Multiple sequence alignment - TraesCS6D01G070400

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 TraesCS6D01G070400 chr6D 100.000 3946 0 0 1 3946 35624952 35621007 0.000000e+00 7287.0
1 TraesCS6D01G070400 chr6A 92.927 2559 107 25 1 2522 39495940 39493419 0.000000e+00 3655.0
2 TraesCS6D01G070400 chr6A 89.427 785 47 16 2707 3474 39493300 39492535 0.000000e+00 957.0
3 TraesCS6D01G070400 chr6A 92.222 90 6 1 3857 3946 39489979 39489891 4.140000e-25 126.0
4 TraesCS6D01G070400 chr6B 89.952 1652 122 25 900 2522 73902799 73901163 0.000000e+00 2091.0
5 TraesCS6D01G070400 chr6B 93.316 763 38 6 1781 2533 75027580 75026821 0.000000e+00 1114.0
6 TraesCS6D01G070400 chr6B 89.052 886 72 12 923 1793 75028477 75027602 0.000000e+00 1075.0
7 TraesCS6D01G070400 chr6B 93.566 544 27 6 1 539 75029478 75028938 0.000000e+00 804.0
8 TraesCS6D01G070400 chr6B 93.173 498 25 4 2684 3173 75026758 75026262 0.000000e+00 723.0
9 TraesCS6D01G070400 chr6B 94.595 370 15 5 592 956 75028847 75028478 5.720000e-158 568.0
10 TraesCS6D01G070400 chr6B 91.045 402 31 4 12 409 73947782 73947382 4.490000e-149 538.0
11 TraesCS6D01G070400 chr6B 91.437 327 21 6 12 333 73903352 73903028 3.620000e-120 442.0
12 TraesCS6D01G070400 chr6B 86.305 387 50 1 900 1286 73947385 73947002 6.100000e-113 418.0
13 TraesCS6D01G070400 chr6B 92.917 240 17 0 2707 2946 73900978 73900739 2.260000e-92 350.0
14 TraesCS6D01G070400 chr6B 93.939 99 6 0 311 409 73902894 73902796 2.460000e-32 150.0
15 TraesCS6D01G070400 chr1B 94.444 72 4 0 788 859 393120101 393120172 1.160000e-20 111.0
16 TraesCS6D01G070400 chr1B 90.385 52 5 0 3630 3681 422480836 422480887 7.080000e-08 69.4
17 TraesCS6D01G070400 chr7D 93.617 47 2 1 2616 2661 467999663 467999617 7.080000e-08 69.4
18 TraesCS6D01G070400 chr4B 91.837 49 4 0 3633 3681 136610065 136610017 7.080000e-08 69.4
19 TraesCS6D01G070400 chr4B 91.837 49 4 0 3633 3681 240057695 240057647 7.080000e-08 69.4
20 TraesCS6D01G070400 chr4B 90.385 52 5 0 3630 3681 580307869 580307920 7.080000e-08 69.4
21 TraesCS6D01G070400 chr4B 91.667 48 4 0 3634 3681 580300247 580300294 2.540000e-07 67.6
22 TraesCS6D01G070400 chr3B 91.837 49 4 0 3633 3681 558869038 558868990 7.080000e-08 69.4
23 TraesCS6D01G070400 chr3B 87.931 58 4 2 2616 2673 75901578 75901632 9.150000e-07 65.8
24 TraesCS6D01G070400 chr3B 89.796 49 5 0 3633 3681 558876821 558876773 3.290000e-06 63.9
25 TraesCS6D01G070400 chr2B 90.385 52 5 0 3630 3681 463735740 463735791 7.080000e-08 69.4
26 TraesCS6D01G070400 chr5B 91.667 48 4 0 3630 3677 177592697 177592744 2.540000e-07 67.6


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 TraesCS6D01G070400 chr6D 35621007 35624952 3945 True 7287.000000 7287 100.000000 1 3946 1 chr6D.!!$R1 3945
1 TraesCS6D01G070400 chr6A 39489891 39495940 6049 True 1579.333333 3655 91.525333 1 3946 3 chr6A.!!$R1 3945
2 TraesCS6D01G070400 chr6B 75026262 75029478 3216 True 856.800000 1114 92.740400 1 3173 5 chr6B.!!$R3 3172
3 TraesCS6D01G070400 chr6B 73900739 73903352 2613 True 758.250000 2091 92.061250 12 2946 4 chr6B.!!$R1 2934
4 TraesCS6D01G070400 chr6B 73947002 73947782 780 True 478.000000 538 88.675000 12 1286 2 chr6B.!!$R2 1274

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
996 1249 1.048601 TTGTCTGGTGACTGGAGTCC 58.951 55.0 0.73 0.73 44.15 3.85 F
1251 1504 0.108329 CGACGGGCAGGTTCAGTAAT 60.108 55.0 0.00 0.00 0.00 1.89 F
2601 2929 0.258484 TGCCATAGGGGTTGGATGTG 59.742 55.0 0.00 0.00 39.65 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 2914 0.107214 CACGCACATCCAACCCCTAT 60.107 55.0 0.00 0.0 0.00 2.57 R
2605 2933 0.247301 GCATACACTCGAGCGCAAAC 60.247 55.0 13.61 0.0 0.00 2.93 R
3832 5560 0.032540 GTGGGCAAGAAAGGCAGTTG 59.967 55.0 0.00 0.0 35.46 3.16 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
125 127 5.094134 GCGTAACTCTGACTTAGTTGGTAG 58.906 45.833 0.00 0.00 37.71 3.18
289 295 7.466746 AACAATGTATGTGAAATAGTTGGCT 57.533 32.000 0.00 0.00 42.99 4.75
415 578 1.067000 ATCAGCAGAGATGCGGATAGC 60.067 52.381 13.03 0.00 45.21 2.97
441 604 6.230849 TGTTTACGCATTTTATTCGTGTCT 57.769 33.333 0.00 0.00 37.61 3.41
442 605 6.301108 TGTTTACGCATTTTATTCGTGTCTC 58.699 36.000 0.00 0.00 37.61 3.36
443 606 6.146510 TGTTTACGCATTTTATTCGTGTCTCT 59.853 34.615 0.00 0.00 37.61 3.10
549 737 4.282449 TGAGAAAACAATCGTACTCCCTCA 59.718 41.667 0.00 0.00 0.00 3.86
588 803 6.053005 GCATCAAATGAATTCCCATGTTGAT 58.947 36.000 2.27 7.88 36.24 2.57
589 804 7.147707 TGCATCAAATGAATTCCCATGTTGATA 60.148 33.333 2.27 0.00 35.32 2.15
590 805 7.170320 GCATCAAATGAATTCCCATGTTGATAC 59.830 37.037 2.27 2.94 35.32 2.24
591 806 7.959658 TCAAATGAATTCCCATGTTGATACT 57.040 32.000 2.27 0.00 0.00 2.12
592 807 9.645128 ATCAAATGAATTCCCATGTTGATACTA 57.355 29.630 2.27 0.00 35.32 1.82
593 808 9.645128 TCAAATGAATTCCCATGTTGATACTAT 57.355 29.630 2.27 0.00 0.00 2.12
597 812 8.236585 TGAATTCCCATGTTGATACTATTTGG 57.763 34.615 2.27 0.00 0.00 3.28
697 914 3.721575 TCCCATGCTGATACTATTTGGGT 59.278 43.478 5.09 0.00 42.41 4.51
717 936 6.683715 TGGGTGGACTTTTTAAATTCGAATC 58.316 36.000 11.83 0.00 0.00 2.52
735 954 3.909776 ATCACTGATGTGTTGTGCAAG 57.090 42.857 0.00 0.00 44.14 4.01
743 962 6.141560 TGATGTGTTGTGCAAGTTGATTTA 57.858 33.333 7.16 0.00 0.00 1.40
786 1005 2.103373 TGGCAGCTAGAACCTAGACAG 58.897 52.381 5.27 0.00 0.00 3.51
974 1227 4.234530 AGCAAAGCATCAGAAGTTGTTC 57.765 40.909 0.00 0.00 0.00 3.18
996 1249 1.048601 TTGTCTGGTGACTGGAGTCC 58.951 55.000 0.73 0.73 44.15 3.85
1071 1324 4.160635 GCGATCCGGTTGCCGTTG 62.161 66.667 0.00 0.00 46.80 4.10
1106 1359 4.436998 CACCGTCGTCTCCAGGGC 62.437 72.222 0.00 0.00 0.00 5.19
1107 1360 4.988716 ACCGTCGTCTCCAGGGCA 62.989 66.667 0.00 0.00 0.00 5.36
1108 1361 3.691342 CCGTCGTCTCCAGGGCAA 61.691 66.667 0.00 0.00 0.00 4.52
1119 1372 3.978193 AGGGCAATGGTTCCGGCA 61.978 61.111 0.00 0.00 0.00 5.69
1164 1417 1.544724 CCGATGTGGGGAACAACAAT 58.455 50.000 0.00 0.00 43.61 2.71
1221 1474 1.079127 CAATGGCGTCGACTTCCCT 60.079 57.895 14.70 4.93 0.00 4.20
1248 1501 4.003788 CCGACGGGCAGGTTCAGT 62.004 66.667 5.81 0.00 0.00 3.41
1251 1504 0.108329 CGACGGGCAGGTTCAGTAAT 60.108 55.000 0.00 0.00 0.00 1.89
1255 1508 2.493547 GGCAGGTTCAGTAATGGCC 58.506 57.895 0.00 0.00 32.48 5.36
1260 1513 3.209410 CAGGTTCAGTAATGGCCTCATC 58.791 50.000 3.32 0.00 32.24 2.92
1263 1516 1.496060 TCAGTAATGGCCTCATCGGT 58.504 50.000 3.32 0.00 32.24 4.69
1486 1739 1.340795 CCATGAGAGGAGCCAGCTTTT 60.341 52.381 0.00 0.00 0.00 2.27
1509 1762 2.232298 CTGGAGGCTCCGGTGTTCTC 62.232 65.000 30.63 15.71 40.17 2.87
1559 1828 4.753107 TGCCTCTGTTTTTCTAGTTTACCG 59.247 41.667 0.00 0.00 0.00 4.02
1575 1852 2.981859 ACCGGACATATCTGTGGTTC 57.018 50.000 9.46 0.00 35.14 3.62
1592 1870 4.699637 TGGTTCAGTAGAAACATGTCGTT 58.300 39.130 0.00 0.00 46.12 3.85
1630 1908 9.743057 TTTTGTTCAGACATAAATTTCGATTGT 57.257 25.926 0.00 0.00 35.29 2.71
1633 1911 9.214957 TGTTCAGACATAAATTTCGATTGTAGT 57.785 29.630 0.00 0.00 0.00 2.73
1660 1938 5.111989 GGTTAATAACCCCAAGTACGTCTC 58.888 45.833 11.01 0.00 46.12 3.36
1669 1947 4.320935 CCCCAAGTACGTCTCAAATTTTGG 60.321 45.833 9.18 0.00 34.92 3.28
1735 2013 8.529476 AGATGATTCGTTACTACCTAAAGTTGT 58.471 33.333 0.00 0.00 38.10 3.32
1768 2046 6.831727 TCAATTGTTCAATCAAAGCAACAG 57.168 33.333 5.13 0.00 30.66 3.16
1802 2114 7.548097 TGTACTCCATCTCTCTTTAATGTCAC 58.452 38.462 0.00 0.00 0.00 3.67
1829 2141 5.163364 ACCACACACAATTTAAAATCTGGCA 60.163 36.000 0.00 0.00 0.00 4.92
1833 2145 8.011106 CACACACAATTTAAAATCTGGCATTTC 58.989 33.333 0.00 0.00 0.00 2.17
1851 2165 5.352293 GCATTTCCCCTTGCTGAATTAAAAG 59.648 40.000 0.00 0.00 35.95 2.27
1943 2261 2.271800 GGAGACACGATCAACATGACC 58.728 52.381 0.00 0.00 0.00 4.02
2087 2405 1.464734 TCGACTTCTTCTCGCAGGAT 58.535 50.000 0.00 0.00 0.00 3.24
2217 2541 1.876156 CTTCAACTCAGCCAACTCACC 59.124 52.381 0.00 0.00 0.00 4.02
2481 2809 3.900892 GGCAGCGCCTACGAGCTA 61.901 66.667 2.29 0.00 44.07 3.32
2505 2833 2.362503 AGCATCGTCGAGGACCCA 60.363 61.111 11.71 0.00 0.00 4.51
2523 2851 2.571212 CCACAGTCTGCAGGTAAAACA 58.429 47.619 15.13 0.00 0.00 2.83
2524 2852 2.290641 CCACAGTCTGCAGGTAAAACAC 59.709 50.000 15.13 2.28 0.00 3.32
2526 2854 3.002656 CACAGTCTGCAGGTAAAACACAG 59.997 47.826 15.13 2.05 0.00 3.66
2527 2855 2.031682 CAGTCTGCAGGTAAAACACAGC 60.032 50.000 15.13 0.00 0.00 4.40
2528 2856 1.946768 GTCTGCAGGTAAAACACAGCA 59.053 47.619 15.13 0.00 37.37 4.41
2530 2858 1.949525 CTGCAGGTAAAACACAGCAGT 59.050 47.619 5.57 0.00 45.47 4.40
2531 2859 2.358898 CTGCAGGTAAAACACAGCAGTT 59.641 45.455 5.57 0.00 45.47 3.16
2532 2860 2.357637 TGCAGGTAAAACACAGCAGTTC 59.642 45.455 0.00 0.00 35.55 3.01
2533 2861 2.357637 GCAGGTAAAACACAGCAGTTCA 59.642 45.455 0.00 0.00 31.93 3.18
2534 2862 3.792124 GCAGGTAAAACACAGCAGTTCAC 60.792 47.826 0.00 0.00 31.93 3.18
2535 2863 2.949644 AGGTAAAACACAGCAGTTCACC 59.050 45.455 10.10 10.10 37.04 4.02
2536 2864 2.685897 GGTAAAACACAGCAGTTCACCA 59.314 45.455 11.89 0.00 36.89 4.17
2537 2865 3.129638 GGTAAAACACAGCAGTTCACCAA 59.870 43.478 11.89 0.00 36.89 3.67
2538 2866 3.951775 AAAACACAGCAGTTCACCAAA 57.048 38.095 0.00 0.00 0.00 3.28
2541 2869 2.292267 ACACAGCAGTTCACCAAAGAG 58.708 47.619 0.00 0.00 0.00 2.85
2542 2870 2.292267 CACAGCAGTTCACCAAAGAGT 58.708 47.619 0.00 0.00 0.00 3.24
2543 2871 3.118408 ACACAGCAGTTCACCAAAGAGTA 60.118 43.478 0.00 0.00 0.00 2.59
2544 2872 4.067896 CACAGCAGTTCACCAAAGAGTAT 58.932 43.478 0.00 0.00 0.00 2.12
2545 2873 4.516698 CACAGCAGTTCACCAAAGAGTATT 59.483 41.667 0.00 0.00 0.00 1.89
2546 2874 4.757149 ACAGCAGTTCACCAAAGAGTATTC 59.243 41.667 0.00 0.00 0.00 1.75
2547 2875 4.999950 CAGCAGTTCACCAAAGAGTATTCT 59.000 41.667 0.00 0.00 34.29 2.40
2548 2876 4.999950 AGCAGTTCACCAAAGAGTATTCTG 59.000 41.667 0.00 0.00 32.79 3.02
2549 2877 4.154918 GCAGTTCACCAAAGAGTATTCTGG 59.845 45.833 0.00 0.00 32.79 3.86
2550 2878 4.154918 CAGTTCACCAAAGAGTATTCTGGC 59.845 45.833 0.00 0.00 32.79 4.85
2553 2881 4.264253 TCACCAAAGAGTATTCTGGCATG 58.736 43.478 0.00 0.00 32.79 4.06
2555 2883 4.012374 ACCAAAGAGTATTCTGGCATGTG 58.988 43.478 0.00 0.00 32.79 3.21
2556 2884 4.263462 ACCAAAGAGTATTCTGGCATGTGA 60.263 41.667 0.00 0.00 32.79 3.58
2559 2887 4.399004 AGAGTATTCTGGCATGTGACTC 57.601 45.455 10.21 10.21 33.58 3.36
2561 2889 2.840038 AGTATTCTGGCATGTGACTCCA 59.160 45.455 0.00 0.00 0.00 3.86
2562 2890 2.119801 ATTCTGGCATGTGACTCCAC 57.880 50.000 0.00 0.00 43.46 4.02
2571 2899 3.540211 GTGACTCCACACCTCATGG 57.460 57.895 0.00 0.00 42.72 3.66
2572 2900 0.976641 GTGACTCCACACCTCATGGA 59.023 55.000 0.00 0.00 44.20 3.41
2573 2901 1.556911 GTGACTCCACACCTCATGGAT 59.443 52.381 0.00 0.00 45.27 3.41
2576 2904 0.531532 CTCCACACCTCATGGATCGC 60.532 60.000 0.00 0.00 45.27 4.58
2577 2905 1.524621 CCACACCTCATGGATCGCC 60.525 63.158 0.00 0.00 39.87 5.54
2586 2914 4.430721 TGGATCGCCATTTTGCCA 57.569 50.000 0.00 0.00 39.92 4.92
2587 2915 2.899122 TGGATCGCCATTTTGCCAT 58.101 47.368 0.00 0.00 39.92 4.40
2588 2916 2.064434 TGGATCGCCATTTTGCCATA 57.936 45.000 0.00 0.00 39.92 2.74
2589 2917 1.955778 TGGATCGCCATTTTGCCATAG 59.044 47.619 0.00 0.00 39.92 2.23
2590 2918 1.270550 GGATCGCCATTTTGCCATAGG 59.729 52.381 0.00 0.00 0.00 2.57
2591 2919 1.270550 GATCGCCATTTTGCCATAGGG 59.729 52.381 0.00 0.00 37.18 3.53
2592 2920 0.754957 TCGCCATTTTGCCATAGGGG 60.755 55.000 0.00 0.00 40.85 4.79
2593 2921 1.042559 CGCCATTTTGCCATAGGGGT 61.043 55.000 0.00 0.00 39.65 4.95
2594 2922 1.203237 GCCATTTTGCCATAGGGGTT 58.797 50.000 0.00 0.00 39.65 4.11
2595 2923 1.134431 GCCATTTTGCCATAGGGGTTG 60.134 52.381 0.00 0.00 39.65 3.77
2596 2924 1.485895 CCATTTTGCCATAGGGGTTGG 59.514 52.381 0.00 0.00 39.65 3.77
2597 2925 2.465813 CATTTTGCCATAGGGGTTGGA 58.534 47.619 0.00 0.00 39.65 3.53
2599 2927 2.157640 TTTGCCATAGGGGTTGGATG 57.842 50.000 0.00 0.00 39.65 3.51
2600 2928 1.006813 TTGCCATAGGGGTTGGATGT 58.993 50.000 0.00 0.00 39.65 3.06
2601 2929 0.258484 TGCCATAGGGGTTGGATGTG 59.742 55.000 0.00 0.00 39.65 3.21
2602 2930 1.109323 GCCATAGGGGTTGGATGTGC 61.109 60.000 0.00 0.00 39.65 4.57
2603 2931 0.819259 CCATAGGGGTTGGATGTGCG 60.819 60.000 0.00 0.00 36.26 5.34
2605 2933 0.107214 ATAGGGGTTGGATGTGCGTG 60.107 55.000 0.00 0.00 0.00 5.34
2606 2934 1.485294 TAGGGGTTGGATGTGCGTGT 61.485 55.000 0.00 0.00 0.00 4.49
2607 2935 1.901464 GGGGTTGGATGTGCGTGTT 60.901 57.895 0.00 0.00 0.00 3.32
2609 2937 0.318614 GGGTTGGATGTGCGTGTTTG 60.319 55.000 0.00 0.00 0.00 2.93
2610 2938 0.939106 GGTTGGATGTGCGTGTTTGC 60.939 55.000 0.00 0.00 0.00 3.68
2611 2939 1.009108 TTGGATGTGCGTGTTTGCG 60.009 52.632 0.00 0.00 37.81 4.85
2621 2949 1.272784 CGTGTTTGCGCTCGAGTGTA 61.273 55.000 25.72 19.87 0.00 2.90
2622 2950 1.068474 GTGTTTGCGCTCGAGTGTAT 58.932 50.000 25.72 0.00 0.00 2.29
2624 2952 0.247301 GTTTGCGCTCGAGTGTATGC 60.247 55.000 25.72 16.04 0.00 3.14
2627 2955 3.672397 CGCTCGAGTGTATGCGCG 61.672 66.667 17.90 0.00 41.85 6.86
2628 2956 2.579787 GCTCGAGTGTATGCGCGT 60.580 61.111 15.13 7.55 33.56 6.01
2630 2958 0.660595 GCTCGAGTGTATGCGCGTAT 60.661 55.000 15.52 15.52 33.56 3.06
2631 2959 1.399343 GCTCGAGTGTATGCGCGTATA 60.399 52.381 13.13 13.13 33.56 1.47
2633 2961 3.484721 GCTCGAGTGTATGCGCGTATATA 60.485 47.826 19.79 14.59 33.56 0.86
2634 2962 4.785658 GCTCGAGTGTATGCGCGTATATAT 60.786 45.833 19.79 9.03 33.56 0.86
2635 2963 5.557703 GCTCGAGTGTATGCGCGTATATATA 60.558 44.000 19.79 7.33 33.56 0.86
2637 2965 6.360329 TCGAGTGTATGCGCGTATATATATG 58.640 40.000 19.79 10.46 33.56 1.78
2641 2969 7.015877 AGTGTATGCGCGTATATATATGATCG 58.984 38.462 19.79 10.70 0.00 3.69
2642 2970 5.793457 TGTATGCGCGTATATATATGATCGC 59.207 40.000 19.79 20.86 41.41 4.58
2645 2973 4.675114 TGCGCGTATATATATGATCGCTTG 59.325 41.667 24.64 17.14 41.57 4.01
2648 2976 5.681543 CGCGTATATATATGATCGCTTGTGT 59.318 40.000 24.49 0.00 41.17 3.72
2649 2977 6.129691 CGCGTATATATATGATCGCTTGTGTC 60.130 42.308 24.49 8.10 41.17 3.67
2650 2978 6.913132 GCGTATATATATGATCGCTTGTGTCT 59.087 38.462 22.31 0.00 40.39 3.41
2651 2979 7.096844 GCGTATATATATGATCGCTTGTGTCTG 60.097 40.741 22.31 0.00 40.39 3.51
2652 2980 7.910683 CGTATATATATGATCGCTTGTGTCTGT 59.089 37.037 6.13 0.00 0.00 3.41
2655 2983 3.876274 ATGATCGCTTGTGTCTGTACT 57.124 42.857 0.00 0.00 0.00 2.73
2657 2985 2.296190 TGATCGCTTGTGTCTGTACTGT 59.704 45.455 0.00 0.00 0.00 3.55
2658 2986 2.134201 TCGCTTGTGTCTGTACTGTG 57.866 50.000 0.00 0.00 0.00 3.66
2659 2987 1.407618 TCGCTTGTGTCTGTACTGTGT 59.592 47.619 0.00 0.00 0.00 3.72
2661 2989 2.033747 CGCTTGTGTCTGTACTGTGTTG 60.034 50.000 0.00 0.00 0.00 3.33
2662 2990 2.287915 GCTTGTGTCTGTACTGTGTTGG 59.712 50.000 0.00 0.00 0.00 3.77
2665 2993 4.209307 TGTGTCTGTACTGTGTTGGAAA 57.791 40.909 0.00 0.00 0.00 3.13
2666 2994 4.580868 TGTGTCTGTACTGTGTTGGAAAA 58.419 39.130 0.00 0.00 0.00 2.29
2667 2995 5.004448 TGTGTCTGTACTGTGTTGGAAAAA 58.996 37.500 0.00 0.00 0.00 1.94
2705 3034 4.402155 CCATACTTGCACCAACCATGTAAT 59.598 41.667 0.00 0.00 0.00 1.89
2712 3048 3.554752 GCACCAACCATGTAATGCTTTGT 60.555 43.478 0.00 0.00 44.97 2.83
2715 3051 4.100808 ACCAACCATGTAATGCTTTGTTGT 59.899 37.500 9.91 0.30 44.97 3.32
2729 3065 0.322906 TGTTGTGTGCAGGGTTGACA 60.323 50.000 0.00 0.00 0.00 3.58
3003 3339 6.368516 AGACTCAAATGTGGTTTTGTGTTTTG 59.631 34.615 6.21 0.00 41.07 2.44
3007 3344 2.257207 TGTGGTTTTGTGTTTTGGGGA 58.743 42.857 0.00 0.00 0.00 4.81
3098 3437 5.046014 TCCAAATTGGGGGTTGATTAATGTG 60.046 40.000 12.67 0.00 38.32 3.21
3104 3456 3.380320 GGGGGTTGATTAATGTGCTACAC 59.620 47.826 0.00 0.00 34.56 2.90
3128 3480 0.107831 TTGGGGCAGACACACACTAC 59.892 55.000 0.00 0.00 0.00 2.73
3135 3487 3.576648 GCAGACACACACTACTTACTCC 58.423 50.000 0.00 0.00 0.00 3.85
3156 3509 1.065551 TCGATCGATTCTCGTGCACAT 59.934 47.619 15.15 1.81 41.35 3.21
3176 3529 3.527507 TTGACCTGAGTACTGGAGACT 57.472 47.619 0.00 0.00 38.29 3.24
3222 3575 5.023452 TCAACTTATGAGCTGAGGGAGTAA 58.977 41.667 0.00 0.00 33.04 2.24
3247 3600 1.607628 AGTAGACGACGCTCAACAAGT 59.392 47.619 0.00 0.00 0.00 3.16
3251 3604 3.650139 AGACGACGCTCAACAAGTTAAT 58.350 40.909 0.00 0.00 0.00 1.40
3353 3706 9.817365 GTGATTCTTATGTTTATGATCCAATCG 57.183 33.333 0.00 0.00 0.00 3.34
3365 3718 1.808411 TCCAATCGTTGTTCTGGCTC 58.192 50.000 0.00 0.00 0.00 4.70
3366 3719 0.443869 CCAATCGTTGTTCTGGCTCG 59.556 55.000 0.00 0.00 0.00 5.03
3367 3720 1.428448 CAATCGTTGTTCTGGCTCGA 58.572 50.000 0.00 0.00 35.14 4.04
3368 3721 2.002586 CAATCGTTGTTCTGGCTCGAT 58.997 47.619 0.00 0.00 41.82 3.59
3369 3722 1.927895 ATCGTTGTTCTGGCTCGATC 58.072 50.000 0.00 0.00 36.72 3.69
3370 3723 0.888619 TCGTTGTTCTGGCTCGATCT 59.111 50.000 0.00 0.00 0.00 2.75
3371 3724 2.089201 TCGTTGTTCTGGCTCGATCTA 58.911 47.619 0.00 0.00 0.00 1.98
3372 3725 2.097629 TCGTTGTTCTGGCTCGATCTAG 59.902 50.000 0.00 0.00 0.00 2.43
3373 3726 2.159366 CGTTGTTCTGGCTCGATCTAGT 60.159 50.000 0.00 0.00 0.00 2.57
3374 3727 3.064958 CGTTGTTCTGGCTCGATCTAGTA 59.935 47.826 0.00 0.00 0.00 1.82
3375 3728 4.352887 GTTGTTCTGGCTCGATCTAGTAC 58.647 47.826 3.07 3.07 0.00 2.73
3376 3729 3.887352 TGTTCTGGCTCGATCTAGTACT 58.113 45.455 9.95 0.00 0.00 2.73
3377 3730 5.032327 TGTTCTGGCTCGATCTAGTACTA 57.968 43.478 9.95 1.89 0.00 1.82
3378 3731 5.057819 TGTTCTGGCTCGATCTAGTACTAG 58.942 45.833 21.87 21.87 34.56 2.57
3379 3732 3.666274 TCTGGCTCGATCTAGTACTAGC 58.334 50.000 22.87 13.85 33.32 3.42
3380 3733 3.325425 TCTGGCTCGATCTAGTACTAGCT 59.675 47.826 22.87 15.00 33.32 3.32
3381 3734 3.666274 TGGCTCGATCTAGTACTAGCTC 58.334 50.000 22.87 21.04 33.32 4.09
3382 3735 3.004862 GGCTCGATCTAGTACTAGCTCC 58.995 54.545 22.87 13.42 33.32 4.70
3388 3741 2.831333 TCTAGTACTAGCTCCGGTTCG 58.169 52.381 22.87 0.00 33.32 3.95
3404 3757 4.615541 CCGGTTCGCTAAAAGTTTCATTTC 59.384 41.667 0.00 0.00 0.00 2.17
3428 3781 8.310406 TCGAATATCAGCATAAATGTAACAGG 57.690 34.615 0.00 0.00 0.00 4.00
3437 3790 0.610785 AATGTAACAGGCCCAACCCG 60.611 55.000 0.00 0.00 40.58 5.28
3441 3794 0.537828 TAACAGGCCCAACCCGAAAC 60.538 55.000 0.00 0.00 40.58 2.78
3442 3795 2.989253 CAGGCCCAACCCGAAACC 60.989 66.667 0.00 0.00 40.58 3.27
3455 3808 2.817844 CCCGAAACCCTAGTTCCTTTTG 59.182 50.000 0.00 0.00 34.19 2.44
3632 5154 6.465439 TCCTTTTCTCTTCCAAAGGTTTTC 57.535 37.500 9.87 0.00 46.44 2.29
3647 5169 3.081061 GGTTTTCAAAAATCCCATGCCC 58.919 45.455 0.00 0.00 0.00 5.36
3650 5172 4.720775 TTTCAAAAATCCCATGCCCTTT 57.279 36.364 0.00 0.00 0.00 3.11
3658 5180 1.564348 TCCCATGCCCTTTCTACTTCC 59.436 52.381 0.00 0.00 0.00 3.46
3659 5181 1.284785 CCCATGCCCTTTCTACTTCCA 59.715 52.381 0.00 0.00 0.00 3.53
3681 5203 0.536460 TTGGACTCCAAACTTCGCCC 60.536 55.000 8.15 0.00 40.92 6.13
3682 5204 2.033194 GGACTCCAAACTTCGCCCG 61.033 63.158 0.00 0.00 0.00 6.13
3683 5205 2.668550 ACTCCAAACTTCGCCCGC 60.669 61.111 0.00 0.00 0.00 6.13
3684 5206 3.788766 CTCCAAACTTCGCCCGCG 61.789 66.667 0.00 0.00 41.35 6.46
3697 5219 2.112198 CCCGCGCCATGCTTTTCTA 61.112 57.895 0.00 0.00 43.27 2.10
3698 5220 1.353103 CCGCGCCATGCTTTTCTAG 59.647 57.895 0.00 0.00 43.27 2.43
3699 5221 1.089481 CCGCGCCATGCTTTTCTAGA 61.089 55.000 0.00 0.00 43.27 2.43
3701 5223 1.267732 CGCGCCATGCTTTTCTAGAAG 60.268 52.381 5.12 0.00 43.27 2.85
3702 5224 1.740025 GCGCCATGCTTTTCTAGAAGT 59.260 47.619 5.12 0.00 41.73 3.01
3703 5225 2.223135 GCGCCATGCTTTTCTAGAAGTC 60.223 50.000 5.12 0.06 41.73 3.01
3704 5226 3.265791 CGCCATGCTTTTCTAGAAGTCT 58.734 45.455 5.12 0.00 0.00 3.24
3705 5227 3.686726 CGCCATGCTTTTCTAGAAGTCTT 59.313 43.478 5.12 0.00 0.00 3.01
3706 5228 4.154918 CGCCATGCTTTTCTAGAAGTCTTT 59.845 41.667 5.12 0.00 0.00 2.52
3707 5229 5.335191 CGCCATGCTTTTCTAGAAGTCTTTT 60.335 40.000 5.12 0.00 0.00 2.27
3708 5230 6.128282 CGCCATGCTTTTCTAGAAGTCTTTTA 60.128 38.462 5.12 0.00 0.00 1.52
3709 5231 7.414540 CGCCATGCTTTTCTAGAAGTCTTTTAT 60.415 37.037 5.12 0.00 0.00 1.40
3710 5232 8.246871 GCCATGCTTTTCTAGAAGTCTTTTATT 58.753 33.333 5.12 0.00 0.00 1.40
3751 5479 6.015095 AGGAAAAGGCAGAAAAGTAAATCAGG 60.015 38.462 0.00 0.00 0.00 3.86
3755 5483 6.128138 AGGCAGAAAAGTAAATCAGGTAGT 57.872 37.500 0.00 0.00 0.00 2.73
3771 5499 0.615331 TAGTGAGAAGCCCAAGCCAG 59.385 55.000 0.00 0.00 41.25 4.85
3790 5518 4.227134 CAGCGCCGTAGCCCATCT 62.227 66.667 2.29 0.00 38.01 2.90
3792 5520 2.131709 AGCGCCGTAGCCCATCTAA 61.132 57.895 2.29 0.00 38.01 2.10
3794 5522 1.014564 GCGCCGTAGCCCATCTAATC 61.015 60.000 0.00 0.00 34.57 1.75
3805 5533 0.954452 CATCTAATCAAAGCCGGCCC 59.046 55.000 26.15 0.00 0.00 5.80
3807 5535 0.393808 TCTAATCAAAGCCGGCCCAC 60.394 55.000 26.15 0.00 0.00 4.61
3811 5539 1.847798 ATCAAAGCCGGCCCACTACA 61.848 55.000 26.15 0.35 0.00 2.74
3818 5546 1.002624 CGGCCCACTACAACCACAT 60.003 57.895 0.00 0.00 0.00 3.21
3821 5549 1.453155 GCCCACTACAACCACATGAG 58.547 55.000 0.00 0.00 0.00 2.90
3847 5575 1.005748 GCCCAACTGCCTTTCTTGC 60.006 57.895 0.00 0.00 0.00 4.01
3850 5578 1.114722 CCAACTGCCTTTCTTGCCCA 61.115 55.000 0.00 0.00 0.00 5.36
3851 5579 0.032540 CAACTGCCTTTCTTGCCCAC 59.967 55.000 0.00 0.00 0.00 4.61
3853 5581 1.228675 CTGCCTTTCTTGCCCACCT 60.229 57.895 0.00 0.00 0.00 4.00
3854 5582 0.038166 CTGCCTTTCTTGCCCACCTA 59.962 55.000 0.00 0.00 0.00 3.08
3855 5583 0.251165 TGCCTTTCTTGCCCACCTAC 60.251 55.000 0.00 0.00 0.00 3.18
3886 6441 1.607225 AACCTAGCCCAATCCATCCA 58.393 50.000 0.00 0.00 0.00 3.41
3892 6447 0.533755 GCCCAATCCATCCACGAGAG 60.534 60.000 0.00 0.00 0.00 3.20
3927 6482 1.099689 AGCGAGACTGTAGCTTCTCC 58.900 55.000 7.42 1.87 38.13 3.71
3928 6483 0.101579 GCGAGACTGTAGCTTCTCCC 59.898 60.000 7.42 0.00 35.74 4.30
3932 6487 2.583593 CTGTAGCTTCTCCCGCGC 60.584 66.667 0.00 0.00 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
424 587 6.911484 AAAAAGAGACACGAATAAAATGCG 57.089 33.333 0.00 0.00 0.00 4.73
540 728 7.113437 GCAGAGTGATATATACTGAGGGAGTA 58.887 42.308 0.00 0.00 41.57 2.59
541 729 5.949354 GCAGAGTGATATATACTGAGGGAGT 59.051 44.000 0.00 0.00 38.88 3.85
542 730 5.948758 TGCAGAGTGATATATACTGAGGGAG 59.051 44.000 0.00 0.00 0.00 4.30
544 732 6.379417 TGATGCAGAGTGATATATACTGAGGG 59.621 42.308 0.00 0.00 0.00 4.30
588 803 4.295905 ACTCCCTCCATCCCAAATAGTA 57.704 45.455 0.00 0.00 0.00 1.82
589 804 3.151542 ACTCCCTCCATCCCAAATAGT 57.848 47.619 0.00 0.00 0.00 2.12
590 805 4.235372 ACTACTCCCTCCATCCCAAATAG 58.765 47.826 0.00 0.00 0.00 1.73
591 806 4.295905 ACTACTCCCTCCATCCCAAATA 57.704 45.455 0.00 0.00 0.00 1.40
592 807 3.151542 ACTACTCCCTCCATCCCAAAT 57.848 47.619 0.00 0.00 0.00 2.32
593 808 2.661176 ACTACTCCCTCCATCCCAAA 57.339 50.000 0.00 0.00 0.00 3.28
594 809 2.045885 AGAACTACTCCCTCCATCCCAA 59.954 50.000 0.00 0.00 0.00 4.12
595 810 1.651770 AGAACTACTCCCTCCATCCCA 59.348 52.381 0.00 0.00 0.00 4.37
596 811 2.043227 CAGAACTACTCCCTCCATCCC 58.957 57.143 0.00 0.00 0.00 3.85
597 812 3.033659 TCAGAACTACTCCCTCCATCC 57.966 52.381 0.00 0.00 0.00 3.51
697 914 8.160521 TCAGTGATTCGAATTTAAAAAGTCCA 57.839 30.769 12.81 0.00 29.78 4.02
743 962 7.416664 GCCACAATTATCACATGGTACTGAAAT 60.417 37.037 0.00 0.00 32.71 2.17
786 1005 4.354587 CTGAAGAGAAAACAAGCCACAAC 58.645 43.478 0.00 0.00 0.00 3.32
1067 1320 2.203139 TCACCACAGCCACCAACG 60.203 61.111 0.00 0.00 0.00 4.10
1071 1324 2.670934 CTGCTCACCACAGCCACC 60.671 66.667 0.00 0.00 38.80 4.61
1097 1350 1.691219 GGAACCATTGCCCTGGAGA 59.309 57.895 8.54 0.00 39.73 3.71
1106 1359 2.029110 ACAAAGATTGCCGGAACCATTG 60.029 45.455 5.05 5.16 0.00 2.82
1107 1360 2.029110 CACAAAGATTGCCGGAACCATT 60.029 45.455 5.05 0.00 0.00 3.16
1108 1361 1.545582 CACAAAGATTGCCGGAACCAT 59.454 47.619 5.05 0.00 0.00 3.55
1119 1372 1.798813 GAGTCGCCGAACACAAAGATT 59.201 47.619 0.00 0.00 0.00 2.40
1164 1417 1.844289 ACTGGTCCCCGGCAAGTAA 60.844 57.895 0.00 0.00 32.02 2.24
1248 1501 1.148273 GGCACCGATGAGGCCATTA 59.852 57.895 5.01 0.00 46.92 1.90
1260 1513 2.742372 CCCAAGAAGTCGGCACCG 60.742 66.667 1.73 1.73 41.35 4.94
1263 1516 1.371183 CTCACCCAAGAAGTCGGCA 59.629 57.895 0.00 0.00 0.00 5.69
1432 1685 2.175078 CGGCTTCTTCGTCGTCGA 59.825 61.111 0.00 0.00 44.66 4.20
1455 1708 0.468648 CTCTCATGGAGGCATCAGCA 59.531 55.000 0.00 0.00 44.61 4.41
1509 1762 1.855213 TTGGACGTACCGTGGAGTCG 61.855 60.000 0.00 0.00 41.37 4.18
1642 1920 4.895668 TTTGAGACGTACTTGGGGTTAT 57.104 40.909 0.00 0.00 0.00 1.89
1683 1961 5.947663 TCCACCTAAATTCTTCCAGTGAAA 58.052 37.500 0.00 0.00 0.00 2.69
1768 2046 3.704061 AGAGATGGAGTACAGGAGAAAGC 59.296 47.826 0.00 0.00 0.00 3.51
1802 2114 6.143758 CCAGATTTTAAATTGTGTGTGGTTCG 59.856 38.462 6.52 0.00 0.00 3.95
1829 2141 6.269769 TGACTTTTAATTCAGCAAGGGGAAAT 59.730 34.615 0.00 0.00 0.00 2.17
1833 2145 5.064441 CTGACTTTTAATTCAGCAAGGGG 57.936 43.478 0.00 0.00 33.23 4.79
1851 2165 5.107065 GGTGTCAATTGTAGTACTTGCTGAC 60.107 44.000 0.00 8.27 34.03 3.51
2165 2483 1.833630 TGATCATCACTGGTCAGGTCC 59.166 52.381 0.00 0.00 37.60 4.46
2217 2541 6.466308 TGATTCAGAGTTGAACATAACACG 57.534 37.500 0.00 0.00 45.54 4.49
2364 2692 4.717629 CGGTTCAGCGGCTCGACA 62.718 66.667 0.00 0.00 0.00 4.35
2431 2759 1.763655 TGCCCTGCATCTCGGAGAT 60.764 57.895 14.68 14.68 34.28 2.75
2481 2809 4.203618 TCGACGATGCTCGAGACT 57.796 55.556 18.75 0.90 43.74 3.24
2487 2815 2.413765 GGGTCCTCGACGATGCTC 59.586 66.667 0.00 0.00 32.65 4.26
2499 2827 1.192146 TACCTGCAGACTGTGGGTCC 61.192 60.000 17.39 0.00 45.54 4.46
2505 2833 3.206150 CTGTGTTTTACCTGCAGACTGT 58.794 45.455 17.39 7.36 0.00 3.55
2523 2851 2.717639 ACTCTTTGGTGAACTGCTGT 57.282 45.000 0.00 0.00 0.00 4.40
2524 2852 4.999950 AGAATACTCTTTGGTGAACTGCTG 59.000 41.667 0.00 0.00 0.00 4.41
2526 2854 4.154918 CCAGAATACTCTTTGGTGAACTGC 59.845 45.833 0.00 0.00 0.00 4.40
2527 2855 4.154918 GCCAGAATACTCTTTGGTGAACTG 59.845 45.833 0.00 0.00 33.21 3.16
2528 2856 4.202461 TGCCAGAATACTCTTTGGTGAACT 60.202 41.667 0.00 0.00 33.21 3.01
2530 2858 4.365514 TGCCAGAATACTCTTTGGTGAA 57.634 40.909 0.00 0.00 33.21 3.18
2531 2859 4.263462 ACATGCCAGAATACTCTTTGGTGA 60.263 41.667 0.00 0.00 33.21 4.02
2532 2860 4.012374 ACATGCCAGAATACTCTTTGGTG 58.988 43.478 0.00 0.00 33.21 4.17
2533 2861 4.012374 CACATGCCAGAATACTCTTTGGT 58.988 43.478 0.00 0.00 33.21 3.67
2534 2862 4.095483 GTCACATGCCAGAATACTCTTTGG 59.905 45.833 0.00 0.00 0.00 3.28
2535 2863 4.940046 AGTCACATGCCAGAATACTCTTTG 59.060 41.667 0.00 0.00 0.00 2.77
2536 2864 5.171339 AGTCACATGCCAGAATACTCTTT 57.829 39.130 0.00 0.00 0.00 2.52
2537 2865 4.383552 GGAGTCACATGCCAGAATACTCTT 60.384 45.833 0.00 0.00 33.92 2.85
2538 2866 3.133721 GGAGTCACATGCCAGAATACTCT 59.866 47.826 0.00 0.00 33.92 3.24
2541 2869 2.939103 GTGGAGTCACATGCCAGAATAC 59.061 50.000 0.00 0.00 43.13 1.89
2542 2870 3.266510 GTGGAGTCACATGCCAGAATA 57.733 47.619 0.00 0.00 43.13 1.75
2543 2871 2.119801 GTGGAGTCACATGCCAGAAT 57.880 50.000 0.00 0.00 43.13 2.40
2544 2872 3.631453 GTGGAGTCACATGCCAGAA 57.369 52.632 0.00 0.00 43.13 3.02
2553 2881 0.976641 TCCATGAGGTGTGGAGTCAC 59.023 55.000 0.00 0.00 40.72 3.67
2559 2887 1.524621 GGCGATCCATGAGGTGTGG 60.525 63.158 0.00 0.00 38.11 4.17
2561 2889 3.726004 TGGCGATCCATGAGGTGT 58.274 55.556 0.00 0.00 37.47 4.16
2576 2904 1.485895 CCAACCCCTATGGCAAAATGG 59.514 52.381 0.00 0.00 37.83 3.16
2577 2905 2.465813 TCCAACCCCTATGGCAAAATG 58.534 47.619 0.00 0.00 37.88 2.32
2578 2906 2.938428 TCCAACCCCTATGGCAAAAT 57.062 45.000 0.00 0.00 37.88 1.82
2580 2908 1.360852 ACATCCAACCCCTATGGCAAA 59.639 47.619 0.00 0.00 37.88 3.68
2582 2910 0.258484 CACATCCAACCCCTATGGCA 59.742 55.000 0.00 0.00 37.88 4.92
2583 2911 1.109323 GCACATCCAACCCCTATGGC 61.109 60.000 0.00 0.00 37.88 4.40
2584 2912 0.819259 CGCACATCCAACCCCTATGG 60.819 60.000 0.00 0.00 39.41 2.74
2586 2914 0.107214 CACGCACATCCAACCCCTAT 60.107 55.000 0.00 0.00 0.00 2.57
2587 2915 1.298340 CACGCACATCCAACCCCTA 59.702 57.895 0.00 0.00 0.00 3.53
2588 2916 2.034066 CACGCACATCCAACCCCT 59.966 61.111 0.00 0.00 0.00 4.79
2589 2917 1.460273 AAACACGCACATCCAACCCC 61.460 55.000 0.00 0.00 0.00 4.95
2590 2918 0.318614 CAAACACGCACATCCAACCC 60.319 55.000 0.00 0.00 0.00 4.11
2591 2919 0.939106 GCAAACACGCACATCCAACC 60.939 55.000 0.00 0.00 0.00 3.77
2592 2920 1.268113 CGCAAACACGCACATCCAAC 61.268 55.000 0.00 0.00 0.00 3.77
2593 2921 1.009108 CGCAAACACGCACATCCAA 60.009 52.632 0.00 0.00 0.00 3.53
2594 2922 2.636462 CGCAAACACGCACATCCA 59.364 55.556 0.00 0.00 0.00 3.41
2602 2930 1.272784 TACACTCGAGCGCAAACACG 61.273 55.000 13.61 7.39 0.00 4.49
2603 2931 1.068474 ATACACTCGAGCGCAAACAC 58.932 50.000 13.61 0.00 0.00 3.32
2605 2933 0.247301 GCATACACTCGAGCGCAAAC 60.247 55.000 13.61 0.00 0.00 2.93
2606 2934 1.682867 CGCATACACTCGAGCGCAAA 61.683 55.000 13.61 0.00 43.80 3.68
2607 2935 2.158330 CGCATACACTCGAGCGCAA 61.158 57.895 13.61 0.00 43.80 4.85
2611 2939 0.660595 ATACGCGCATACACTCGAGC 60.661 55.000 13.61 0.00 0.00 5.03
2612 2940 2.589338 TATACGCGCATACACTCGAG 57.411 50.000 11.84 11.84 0.00 4.04
2614 2942 6.360329 TCATATATATACGCGCATACACTCG 58.640 40.000 5.73 0.00 0.00 4.18
2615 2943 7.214635 CGATCATATATATACGCGCATACACTC 59.785 40.741 5.73 0.00 0.00 3.51
2617 2945 6.236967 GCGATCATATATATACGCGCATACAC 60.237 42.308 20.84 0.00 42.41 2.90
2625 2953 6.913132 AGACACAAGCGATCATATATATACGC 59.087 38.462 22.07 22.07 45.03 4.42
2626 2954 7.910683 ACAGACACAAGCGATCATATATATACG 59.089 37.037 0.00 3.81 0.00 3.06
2630 2958 8.237267 CAGTACAGACACAAGCGATCATATATA 58.763 37.037 0.00 0.00 0.00 0.86
2631 2959 7.087007 CAGTACAGACACAAGCGATCATATAT 58.913 38.462 0.00 0.00 0.00 0.86
2633 2961 5.163509 ACAGTACAGACACAAGCGATCATAT 60.164 40.000 0.00 0.00 0.00 1.78
2634 2962 4.157840 ACAGTACAGACACAAGCGATCATA 59.842 41.667 0.00 0.00 0.00 2.15
2635 2963 3.056536 ACAGTACAGACACAAGCGATCAT 60.057 43.478 0.00 0.00 0.00 2.45
2637 2965 2.663602 CACAGTACAGACACAAGCGATC 59.336 50.000 0.00 0.00 0.00 3.69
2641 2969 2.287915 CCAACACAGTACAGACACAAGC 59.712 50.000 0.00 0.00 0.00 4.01
2642 2970 3.792401 TCCAACACAGTACAGACACAAG 58.208 45.455 0.00 0.00 0.00 3.16
2645 2973 5.554822 TTTTTCCAACACAGTACAGACAC 57.445 39.130 0.00 0.00 0.00 3.67
2666 2994 6.037391 GCAAGTATGGCATGCATTATGTTTTT 59.963 34.615 21.36 0.00 41.07 1.94
2667 2995 5.524646 GCAAGTATGGCATGCATTATGTTTT 59.475 36.000 21.36 0.21 41.07 2.43
2670 2998 3.637694 TGCAAGTATGGCATGCATTATGT 59.362 39.130 21.36 0.00 42.69 2.29
2671 2999 4.245845 TGCAAGTATGGCATGCATTATG 57.754 40.909 21.36 11.09 42.69 1.90
2681 3009 1.135024 CATGGTTGGTGCAAGTATGGC 60.135 52.381 0.00 0.00 33.57 4.40
2682 3010 2.170166 ACATGGTTGGTGCAAGTATGG 58.830 47.619 0.00 0.00 0.00 2.74
2686 3014 2.029110 GCATTACATGGTTGGTGCAAGT 60.029 45.455 0.00 0.00 33.07 3.16
2705 3034 0.969917 ACCCTGCACACAACAAAGCA 60.970 50.000 0.00 0.00 35.43 3.91
2712 3048 0.254462 TCTGTCAACCCTGCACACAA 59.746 50.000 0.00 0.00 0.00 3.33
2715 3051 0.546122 AACTCTGTCAACCCTGCACA 59.454 50.000 0.00 0.00 0.00 4.57
2729 3065 2.024319 GCACGCGCTCTTCAACTCT 61.024 57.895 5.73 0.00 34.30 3.24
2811 3147 2.668550 GAGGAACTTGCCGCGGTT 60.669 61.111 28.70 13.40 41.55 4.44
3007 3344 1.141657 CCATGATTGACCTGGATCGGT 59.858 52.381 0.00 0.00 40.80 4.69
3016 3353 2.450476 AGGCAAAGACCATGATTGACC 58.550 47.619 0.00 1.07 32.34 4.02
3024 3363 1.247567 CCACGAAAGGCAAAGACCAT 58.752 50.000 0.00 0.00 0.00 3.55
3050 3389 0.948678 TGGCGCCAGTTGTTAAACTC 59.051 50.000 29.03 0.00 45.07 3.01
3098 3437 0.527565 CTGCCCCAATTGTGTGTAGC 59.472 55.000 4.43 0.00 0.00 3.58
3104 3456 0.314935 GTGTGTCTGCCCCAATTGTG 59.685 55.000 4.43 0.00 0.00 3.33
3156 3509 3.527507 AGTCTCCAGTACTCAGGTCAA 57.472 47.619 0.00 0.00 0.00 3.18
3203 3556 9.030452 ACTTATATTACTCCCTCAGCTCATAAG 57.970 37.037 0.00 0.00 0.00 1.73
3222 3575 5.746307 TGTTGAGCGTCGTCTACTTATAT 57.254 39.130 0.00 0.00 0.00 0.86
3282 3635 4.455190 CCAAATTAATGGCCCAGTGTTTTG 59.545 41.667 0.00 11.45 32.78 2.44
3290 3643 2.183679 GTCCACCAAATTAATGGCCCA 58.816 47.619 0.00 0.00 44.75 5.36
3345 3698 2.359900 GAGCCAGAACAACGATTGGAT 58.640 47.619 0.00 0.00 32.34 3.41
3351 3704 0.888619 AGATCGAGCCAGAACAACGA 59.111 50.000 0.00 0.00 37.39 3.85
3353 3706 3.512033 ACTAGATCGAGCCAGAACAAC 57.488 47.619 2.39 0.00 0.00 3.32
3365 3718 3.042871 ACCGGAGCTAGTACTAGATCG 57.957 52.381 31.47 26.41 46.39 3.69
3366 3719 3.432933 CGAACCGGAGCTAGTACTAGATC 59.567 52.174 31.27 31.27 45.14 2.75
3367 3720 3.401182 CGAACCGGAGCTAGTACTAGAT 58.599 50.000 30.09 25.54 35.21 1.98
3368 3721 2.831333 CGAACCGGAGCTAGTACTAGA 58.169 52.381 30.09 0.00 35.21 2.43
3369 3722 1.263752 GCGAACCGGAGCTAGTACTAG 59.736 57.143 23.25 23.25 36.29 2.57
3370 3723 1.134280 AGCGAACCGGAGCTAGTACTA 60.134 52.381 18.90 1.89 42.60 1.82
3371 3724 0.394080 AGCGAACCGGAGCTAGTACT 60.394 55.000 18.90 0.00 42.60 2.73
3372 3725 1.303309 TAGCGAACCGGAGCTAGTAC 58.697 55.000 20.78 0.00 44.15 2.73
3373 3726 2.042686 TTAGCGAACCGGAGCTAGTA 57.957 50.000 22.44 12.22 45.31 1.82
3374 3727 1.180029 TTTAGCGAACCGGAGCTAGT 58.820 50.000 22.44 8.29 45.31 2.57
3375 3728 2.194271 CTTTTAGCGAACCGGAGCTAG 58.806 52.381 22.44 14.28 45.31 3.42
3376 3729 1.547372 ACTTTTAGCGAACCGGAGCTA 59.453 47.619 20.78 20.78 44.15 3.32
3377 3730 0.320697 ACTTTTAGCGAACCGGAGCT 59.679 50.000 22.44 22.44 46.53 4.09
3378 3731 1.154197 AACTTTTAGCGAACCGGAGC 58.846 50.000 9.46 11.16 0.00 4.70
3379 3732 2.803956 TGAAACTTTTAGCGAACCGGAG 59.196 45.455 9.46 0.00 0.00 4.63
3380 3733 2.836262 TGAAACTTTTAGCGAACCGGA 58.164 42.857 9.46 0.00 0.00 5.14
3381 3734 3.824414 ATGAAACTTTTAGCGAACCGG 57.176 42.857 0.00 0.00 0.00 5.28
3382 3735 4.317291 CGAAATGAAACTTTTAGCGAACCG 59.683 41.667 0.00 0.00 0.00 4.44
3388 3741 8.737648 GCTGATATTCGAAATGAAACTTTTAGC 58.262 33.333 0.00 0.00 40.71 3.09
3404 3757 7.017645 GCCTGTTACATTTATGCTGATATTCG 58.982 38.462 0.00 0.00 0.00 3.34
3416 3769 2.810164 GGGTTGGGCCTGTTACATTTA 58.190 47.619 4.53 0.00 37.43 1.40
3417 3770 1.639722 GGGTTGGGCCTGTTACATTT 58.360 50.000 4.53 0.00 37.43 2.32
3418 3771 0.610785 CGGGTTGGGCCTGTTACATT 60.611 55.000 4.53 0.00 38.84 2.71
3419 3772 1.001393 CGGGTTGGGCCTGTTACAT 60.001 57.895 4.53 0.00 38.84 2.29
3423 3776 1.830847 GTTTCGGGTTGGGCCTGTT 60.831 57.895 4.53 0.00 44.16 3.16
3424 3777 2.203437 GTTTCGGGTTGGGCCTGT 60.203 61.111 4.53 0.00 44.16 4.00
3428 3781 1.378119 CTAGGGTTTCGGGTTGGGC 60.378 63.158 0.00 0.00 0.00 5.36
3437 3790 6.181190 AGATAGCAAAAGGAACTAGGGTTTC 58.819 40.000 0.00 0.00 38.49 2.78
3441 3794 5.946377 ACAAAGATAGCAAAAGGAACTAGGG 59.054 40.000 0.00 0.00 38.49 3.53
3442 3795 7.454260 AACAAAGATAGCAAAAGGAACTAGG 57.546 36.000 0.00 0.00 38.49 3.02
3597 5119 9.250246 TGGAAGAGAAAAGGAAAAGAACTTAAA 57.750 29.630 0.00 0.00 0.00 1.52
3598 5120 8.817092 TGGAAGAGAAAAGGAAAAGAACTTAA 57.183 30.769 0.00 0.00 0.00 1.85
3599 5121 8.817092 TTGGAAGAGAAAAGGAAAAGAACTTA 57.183 30.769 0.00 0.00 0.00 2.24
3600 5122 7.718334 TTGGAAGAGAAAAGGAAAAGAACTT 57.282 32.000 0.00 0.00 0.00 2.66
3601 5123 7.718334 TTTGGAAGAGAAAAGGAAAAGAACT 57.282 32.000 0.00 0.00 0.00 3.01
3602 5124 7.993821 CTTTGGAAGAGAAAAGGAAAAGAAC 57.006 36.000 0.00 0.00 31.15 3.01
3611 5133 8.546597 TTTTGAAAACCTTTGGAAGAGAAAAG 57.453 30.769 0.00 0.00 33.95 2.27
3632 5154 3.986996 AGAAAGGGCATGGGATTTTTG 57.013 42.857 0.00 0.00 0.00 2.44
3682 5204 1.740025 ACTTCTAGAAAAGCATGGCGC 59.260 47.619 6.63 0.00 42.91 6.53
3683 5205 3.265791 AGACTTCTAGAAAAGCATGGCG 58.734 45.455 6.63 0.00 0.00 5.69
3684 5206 5.635417 AAAGACTTCTAGAAAAGCATGGC 57.365 39.130 6.63 0.00 0.00 4.40
3721 5243 5.675684 ACTTTTCTGCCTTTTCCTCAAAA 57.324 34.783 0.00 0.00 0.00 2.44
3722 5244 6.783708 TTACTTTTCTGCCTTTTCCTCAAA 57.216 33.333 0.00 0.00 0.00 2.69
3723 5245 6.783708 TTTACTTTTCTGCCTTTTCCTCAA 57.216 33.333 0.00 0.00 0.00 3.02
3724 5246 6.549364 TGATTTACTTTTCTGCCTTTTCCTCA 59.451 34.615 0.00 0.00 0.00 3.86
3725 5247 6.981722 TGATTTACTTTTCTGCCTTTTCCTC 58.018 36.000 0.00 0.00 0.00 3.71
3727 5249 6.159293 CCTGATTTACTTTTCTGCCTTTTCC 58.841 40.000 0.00 0.00 0.00 3.13
3728 5250 6.749139 ACCTGATTTACTTTTCTGCCTTTTC 58.251 36.000 0.00 0.00 0.00 2.29
3729 5251 6.731292 ACCTGATTTACTTTTCTGCCTTTT 57.269 33.333 0.00 0.00 0.00 2.27
3730 5252 7.004691 ACTACCTGATTTACTTTTCTGCCTTT 58.995 34.615 0.00 0.00 0.00 3.11
3751 5479 0.324943 TGGCTTGGGCTTCTCACTAC 59.675 55.000 0.00 0.00 38.73 2.73
3755 5483 2.034687 GCTGGCTTGGGCTTCTCA 59.965 61.111 0.00 0.00 38.73 3.27
3779 5507 2.808543 GGCTTTGATTAGATGGGCTACG 59.191 50.000 0.00 0.00 0.00 3.51
3782 5510 1.477558 CCGGCTTTGATTAGATGGGCT 60.478 52.381 0.00 0.00 0.00 5.19
3786 5514 0.954452 GGGCCGGCTTTGATTAGATG 59.046 55.000 28.56 0.00 0.00 2.90
3787 5515 0.550914 TGGGCCGGCTTTGATTAGAT 59.449 50.000 28.56 0.00 0.00 1.98
3788 5516 0.393808 GTGGGCCGGCTTTGATTAGA 60.394 55.000 28.56 0.00 0.00 2.10
3789 5517 0.394352 AGTGGGCCGGCTTTGATTAG 60.394 55.000 28.56 0.00 0.00 1.73
3790 5518 0.913205 TAGTGGGCCGGCTTTGATTA 59.087 50.000 28.56 8.99 0.00 1.75
3792 5520 1.077716 GTAGTGGGCCGGCTTTGAT 60.078 57.895 28.56 11.55 0.00 2.57
3794 5522 1.602323 TTGTAGTGGGCCGGCTTTG 60.602 57.895 28.56 0.00 0.00 2.77
3805 5533 2.079158 CTGGCTCATGTGGTTGTAGTG 58.921 52.381 0.00 0.00 0.00 2.74
3807 5535 2.350522 GACTGGCTCATGTGGTTGTAG 58.649 52.381 0.00 0.00 0.00 2.74
3811 5539 1.003355 CCGACTGGCTCATGTGGTT 60.003 57.895 0.00 0.00 0.00 3.67
3831 5559 1.114722 TGGGCAAGAAAGGCAGTTGG 61.115 55.000 0.00 0.00 35.46 3.77
3832 5560 0.032540 GTGGGCAAGAAAGGCAGTTG 59.967 55.000 0.00 0.00 35.46 3.16
3835 5563 0.038166 TAGGTGGGCAAGAAAGGCAG 59.962 55.000 0.00 0.00 35.46 4.85
3841 5569 1.765074 GTGGGTAGGTGGGCAAGAA 59.235 57.895 0.00 0.00 0.00 2.52
3847 5575 3.339713 TTAGATAGGTGGGTAGGTGGG 57.660 52.381 0.00 0.00 0.00 4.61
3850 5578 4.639019 AGGTTTAGATAGGTGGGTAGGT 57.361 45.455 0.00 0.00 0.00 3.08
3851 5579 4.527427 GCTAGGTTTAGATAGGTGGGTAGG 59.473 50.000 0.00 0.00 0.00 3.18
3853 5581 4.486839 GGCTAGGTTTAGATAGGTGGGTA 58.513 47.826 0.00 0.00 0.00 3.69
3854 5582 3.315596 GGCTAGGTTTAGATAGGTGGGT 58.684 50.000 0.00 0.00 0.00 4.51
3855 5583 2.638363 GGGCTAGGTTTAGATAGGTGGG 59.362 54.545 0.00 0.00 0.00 4.61
3910 6465 0.378962 CGGGAGAAGCTACAGTCTCG 59.621 60.000 6.99 0.61 41.07 4.04
3927 6482 4.111016 TGTAGACACTCGGCGCGG 62.111 66.667 8.83 8.94 0.00 6.46
3928 6483 2.577112 CTGTAGACACTCGGCGCG 60.577 66.667 0.00 0.00 0.00 6.86


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

AutoCloner maintained by Alex Coulton.