45
2142 2192 2.237143 TCCAAATACAGAGCTGTCAGGG 59.763 50.000 6.38 5.49 43.74 4.45
2143 2193 3.529533 CTCCAAATACAGAGCTGTCAGG 58.470 50.000 6.38 5.51 43.74 3.86
2213 2265 5.500234 CCTGAAATTCTGGGTGTTGATCTA 58.500 41.667 10.63 0.00 32.51 1.98
2311 2363 1.180456 TTGTCATTGTGGGGCTGCAG 61.180 55.000 10.11 10.11 0.00 4.41
2380 2433 5.453339 GGGACTACTTGCAGCATATCTGTAA 60.453 44.000 0.00 5.88 43.58 2.41
2404 2457 2.093764 AGAGTCAAATGAGGAGCTTCCG 60.094 50.000 0.00 0.00 42.75 4.30
2443 2496 0.394899 AACATTAGCAGAGCCAGGGC 60.395 55.000 0.97 0.97 42.33 5.19
2464 2517 4.832266 TGTTTTGGTTGACCTTCATAGCAT 59.168 37.500 1.34 0.00 36.82 3.79
2493 2546 0.250727 GTAGGCTTTGGAGGTGCACA 60.251 55.000 20.43 0.00 0.00 4.57
2584 2662 4.016444 TCCTGTGGAATAAGATTTGCCAC 58.984 43.478 0.00 0.00 46.97 5.01
2672 2750 5.048364 ACAGTAACTGCAACACTGAAAACAA 60.048 36.000 22.13 0.00 41.80 2.83
2674 2752 4.981794 ACAGTAACTGCAACACTGAAAAC 58.018 39.130 22.13 0.00 41.80 2.43
2681 2759 6.725246 ACATTAGAAACAGTAACTGCAACAC 58.275 36.000 0.00 0.00 34.37 3.32
2723 2801 6.749036 TTAGGTCTCTAATTTGAGGATCCC 57.251 41.667 15.49 10.79 34.98 3.85
2789 2867 1.267121 TCCACAGCTCCAGACCTTAC 58.733 55.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.