Multiple sequence alignment - TraesCS6B01G440400

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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 TraesCS6B01G440400 chr6B 100.000 3969 0 0 1 3969 705489657 705493625 0.000000e+00 7330
1 TraesCS6B01G440400 chr6B 81.913 1056 172 15 1577 2619 705473752 705474801 0.000000e+00 874
2 TraesCS6B01G440400 chr6B 89.308 159 15 2 1310 1467 705473594 705473751 8.700000e-47 198
3 TraesCS6B01G440400 chr6A 90.986 3306 173 62 1 3242 609550294 609553538 0.000000e+00 4338
4 TraesCS6B01G440400 chr6A 82.336 1036 167 12 1581 2605 609480485 609479455 0.000000e+00 885
5 TraesCS6B01G440400 chr6A 88.298 376 34 8 3306 3677 609553570 609553939 3.640000e-120 442
6 TraesCS6B01G440400 chr6A 92.568 296 21 1 3675 3969 609554012 609554307 1.320000e-114 424
7 TraesCS6B01G440400 chr6A 87.500 160 18 2 1310 1468 609480647 609480489 2.440000e-42 183
8 TraesCS6B01G440400 chr6D 91.138 2460 119 42 803 3217 462689331 462691736 0.000000e+00 3243
9 TraesCS6B01G440400 chr6D 82.739 1037 161 14 1581 2605 462635747 462634717 0.000000e+00 907
10 TraesCS6B01G440400 chr6D 88.750 160 16 2 1310 1468 462635909 462635751 1.130000e-45 195
11 TraesCS6B01G440400 chr7B 84.232 501 62 12 149 638 608295765 608295271 4.640000e-129 472
12 TraesCS6B01G440400 chr7B 75.218 573 124 17 1569 2132 32344792 32345355 5.090000e-64 255
13 TraesCS6B01G440400 chr7B 76.923 286 60 6 1581 1863 242987662 242987380 1.480000e-34 158
14 TraesCS6B01G440400 chr7B 75.490 306 65 10 2203 2503 650129034 650128734 1.490000e-29 141
15 TraesCS6B01G440400 chr7D 82.732 527 69 17 126 640 593637239 593637755 2.180000e-122 449
16 TraesCS6B01G440400 chr7D 75.965 570 117 18 1573 2132 205132071 205132630 3.910000e-70 276
17 TraesCS6B01G440400 chr7D 76.140 285 62 6 1581 1862 263506275 263505994 1.150000e-30 145
18 TraesCS6B01G440400 chr7A 81.168 531 74 16 117 640 2234248 2234759 1.720000e-108 403
19 TraesCS6B01G440400 chr7A 80.114 176 27 7 116 286 372778877 372779049 1.500000e-24 124
20 TraesCS6B01G440400 chr2A 80.899 534 70 22 120 640 10487755 10487241 3.720000e-105 392
21 TraesCS6B01G440400 chr4D 79.110 292 55 6 1573 1861 44422855 44423143 3.130000e-46 196
22 TraesCS6B01G440400 chr5A 76.333 300 53 17 1569 1859 552374827 552375117 1.150000e-30 145
23 TraesCS6B01G440400 chr4A 79.670 182 29 5 114 290 654624294 654624472 1.500000e-24 124


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 TraesCS6B01G440400 chr6B 705489657 705493625 3968 False 7330.000000 7330 100.000000 1 3969 1 chr6B.!!$F1 3968
1 TraesCS6B01G440400 chr6B 705473594 705474801 1207 False 536.000000 874 85.610500 1310 2619 2 chr6B.!!$F2 1309
2 TraesCS6B01G440400 chr6A 609550294 609554307 4013 False 1734.666667 4338 90.617333 1 3969 3 chr6A.!!$F1 3968
3 TraesCS6B01G440400 chr6A 609479455 609480647 1192 True 534.000000 885 84.918000 1310 2605 2 chr6A.!!$R1 1295
4 TraesCS6B01G440400 chr6D 462689331 462691736 2405 False 3243.000000 3243 91.138000 803 3217 1 chr6D.!!$F1 2414
5 TraesCS6B01G440400 chr6D 462634717 462635909 1192 True 551.000000 907 85.744500 1310 2605 2 chr6D.!!$R1 1295
6 TraesCS6B01G440400 chr7B 32344792 32345355 563 False 255.000000 255 75.218000 1569 2132 1 chr7B.!!$F1 563
7 TraesCS6B01G440400 chr7D 593637239 593637755 516 False 449.000000 449 82.732000 126 640 1 chr7D.!!$F2 514
8 TraesCS6B01G440400 chr7D 205132071 205132630 559 False 276.000000 276 75.965000 1573 2132 1 chr7D.!!$F1 559
9 TraesCS6B01G440400 chr7A 2234248 2234759 511 False 403.000000 403 81.168000 117 640 1 chr7A.!!$F1 523
10 TraesCS6B01G440400 chr2A 10487241 10487755 514 True 392.000000 392 80.899000 120 640 1 chr2A.!!$R1 520

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
118 119 0.106318 AGAAGCTTCATCCATGGGCC 60.106 55.0 27.57 0.00 0.00 5.80 F
528 541 0.252696 TGGATGCACCTAGGAGTGGT 60.253 55.0 17.98 0.00 38.24 4.16 F
763 793 1.133809 TCCTAGCACTGCCTTGGGTT 61.134 55.0 0.00 0.00 0.00 4.11 F
1725 1769 0.744874 CTCTACATCTTCGCCGGGAA 59.255 55.0 2.18 4.24 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1409 1.519455 GTGGCCGACGAAGATCTGG 60.519 63.158 0.00 0.0 0.00 3.86 R
1552 1594 1.558233 TGCAATGTTCCATGCATCCA 58.442 45.000 0.00 0.0 46.87 3.41 R
2663 2749 0.528924 GCATTGCAGCAAGGTGATCA 59.471 50.000 20.36 0.0 0.00 2.92 R
3276 3386 0.030101 GAGCCGAGGAAGATCGACAG 59.970 60.000 0.00 0.0 45.56 3.51 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
46 47 2.315925 TCATCCATGTTTCCGAGAGC 57.684 50.000 0.00 0.00 0.00 4.09
52 53 1.536766 CATGTTTCCGAGAGCTGCAAA 59.463 47.619 1.02 0.00 0.00 3.68
85 86 4.988598 CGGGCGGGCGAATGCTAT 62.989 66.667 0.00 0.00 42.25 2.97
118 119 0.106318 AGAAGCTTCATCCATGGGCC 60.106 55.000 27.57 0.00 0.00 5.80
208 213 4.164087 ACCGTGGTGTCGTTGCCA 62.164 61.111 0.00 0.00 0.00 4.92
209 214 2.668212 CCGTGGTGTCGTTGCCAT 60.668 61.111 0.00 0.00 37.09 4.40
247 253 4.621034 GCATCAATTTGTTTCCTACAACCG 59.379 41.667 0.00 0.00 46.09 4.44
273 283 3.309954 CCGATTTTTGCTACTACCAGCTC 59.690 47.826 0.00 0.00 42.30 4.09
313 324 3.509967 AGCAGCCATTTTTGTTACTACCC 59.490 43.478 0.00 0.00 0.00 3.69
314 325 3.509967 GCAGCCATTTTTGTTACTACCCT 59.490 43.478 0.00 0.00 0.00 4.34
318 329 6.645003 CAGCCATTTTTGTTACTACCCTTTTC 59.355 38.462 0.00 0.00 0.00 2.29
322 333 9.607988 CCATTTTTGTTACTACCCTTTTCTTTT 57.392 29.630 0.00 0.00 0.00 2.27
340 351 1.573108 TTGGGTTTTGCTGGGACAAA 58.427 45.000 0.00 0.00 38.70 2.83
438 450 1.031235 CCGCCATGGTTGCATGAATA 58.969 50.000 14.67 0.00 34.66 1.75
462 474 1.779061 AACTGGAGGGACGGCAACAT 61.779 55.000 0.00 0.00 0.00 2.71
464 476 2.184020 CTGGAGGGACGGCAACATCA 62.184 60.000 0.00 0.00 0.00 3.07
471 483 3.197790 CGGCAACATCAGCGAGGG 61.198 66.667 0.00 0.00 0.00 4.30
520 533 0.620030 AGCACACATGGATGCACCTA 59.380 50.000 21.33 0.00 44.59 3.08
525 538 1.487976 CACATGGATGCACCTAGGAGT 59.512 52.381 17.98 0.00 39.86 3.85
528 541 0.252696 TGGATGCACCTAGGAGTGGT 60.253 55.000 17.98 0.00 38.24 4.16
564 579 1.153978 CTACGCGTCAACGGCCTAA 60.154 57.895 18.63 0.00 40.23 2.69
569 584 1.400500 CGCGTCAACGGCCTAATTTTT 60.400 47.619 0.00 0.00 40.23 1.94
657 673 4.787286 TGGTTACGCCCGCCATGG 62.787 66.667 7.63 7.63 36.04 3.66
688 704 3.119955 CGTGTTGACCAGATCGAAGACTA 60.120 47.826 0.00 0.00 42.51 2.59
697 715 3.568007 CAGATCGAAGACTAGGGGAGAAG 59.432 52.174 0.00 0.00 42.51 2.85
712 730 4.074970 GGGAGAAGAAAGAAGATGCACAA 58.925 43.478 0.00 0.00 0.00 3.33
713 731 4.083057 GGGAGAAGAAAGAAGATGCACAAC 60.083 45.833 0.00 0.00 0.00 3.32
716 734 4.518211 AGAAGAAAGAAGATGCACAACTGG 59.482 41.667 0.00 0.00 0.00 4.00
755 785 3.775654 ACCGGCTCCTAGCACTGC 61.776 66.667 0.00 0.00 44.75 4.40
758 788 2.993853 GGCTCCTAGCACTGCCTT 59.006 61.111 0.00 0.00 44.75 4.35
759 789 1.451028 GGCTCCTAGCACTGCCTTG 60.451 63.158 0.00 0.00 44.75 3.61
760 790 1.451028 GCTCCTAGCACTGCCTTGG 60.451 63.158 0.00 0.00 41.89 3.61
761 791 1.222936 CTCCTAGCACTGCCTTGGG 59.777 63.158 0.00 0.00 0.00 4.12
762 792 1.538876 TCCTAGCACTGCCTTGGGT 60.539 57.895 0.00 0.00 0.00 4.51
763 793 1.133809 TCCTAGCACTGCCTTGGGTT 61.134 55.000 0.00 0.00 0.00 4.11
772 802 4.508662 CACTGCCTTGGGTTGTTTTAAAA 58.491 39.130 0.00 0.00 0.00 1.52
777 807 4.261405 GCCTTGGGTTGTTTTAAAAATGGC 60.261 41.667 1.31 5.82 0.00 4.40
778 808 4.024472 CCTTGGGTTGTTTTAAAAATGGCG 60.024 41.667 1.31 0.00 0.00 5.69
784 814 6.128661 GGGTTGTTTTAAAAATGGCGATCTTC 60.129 38.462 1.31 0.00 0.00 2.87
801 831 7.329226 GGCGATCTTCTTTTCATTTTTGAATCA 59.671 33.333 0.00 0.00 0.00 2.57
1140 1172 1.224069 AAGACGACGACGACGAGGAA 61.224 55.000 25.15 0.00 42.66 3.36
1377 1409 2.597510 GGCACCAACTCCACCACC 60.598 66.667 0.00 0.00 0.00 4.61
1505 1539 6.131972 TCCTTTCATGATTGTTCTTCCTCT 57.868 37.500 0.00 0.00 0.00 3.69
1506 1540 6.176183 TCCTTTCATGATTGTTCTTCCTCTC 58.824 40.000 0.00 0.00 0.00 3.20
1548 1590 5.354054 GATCCAGATCGAATTGACAATGG 57.646 43.478 0.34 0.00 0.00 3.16
1549 1591 4.486125 TCCAGATCGAATTGACAATGGA 57.514 40.909 0.34 0.82 34.88 3.41
1550 1592 4.842574 TCCAGATCGAATTGACAATGGAA 58.157 39.130 0.34 0.00 34.54 3.53
1551 1593 5.252547 TCCAGATCGAATTGACAATGGAAA 58.747 37.500 0.34 0.00 34.54 3.13
1552 1594 5.887598 TCCAGATCGAATTGACAATGGAAAT 59.112 36.000 0.34 0.00 34.54 2.17
1553 1595 5.975344 CCAGATCGAATTGACAATGGAAATG 59.025 40.000 0.34 6.05 31.49 2.32
1556 1598 6.548622 AGATCGAATTGACAATGGAAATGGAT 59.451 34.615 0.34 0.00 0.00 3.41
1724 1768 1.735376 GCTCTACATCTTCGCCGGGA 61.735 60.000 2.18 0.00 0.00 5.14
1725 1769 0.744874 CTCTACATCTTCGCCGGGAA 59.255 55.000 2.18 4.24 0.00 3.97
1753 1797 3.847602 CTGCTCGGCCAGGAGGAG 61.848 72.222 13.35 13.35 44.35 3.69
2083 2144 2.743928 GAGCTGTGGGCCTTCGTG 60.744 66.667 4.53 0.00 43.05 4.35
2143 2204 2.696989 TCTGGTACATGATGGTGCTG 57.303 50.000 0.00 0.00 38.20 4.41
2152 2213 2.282674 ATGGTGCTGGTGGTGCTG 60.283 61.111 0.00 0.00 0.00 4.41
2622 2683 1.146263 GATGGGGCGTCAGGGTAAG 59.854 63.158 0.00 0.00 0.00 2.34
2623 2684 2.942648 GATGGGGCGTCAGGGTAAGC 62.943 65.000 0.00 0.00 0.00 3.09
2624 2685 3.400054 GGGGCGTCAGGGTAAGCT 61.400 66.667 0.00 0.00 0.00 3.74
2632 2718 0.899720 TCAGGGTAAGCTAACCACCG 59.100 55.000 4.34 0.00 41.67 4.94
2635 2721 1.812507 GGTAAGCTAACCACCGCCG 60.813 63.158 0.00 0.00 39.50 6.46
2663 2749 2.024655 AGTTCCAGCATCCACCATGATT 60.025 45.455 0.00 0.00 33.80 2.57
2670 2756 2.295349 GCATCCACCATGATTGATCACC 59.705 50.000 0.00 0.00 40.03 4.02
2692 2791 1.947456 TGCTGCAATGCTGATCTGATC 59.053 47.619 16.29 10.72 0.00 2.92
2693 2792 2.222886 GCTGCAATGCTGATCTGATCT 58.777 47.619 16.29 0.00 0.00 2.75
2714 2813 4.839706 CAGGGGATTTGGGCGGGG 62.840 72.222 0.00 0.00 0.00 5.73
2790 2889 1.134965 CCGACTGGAAAGCAGAGGTAG 60.135 57.143 0.00 0.00 37.49 3.18
2791 2890 1.737363 CGACTGGAAAGCAGAGGTAGC 60.737 57.143 0.00 0.00 0.00 3.58
2792 2891 1.552792 GACTGGAAAGCAGAGGTAGCT 59.447 52.381 0.00 0.00 45.97 3.32
2793 2892 2.761208 GACTGGAAAGCAGAGGTAGCTA 59.239 50.000 0.00 0.00 42.53 3.32
2798 2897 5.186198 TGGAAAGCAGAGGTAGCTAATTTC 58.814 41.667 0.00 3.61 42.53 2.17
2799 2898 4.576873 GGAAAGCAGAGGTAGCTAATTTCC 59.423 45.833 17.03 17.03 42.53 3.13
2802 2901 2.875317 GCAGAGGTAGCTAATTTCCTGC 59.125 50.000 13.23 13.23 38.88 4.85
2811 2910 6.374613 GGTAGCTAATTTCCTGCTGTTTAGTT 59.625 38.462 0.00 0.00 37.62 2.24
2812 2911 6.502136 AGCTAATTTCCTGCTGTTTAGTTC 57.498 37.500 0.00 0.00 35.54 3.01
2813 2912 6.003950 AGCTAATTTCCTGCTGTTTAGTTCA 58.996 36.000 0.00 0.00 35.54 3.18
2814 2913 6.150140 AGCTAATTTCCTGCTGTTTAGTTCAG 59.850 38.462 0.00 0.00 35.54 3.02
2823 2922 6.428159 CCTGCTGTTTAGTTCAGATTTGTACT 59.572 38.462 1.22 1.22 38.35 2.73
2824 2923 7.189693 TGCTGTTTAGTTCAGATTTGTACTG 57.810 36.000 5.87 0.00 35.92 2.74
2825 2924 6.989759 TGCTGTTTAGTTCAGATTTGTACTGA 59.010 34.615 5.87 0.00 41.70 3.41
2826 2925 7.661437 TGCTGTTTAGTTCAGATTTGTACTGAT 59.339 33.333 5.87 0.00 42.68 2.90
2827 2926 8.171840 GCTGTTTAGTTCAGATTTGTACTGATC 58.828 37.037 5.87 0.00 42.68 2.92
2836 2935 7.623630 TCAGATTTGTACTGATCAATGGAAGA 58.376 34.615 0.00 0.00 39.10 2.87
2843 2948 9.513906 TTGTACTGATCAATGGAAGATTTGTAA 57.486 29.630 0.00 0.00 0.00 2.41
2844 2949 9.513906 TGTACTGATCAATGGAAGATTTGTAAA 57.486 29.630 0.00 0.00 0.00 2.01
2852 2957 9.258826 TCAATGGAAGATTTGTAAAAATGTGTG 57.741 29.630 0.00 0.00 0.00 3.82
2854 2959 8.816640 ATGGAAGATTTGTAAAAATGTGTGTC 57.183 30.769 0.00 0.00 0.00 3.67
2855 2960 7.206687 TGGAAGATTTGTAAAAATGTGTGTCC 58.793 34.615 0.00 0.00 0.00 4.02
2857 2962 7.382218 GGAAGATTTGTAAAAATGTGTGTCCTG 59.618 37.037 0.00 0.00 0.00 3.86
2858 2963 7.581213 AGATTTGTAAAAATGTGTGTCCTGA 57.419 32.000 0.00 0.00 0.00 3.86
2859 2964 8.181904 AGATTTGTAAAAATGTGTGTCCTGAT 57.818 30.769 0.00 0.00 0.00 2.90
2860 2965 8.641541 AGATTTGTAAAAATGTGTGTCCTGATT 58.358 29.630 0.00 0.00 0.00 2.57
2861 2966 9.260002 GATTTGTAAAAATGTGTGTCCTGATTT 57.740 29.630 0.00 0.00 0.00 2.17
2862 2967 8.417780 TTTGTAAAAATGTGTGTCCTGATTTG 57.582 30.769 0.00 0.00 0.00 2.32
2863 2968 7.106439 TGTAAAAATGTGTGTCCTGATTTGT 57.894 32.000 0.00 0.00 0.00 2.83
2864 2969 6.977502 TGTAAAAATGTGTGTCCTGATTTGTG 59.022 34.615 0.00 0.00 0.00 3.33
2865 2970 3.648339 AATGTGTGTCCTGATTTGTGC 57.352 42.857 0.00 0.00 0.00 4.57
2866 2971 1.317613 TGTGTGTCCTGATTTGTGCC 58.682 50.000 0.00 0.00 0.00 5.01
2867 2972 0.238289 GTGTGTCCTGATTTGTGCCG 59.762 55.000 0.00 0.00 0.00 5.69
2868 2973 1.210155 GTGTCCTGATTTGTGCCGC 59.790 57.895 0.00 0.00 0.00 6.53
2888 2993 1.001487 CGTGTTGATTTGAGCAGGCAA 60.001 47.619 0.00 0.00 0.00 4.52
2989 3094 7.795859 GCTAGCTAGCTGATTAAATTCAGAAG 58.204 38.462 33.71 11.84 44.88 2.85
3018 3123 6.868864 TGTACTAGAGCTTAGCTTCAGTTTTG 59.131 38.462 21.04 5.56 39.88 2.44
3042 3147 7.213678 TGTTTTACAGATAGTGTGTGACATCA 58.786 34.615 0.00 0.00 40.69 3.07
3046 3151 5.233225 ACAGATAGTGTGTGACATCAGTTG 58.767 41.667 0.00 0.00 38.28 3.16
3050 3155 6.592994 AGATAGTGTGTGACATCAGTTGATTG 59.407 38.462 0.00 0.00 31.21 2.67
3057 3162 6.148315 GTGTGACATCAGTTGATTGATCAGAA 59.852 38.462 0.00 0.00 38.19 3.02
3058 3163 6.882678 TGTGACATCAGTTGATTGATCAGAAT 59.117 34.615 0.00 0.00 38.19 2.40
3059 3164 7.392393 TGTGACATCAGTTGATTGATCAGAATT 59.608 33.333 0.00 0.00 38.19 2.17
3060 3165 8.886719 GTGACATCAGTTGATTGATCAGAATTA 58.113 33.333 0.00 0.00 38.19 1.40
3061 3166 9.623000 TGACATCAGTTGATTGATCAGAATTAT 57.377 29.630 0.00 0.00 38.19 1.28
3062 3167 9.880064 GACATCAGTTGATTGATCAGAATTATG 57.120 33.333 0.00 0.00 38.19 1.90
3063 3168 9.404848 ACATCAGTTGATTGATCAGAATTATGT 57.595 29.630 0.00 0.00 38.19 2.29
3064 3169 9.665264 CATCAGTTGATTGATCAGAATTATGTG 57.335 33.333 0.00 0.00 38.19 3.21
3065 3170 9.623000 ATCAGTTGATTGATCAGAATTATGTGA 57.377 29.630 0.00 0.00 38.19 3.58
3067 3172 9.717892 CAGTTGATTGATCAGAATTATGTGAAG 57.282 33.333 0.00 0.00 38.19 3.02
3074 3184 8.672823 TGATCAGAATTATGTGAAGATTGAGG 57.327 34.615 0.00 0.00 31.89 3.86
3086 3196 7.717568 TGTGAAGATTGAGGTAGATACTTAGC 58.282 38.462 0.00 0.00 0.00 3.09
3087 3197 7.561722 TGTGAAGATTGAGGTAGATACTTAGCT 59.438 37.037 0.00 0.00 34.28 3.32
3088 3198 8.079809 GTGAAGATTGAGGTAGATACTTAGCTC 58.920 40.741 0.00 5.54 44.49 4.09
3089 3199 8.001875 TGAAGATTGAGGTAGATACTTAGCTCT 58.998 37.037 11.93 0.00 44.52 4.09
3090 3200 7.759489 AGATTGAGGTAGATACTTAGCTCTG 57.241 40.000 11.93 0.00 44.52 3.35
3091 3201 6.719370 AGATTGAGGTAGATACTTAGCTCTGG 59.281 42.308 11.93 0.00 44.52 3.86
3092 3202 4.730966 TGAGGTAGATACTTAGCTCTGGG 58.269 47.826 11.93 0.00 44.52 4.45
3093 3203 3.502356 AGGTAGATACTTAGCTCTGGGC 58.498 50.000 0.00 0.00 42.19 5.36
3103 3213 3.584947 GCTCTGGGCTCTTTTGGAT 57.415 52.632 0.00 0.00 38.06 3.41
3104 3214 1.387539 GCTCTGGGCTCTTTTGGATC 58.612 55.000 0.00 0.00 38.06 3.36
3105 3215 1.064832 GCTCTGGGCTCTTTTGGATCT 60.065 52.381 0.00 0.00 38.06 2.75
3106 3216 2.620108 GCTCTGGGCTCTTTTGGATCTT 60.620 50.000 0.00 0.00 38.06 2.40
3107 3217 3.015327 CTCTGGGCTCTTTTGGATCTTG 58.985 50.000 0.00 0.00 0.00 3.02
3126 3236 2.907634 TGTTTGTAGAAACACCTGCGA 58.092 42.857 13.74 0.00 45.26 5.10
3127 3237 3.271729 TGTTTGTAGAAACACCTGCGAA 58.728 40.909 13.74 0.00 45.26 4.70
3138 3248 5.449107 AACACCTGCGAATATACGTAGAT 57.551 39.130 0.08 0.00 45.73 1.98
3145 3255 7.767659 ACCTGCGAATATACGTAGATCTACATA 59.232 37.037 28.00 20.15 45.73 2.29
3161 3271 9.114952 AGATCTACATACTGGATATATGACACG 57.885 37.037 0.00 0.00 34.65 4.49
3164 3274 8.044908 TCTACATACTGGATATATGACACGCTA 58.955 37.037 0.00 0.00 34.65 4.26
3171 3281 6.447162 TGGATATATGACACGCTAAACTGAG 58.553 40.000 0.00 0.00 0.00 3.35
3201 3311 7.862512 TTTAGAACTTCGTTAGGGTTTTTGA 57.137 32.000 0.00 0.00 0.00 2.69
3202 3312 7.486802 TTAGAACTTCGTTAGGGTTTTTGAG 57.513 36.000 0.00 0.00 0.00 3.02
3203 3313 5.434408 AGAACTTCGTTAGGGTTTTTGAGT 58.566 37.500 0.00 0.00 0.00 3.41
3205 3315 7.049754 AGAACTTCGTTAGGGTTTTTGAGTAA 58.950 34.615 0.00 0.00 0.00 2.24
3207 3317 7.812690 ACTTCGTTAGGGTTTTTGAGTAATT 57.187 32.000 0.00 0.00 0.00 1.40
3213 3323 8.293867 CGTTAGGGTTTTTGAGTAATTTGATGA 58.706 33.333 0.00 0.00 0.00 2.92
3214 3324 9.974980 GTTAGGGTTTTTGAGTAATTTGATGAA 57.025 29.630 0.00 0.00 0.00 2.57
3216 3326 8.250143 AGGGTTTTTGAGTAATTTGATGAAGT 57.750 30.769 0.00 0.00 0.00 3.01
3217 3327 9.362151 AGGGTTTTTGAGTAATTTGATGAAGTA 57.638 29.630 0.00 0.00 0.00 2.24
3231 3341 8.909708 TTTGATGAAGTAAAGTGTTTTGTCAG 57.090 30.769 0.00 0.00 0.00 3.51
3237 3347 2.959507 AAGTGTTTTGTCAGGCAACC 57.040 45.000 0.00 0.00 36.72 3.77
3242 3352 1.269723 GTTTTGTCAGGCAACCCTAGC 59.730 52.381 0.00 0.00 40.33 3.42
3245 3355 0.324943 TGTCAGGCAACCCTAGCTTC 59.675 55.000 0.00 0.00 40.33 3.86
3246 3356 0.393132 GTCAGGCAACCCTAGCTTCC 60.393 60.000 0.00 0.00 40.33 3.46
3248 3358 0.678048 CAGGCAACCCTAGCTTCCAC 60.678 60.000 0.00 0.00 40.33 4.02
3249 3359 1.133809 AGGCAACCCTAGCTTCCACA 61.134 55.000 0.00 0.00 40.58 4.17
3252 3362 1.817740 GCAACCCTAGCTTCCACACAA 60.818 52.381 0.00 0.00 0.00 3.33
3253 3363 1.880027 CAACCCTAGCTTCCACACAAC 59.120 52.381 0.00 0.00 0.00 3.32
3254 3364 0.400594 ACCCTAGCTTCCACACAACC 59.599 55.000 0.00 0.00 0.00 3.77
3255 3365 0.693049 CCCTAGCTTCCACACAACCT 59.307 55.000 0.00 0.00 0.00 3.50
3258 3368 2.354203 CCTAGCTTCCACACAACCTCTC 60.354 54.545 0.00 0.00 0.00 3.20
3259 3369 1.131638 AGCTTCCACACAACCTCTCA 58.868 50.000 0.00 0.00 0.00 3.27
3260 3370 1.701847 AGCTTCCACACAACCTCTCAT 59.298 47.619 0.00 0.00 0.00 2.90
3261 3371 2.079925 GCTTCCACACAACCTCTCATC 58.920 52.381 0.00 0.00 0.00 2.92
3262 3372 2.704572 CTTCCACACAACCTCTCATCC 58.295 52.381 0.00 0.00 0.00 3.51
3263 3373 2.030027 TCCACACAACCTCTCATCCT 57.970 50.000 0.00 0.00 0.00 3.24
3265 3375 2.038952 TCCACACAACCTCTCATCCTTG 59.961 50.000 0.00 0.00 0.00 3.61
3266 3376 1.808945 CACACAACCTCTCATCCTTGC 59.191 52.381 0.00 0.00 0.00 4.01
3267 3377 1.271597 ACACAACCTCTCATCCTTGCC 60.272 52.381 0.00 0.00 0.00 4.52
3269 3379 0.745845 CAACCTCTCATCCTTGCCGG 60.746 60.000 0.00 0.00 0.00 6.13
3270 3380 2.203126 CCTCTCATCCTTGCCGGC 60.203 66.667 22.73 22.73 0.00 6.13
3272 3382 1.523258 CTCTCATCCTTGCCGGCTG 60.523 63.158 29.70 17.49 0.00 4.85
3273 3383 1.964608 CTCTCATCCTTGCCGGCTGA 61.965 60.000 29.70 20.93 35.62 4.26
3274 3384 1.147824 CTCATCCTTGCCGGCTGAT 59.852 57.895 29.70 22.43 37.30 2.90
3275 3385 0.465097 CTCATCCTTGCCGGCTGATT 60.465 55.000 29.70 5.78 37.30 2.57
3276 3386 0.464373 TCATCCTTGCCGGCTGATTC 60.464 55.000 29.70 0.00 33.14 2.52
3277 3387 0.465097 CATCCTTGCCGGCTGATTCT 60.465 55.000 29.70 5.00 30.24 2.40
3278 3388 0.465097 ATCCTTGCCGGCTGATTCTG 60.465 55.000 29.70 9.06 0.00 3.02
3279 3389 1.377725 CCTTGCCGGCTGATTCTGT 60.378 57.895 29.70 0.00 0.00 3.41
3280 3390 1.372087 CCTTGCCGGCTGATTCTGTC 61.372 60.000 29.70 0.00 0.00 3.51
3281 3391 1.699656 CTTGCCGGCTGATTCTGTCG 61.700 60.000 29.70 10.20 0.00 4.35
3282 3392 2.166130 TTGCCGGCTGATTCTGTCGA 62.166 55.000 29.70 0.00 32.46 4.20
3283 3393 1.227380 GCCGGCTGATTCTGTCGAT 60.227 57.895 22.15 0.00 32.46 3.59
3284 3394 1.218230 GCCGGCTGATTCTGTCGATC 61.218 60.000 22.15 6.58 32.46 3.69
3285 3395 0.387202 CCGGCTGATTCTGTCGATCT 59.613 55.000 17.62 0.00 32.46 2.75
3286 3396 1.202463 CCGGCTGATTCTGTCGATCTT 60.202 52.381 17.62 0.00 32.46 2.40
3287 3397 2.123342 CGGCTGATTCTGTCGATCTTC 58.877 52.381 11.56 0.00 32.46 2.87
3288 3398 2.478831 GGCTGATTCTGTCGATCTTCC 58.521 52.381 0.00 0.00 0.00 3.46
3289 3399 2.102252 GGCTGATTCTGTCGATCTTCCT 59.898 50.000 0.00 0.00 0.00 3.36
3290 3400 3.380142 GCTGATTCTGTCGATCTTCCTC 58.620 50.000 0.00 0.00 0.00 3.71
3291 3401 3.626977 CTGATTCTGTCGATCTTCCTCG 58.373 50.000 0.00 0.00 39.99 4.63
3292 3402 2.359214 TGATTCTGTCGATCTTCCTCGG 59.641 50.000 0.00 0.00 39.13 4.63
3293 3403 0.456221 TTCTGTCGATCTTCCTCGGC 59.544 55.000 0.00 0.00 43.36 5.54
3294 3404 0.394488 TCTGTCGATCTTCCTCGGCT 60.394 55.000 0.00 0.00 43.45 5.52
3295 3405 0.030101 CTGTCGATCTTCCTCGGCTC 59.970 60.000 0.00 0.00 43.45 4.70
3296 3406 1.360911 GTCGATCTTCCTCGGCTCC 59.639 63.158 0.00 0.00 40.04 4.70
3297 3407 2.187493 TCGATCTTCCTCGGCTCCG 61.187 63.158 1.14 1.14 39.13 4.63
3298 3408 2.731374 GATCTTCCTCGGCTCCGG 59.269 66.667 8.59 0.00 40.25 5.14
3299 3409 3.507597 GATCTTCCTCGGCTCCGGC 62.508 68.421 8.59 0.00 40.25 6.13
3300 3410 4.761058 TCTTCCTCGGCTCCGGCT 62.761 66.667 8.59 0.00 40.25 5.52
3301 3411 4.521062 CTTCCTCGGCTCCGGCTG 62.521 72.222 8.59 0.00 45.61 4.85
3343 3453 2.545952 CGGGGAACACTATGGATCTTCG 60.546 54.545 0.00 0.00 0.00 3.79
3347 3458 3.385577 GAACACTATGGATCTTCGGCTC 58.614 50.000 0.00 0.00 0.00 4.70
3367 3478 1.335872 CGTTGGCATTTTGGTGTCCTC 60.336 52.381 0.00 0.00 0.00 3.71
3368 3479 1.686052 GTTGGCATTTTGGTGTCCTCA 59.314 47.619 0.00 0.00 0.00 3.86
3373 3484 2.821969 GCATTTTGGTGTCCTCATGTCT 59.178 45.455 0.00 0.00 0.00 3.41
3374 3485 3.119708 GCATTTTGGTGTCCTCATGTCTC 60.120 47.826 0.00 0.00 0.00 3.36
3375 3486 2.455674 TTTGGTGTCCTCATGTCTCG 57.544 50.000 0.00 0.00 0.00 4.04
3376 3487 1.338107 TTGGTGTCCTCATGTCTCGT 58.662 50.000 0.00 0.00 0.00 4.18
3377 3488 1.338107 TGGTGTCCTCATGTCTCGTT 58.662 50.000 0.00 0.00 0.00 3.85
3378 3489 1.272490 TGGTGTCCTCATGTCTCGTTC 59.728 52.381 0.00 0.00 0.00 3.95
3381 3492 3.130516 GGTGTCCTCATGTCTCGTTCATA 59.869 47.826 0.00 0.00 0.00 2.15
3382 3493 4.202161 GGTGTCCTCATGTCTCGTTCATAT 60.202 45.833 0.00 0.00 0.00 1.78
3383 3494 5.009710 GGTGTCCTCATGTCTCGTTCATATA 59.990 44.000 0.00 0.00 0.00 0.86
3392 3503 8.817100 TCATGTCTCGTTCATATACAAACAATC 58.183 33.333 0.00 0.00 0.00 2.67
3448 3559 3.822594 TTTAAGGTTGCGTGCATACAG 57.177 42.857 0.00 0.00 0.00 2.74
3455 3566 0.865111 TGCGTGCATACAGTCAACAC 59.135 50.000 0.00 0.00 0.00 3.32
3457 3568 2.288518 TGCGTGCATACAGTCAACACTA 60.289 45.455 0.00 0.00 0.00 2.74
3458 3569 2.345641 GCGTGCATACAGTCAACACTAG 59.654 50.000 0.00 0.00 0.00 2.57
3460 3571 3.987868 CGTGCATACAGTCAACACTAGTT 59.012 43.478 0.00 0.00 38.88 2.24
3467 3578 8.175716 GCATACAGTCAACACTAGTTTTAATCC 58.824 37.037 0.00 0.00 35.28 3.01
3469 3580 7.492352 ACAGTCAACACTAGTTTTAATCCAC 57.508 36.000 0.00 0.00 35.28 4.02
3470 3581 7.051623 ACAGTCAACACTAGTTTTAATCCACA 58.948 34.615 0.00 0.00 35.28 4.17
3473 3586 9.131791 AGTCAACACTAGTTTTAATCCACATTT 57.868 29.630 0.00 0.00 35.28 2.32
3530 3643 7.759465 AGCAAAGTGAAGATCATCAAACATAG 58.241 34.615 1.48 0.00 0.00 2.23
3531 3644 6.971184 GCAAAGTGAAGATCATCAAACATAGG 59.029 38.462 1.48 0.00 0.00 2.57
3558 3671 8.362639 ACAAAGTGATCTAAAATGCTCAAACAT 58.637 29.630 0.00 0.00 0.00 2.71
3583 3696 1.619827 CATCAAACACCACCATTGCCT 59.380 47.619 0.00 0.00 0.00 4.75
3596 3709 2.624838 CCATTGCCTCACTCAAACTTGT 59.375 45.455 0.00 0.00 0.00 3.16
3604 3717 4.214971 CCTCACTCAAACTTGTCCATCTTG 59.785 45.833 0.00 0.00 0.00 3.02
3630 3743 7.780271 GGAATTGGATGGGACTAATAAGACTTT 59.220 37.037 0.00 0.00 0.00 2.66
3647 3760 3.445008 ACTTTGAGCCATAGTGGAGAGA 58.555 45.455 0.00 0.00 40.96 3.10
3657 3770 5.599732 CCATAGTGGAGAGATTCTGAGTTG 58.400 45.833 0.00 0.00 40.96 3.16
3667 3780 5.471456 AGAGATTCTGAGTTGAATTGCGTTT 59.529 36.000 0.00 0.00 36.86 3.60
3673 3786 3.876914 TGAGTTGAATTGCGTTTGAGACT 59.123 39.130 0.00 0.00 0.00 3.24
3677 3865 4.891627 TGAATTGCGTTTGAGACTTTGA 57.108 36.364 0.00 0.00 0.00 2.69
3716 3904 5.986004 ATTTTATCTAGAAAAGCCCGACG 57.014 39.130 0.00 0.00 32.06 5.12
3790 3979 4.150897 TGCCACCTATCCTATTCAACAC 57.849 45.455 0.00 0.00 0.00 3.32
3797 3986 5.185454 CCTATCCTATTCAACACAGTTGCA 58.815 41.667 5.06 0.00 0.00 4.08
3798 3987 5.824624 CCTATCCTATTCAACACAGTTGCAT 59.175 40.000 5.06 2.98 0.00 3.96
3806 3995 9.442033 CTATTCAACACAGTTGCATATATGTTG 57.558 33.333 20.17 20.17 45.21 3.33
3815 4004 4.445557 TGCATATATGTTGGTTGCCCTA 57.554 40.909 14.14 0.00 32.39 3.53
3817 4006 4.826733 TGCATATATGTTGGTTGCCCTAAG 59.173 41.667 14.14 0.00 32.39 2.18
3868 4057 1.815003 GTGGACTCATTCCTTGCTTGG 59.185 52.381 0.00 0.00 46.10 3.61
3877 4066 0.684535 TCCTTGCTTGGTCGATGTCA 59.315 50.000 0.00 0.00 0.00 3.58
3878 4067 1.071542 TCCTTGCTTGGTCGATGTCAA 59.928 47.619 0.00 0.00 0.00 3.18
3905 4094 8.955388 TGTGTTAGTATTGCATTATGTTGATGT 58.045 29.630 0.00 0.00 0.00 3.06
3946 4135 7.673504 TGGAACATTATCTGGAAAAGGAAATCA 59.326 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.513065 GATGGTGTCGCCGTTTGCAG 62.513 60.000 0.00 0.00 41.33 4.41
72 73 1.526887 CACTGTTATAGCATTCGCCCG 59.473 52.381 0.00 0.00 39.83 6.13
73 74 2.561569 ACACTGTTATAGCATTCGCCC 58.438 47.619 0.00 0.00 39.83 6.13
74 75 4.369182 AGTACACTGTTATAGCATTCGCC 58.631 43.478 0.00 0.00 39.83 5.54
75 76 5.968387 AAGTACACTGTTATAGCATTCGC 57.032 39.130 0.00 0.00 38.99 4.70
76 77 8.851960 TCTTAAGTACACTGTTATAGCATTCG 57.148 34.615 1.63 0.00 0.00 3.34
85 86 7.817962 GGATGAAGCTTCTTAAGTACACTGTTA 59.182 37.037 26.09 1.33 0.00 2.41
234 240 1.017701 CGGGAGCGGTTGTAGGAAAC 61.018 60.000 0.00 0.00 0.00 2.78
247 253 2.612672 GGTAGTAGCAAAAATCGGGAGC 59.387 50.000 0.00 0.00 0.00 4.70
273 283 2.497107 CTGGTTCCAGCAAAACACAG 57.503 50.000 5.89 0.00 0.00 3.66
294 305 6.553476 AGAAAAGGGTAGTAACAAAAATGGCT 59.447 34.615 0.00 0.00 0.00 4.75
313 324 3.627123 CCCAGCAAAACCCAAAAGAAAAG 59.373 43.478 0.00 0.00 0.00 2.27
314 325 3.264450 TCCCAGCAAAACCCAAAAGAAAA 59.736 39.130 0.00 0.00 0.00 2.29
318 329 1.484240 TGTCCCAGCAAAACCCAAAAG 59.516 47.619 0.00 0.00 0.00 2.27
322 333 1.118838 CTTTGTCCCAGCAAAACCCA 58.881 50.000 0.00 0.00 37.82 4.51
419 431 1.031235 TATTCATGCAACCATGGCGG 58.969 50.000 13.04 5.11 47.00 6.13
438 450 1.002134 CCGTCCCTCCAGTTGCAAT 60.002 57.895 0.59 0.00 0.00 3.56
520 533 2.041265 CTGCCCCCTACCACTCCT 59.959 66.667 0.00 0.00 0.00 3.69
525 538 1.140134 AGCTTTTCTGCCCCCTACCA 61.140 55.000 0.00 0.00 0.00 3.25
605 621 1.059369 CGATGCTCGCCGTTGAAAG 59.941 57.895 0.00 0.00 31.14 2.62
657 673 0.250989 TGGTCAACACGGGGGAAATC 60.251 55.000 0.00 0.00 0.00 2.17
688 704 2.915604 TGCATCTTCTTTCTTCTCCCCT 59.084 45.455 0.00 0.00 0.00 4.79
697 715 3.304928 CCACCAGTTGTGCATCTTCTTTC 60.305 47.826 0.00 0.00 44.01 2.62
736 766 3.775654 AGTGCTAGGAGCCGGTGC 61.776 66.667 1.90 0.00 41.51 5.01
744 774 1.133809 AACCCAAGGCAGTGCTAGGA 61.134 55.000 16.11 0.00 0.00 2.94
751 781 4.828072 TTTTAAAACAACCCAAGGCAGT 57.172 36.364 0.00 0.00 0.00 4.40
755 785 4.024472 CGCCATTTTTAAAACAACCCAAGG 60.024 41.667 0.00 0.00 0.00 3.61
758 788 4.402056 TCGCCATTTTTAAAACAACCCA 57.598 36.364 0.00 0.00 0.00 4.51
759 789 5.234752 AGATCGCCATTTTTAAAACAACCC 58.765 37.500 0.00 0.00 0.00 4.11
760 790 6.645003 AGAAGATCGCCATTTTTAAAACAACC 59.355 34.615 0.00 0.00 0.00 3.77
761 791 7.637709 AGAAGATCGCCATTTTTAAAACAAC 57.362 32.000 0.00 0.00 0.00 3.32
762 792 8.655651 AAAGAAGATCGCCATTTTTAAAACAA 57.344 26.923 0.00 0.00 0.00 2.83
763 793 8.655651 AAAAGAAGATCGCCATTTTTAAAACA 57.344 26.923 0.00 0.00 0.00 2.83
772 802 7.153985 TCAAAAATGAAAAGAAGATCGCCATT 58.846 30.769 0.00 0.00 0.00 3.16
801 831 3.801114 TGTTGCTGCGATCTACAGTAT 57.199 42.857 12.56 0.00 37.47 2.12
963 995 1.466025 GGTGGTGGTGGTGTAGACGA 61.466 60.000 0.00 0.00 0.00 4.20
1377 1409 1.519455 GTGGCCGACGAAGATCTGG 60.519 63.158 0.00 0.00 0.00 3.86
1539 1581 4.383226 CCATGCATCCATTTCCATTGTCAA 60.383 41.667 0.00 0.00 0.00 3.18
1548 1590 3.558418 GCAATGTTCCATGCATCCATTTC 59.442 43.478 0.00 0.00 42.12 2.17
1549 1591 3.055021 TGCAATGTTCCATGCATCCATTT 60.055 39.130 0.00 0.00 46.87 2.32
1550 1592 2.502130 TGCAATGTTCCATGCATCCATT 59.498 40.909 0.00 0.41 46.87 3.16
1551 1593 2.112190 TGCAATGTTCCATGCATCCAT 58.888 42.857 0.00 0.00 46.87 3.41
1552 1594 1.558233 TGCAATGTTCCATGCATCCA 58.442 45.000 0.00 0.00 46.87 3.41
2083 2144 2.791868 GGAGGCGAGGGAGAGCTTC 61.792 68.421 0.00 0.00 38.53 3.86
2384 2445 3.255379 GATGCCGGCGAACTCGTC 61.255 66.667 23.90 7.05 42.22 4.20
2397 2458 3.195698 GGTCGCCCGTGAAGATGC 61.196 66.667 0.00 0.00 0.00 3.91
2581 2642 3.491792 GGAAGAGGTAGCCGAAGATGAAG 60.492 52.174 0.00 0.00 0.00 3.02
2623 2684 4.524318 ATCGGCGGCGGTGGTTAG 62.524 66.667 31.73 0.00 0.00 2.34
2624 2685 4.517815 GATCGGCGGCGGTGGTTA 62.518 66.667 31.73 11.47 0.00 2.85
2632 2718 2.892425 CTGGAACTGATCGGCGGC 60.892 66.667 7.21 0.00 0.00 6.53
2635 2721 1.162800 GGATGCTGGAACTGATCGGC 61.163 60.000 0.00 0.00 0.00 5.54
2663 2749 0.528924 GCATTGCAGCAAGGTGATCA 59.471 50.000 20.36 0.00 0.00 2.92
2670 2756 1.743394 TCAGATCAGCATTGCAGCAAG 59.257 47.619 14.47 7.06 36.85 4.01
2692 2791 1.598517 GCCCAAATCCCCTGCAAAG 59.401 57.895 0.00 0.00 0.00 2.77
2693 2792 2.282039 CGCCCAAATCCCCTGCAAA 61.282 57.895 0.00 0.00 0.00 3.68
2790 2889 6.149474 TCTGAACTAAACAGCAGGAAATTAGC 59.851 38.462 0.00 0.00 35.61 3.09
2791 2890 7.672983 TCTGAACTAAACAGCAGGAAATTAG 57.327 36.000 0.00 0.00 35.61 1.73
2792 2891 8.635765 AATCTGAACTAAACAGCAGGAAATTA 57.364 30.769 0.00 0.00 35.61 1.40
2793 2892 7.530426 AATCTGAACTAAACAGCAGGAAATT 57.470 32.000 0.00 0.00 35.61 1.82
2798 2897 5.695851 ACAAATCTGAACTAAACAGCAGG 57.304 39.130 0.00 0.00 35.61 4.85
2799 2898 7.171508 TCAGTACAAATCTGAACTAAACAGCAG 59.828 37.037 0.00 0.00 38.71 4.24
2802 2901 9.208022 TGATCAGTACAAATCTGAACTAAACAG 57.792 33.333 0.00 0.00 43.65 3.16
2811 2910 7.623630 TCTTCCATTGATCAGTACAAATCTGA 58.376 34.615 0.00 0.00 44.37 3.27
2812 2911 7.854557 TCTTCCATTGATCAGTACAAATCTG 57.145 36.000 0.00 0.00 0.00 2.90
2813 2912 9.471702 AAATCTTCCATTGATCAGTACAAATCT 57.528 29.630 0.00 0.00 0.00 2.40
2814 2913 9.512435 CAAATCTTCCATTGATCAGTACAAATC 57.488 33.333 0.00 0.00 0.00 2.17
2826 2925 9.258826 CACACATTTTTACAAATCTTCCATTGA 57.741 29.630 0.00 0.00 29.41 2.57
2827 2926 9.044150 ACACACATTTTTACAAATCTTCCATTG 57.956 29.630 0.00 0.00 29.41 2.82
2836 2935 9.044150 CAAATCAGGACACACATTTTTACAAAT 57.956 29.630 0.00 0.00 32.36 2.32
2843 2948 4.370917 GCACAAATCAGGACACACATTTT 58.629 39.130 0.00 0.00 0.00 1.82
2844 2949 3.243839 GGCACAAATCAGGACACACATTT 60.244 43.478 0.00 0.00 0.00 2.32
2845 2950 2.297033 GGCACAAATCAGGACACACATT 59.703 45.455 0.00 0.00 0.00 2.71
2848 2953 0.238289 CGGCACAAATCAGGACACAC 59.762 55.000 0.00 0.00 0.00 3.82
2849 2954 1.514678 GCGGCACAAATCAGGACACA 61.515 55.000 0.00 0.00 0.00 3.72
2850 2955 1.210155 GCGGCACAAATCAGGACAC 59.790 57.895 0.00 0.00 0.00 3.67
2851 2956 2.324330 CGCGGCACAAATCAGGACA 61.324 57.895 0.00 0.00 0.00 4.02
2852 2957 2.325082 ACGCGGCACAAATCAGGAC 61.325 57.895 12.47 0.00 0.00 3.85
2854 2959 2.128853 AACACGCGGCACAAATCAGG 62.129 55.000 12.47 0.00 0.00 3.86
2855 2960 0.998226 CAACACGCGGCACAAATCAG 60.998 55.000 12.47 0.00 0.00 2.90
2857 2962 0.109781 ATCAACACGCGGCACAAATC 60.110 50.000 12.47 0.00 0.00 2.17
2858 2963 0.313672 AATCAACACGCGGCACAAAT 59.686 45.000 12.47 0.00 0.00 2.32
2859 2964 0.101399 AAATCAACACGCGGCACAAA 59.899 45.000 12.47 0.00 0.00 2.83
2860 2965 0.593518 CAAATCAACACGCGGCACAA 60.594 50.000 12.47 0.00 0.00 3.33
2861 2966 1.009108 CAAATCAACACGCGGCACA 60.009 52.632 12.47 0.00 0.00 4.57
2862 2967 0.725784 CTCAAATCAACACGCGGCAC 60.726 55.000 12.47 0.00 0.00 5.01
2863 2968 1.573932 CTCAAATCAACACGCGGCA 59.426 52.632 12.47 0.00 0.00 5.69
2864 2969 1.797537 GCTCAAATCAACACGCGGC 60.798 57.895 12.47 0.00 0.00 6.53
2865 2970 0.453282 CTGCTCAAATCAACACGCGG 60.453 55.000 12.47 1.27 0.00 6.46
2866 2971 0.453282 CCTGCTCAAATCAACACGCG 60.453 55.000 3.53 3.53 0.00 6.01
2867 2972 0.730494 GCCTGCTCAAATCAACACGC 60.730 55.000 0.00 0.00 0.00 5.34
2868 2973 0.592637 TGCCTGCTCAAATCAACACG 59.407 50.000 0.00 0.00 0.00 4.49
2989 3094 4.142359 TGAAGCTAAGCTCTAGTACACAGC 60.142 45.833 0.00 0.00 38.25 4.40
3018 3123 7.385205 ACTGATGTCACACACTATCTGTAAAAC 59.615 37.037 0.00 0.00 32.35 2.43
3042 3147 9.676861 TCTTCACATAATTCTGATCAATCAACT 57.323 29.630 0.00 0.00 36.18 3.16
3050 3155 8.674263 ACCTCAATCTTCACATAATTCTGATC 57.326 34.615 0.00 0.00 0.00 2.92
3060 3165 8.364142 GCTAAGTATCTACCTCAATCTTCACAT 58.636 37.037 0.00 0.00 0.00 3.21
3061 3166 7.561722 AGCTAAGTATCTACCTCAATCTTCACA 59.438 37.037 0.00 0.00 0.00 3.58
3062 3167 7.947282 AGCTAAGTATCTACCTCAATCTTCAC 58.053 38.462 0.00 0.00 0.00 3.18
3063 3168 8.001875 AGAGCTAAGTATCTACCTCAATCTTCA 58.998 37.037 0.00 0.00 0.00 3.02
3064 3169 8.296713 CAGAGCTAAGTATCTACCTCAATCTTC 58.703 40.741 0.00 0.00 0.00 2.87
3065 3170 7.232534 CCAGAGCTAAGTATCTACCTCAATCTT 59.767 40.741 0.00 0.00 0.00 2.40
3067 3172 6.071616 CCCAGAGCTAAGTATCTACCTCAATC 60.072 46.154 0.00 0.00 0.00 2.67
3069 3179 5.141182 CCCAGAGCTAAGTATCTACCTCAA 58.859 45.833 0.00 0.00 0.00 3.02
3086 3196 3.015327 CAAGATCCAAAAGAGCCCAGAG 58.985 50.000 0.00 0.00 0.00 3.35
3087 3197 2.376518 ACAAGATCCAAAAGAGCCCAGA 59.623 45.455 0.00 0.00 0.00 3.86
3088 3198 2.800250 ACAAGATCCAAAAGAGCCCAG 58.200 47.619 0.00 0.00 0.00 4.45
3089 3199 2.978156 ACAAGATCCAAAAGAGCCCA 57.022 45.000 0.00 0.00 0.00 5.36
3090 3200 3.321968 ACAAACAAGATCCAAAAGAGCCC 59.678 43.478 0.00 0.00 0.00 5.19
3091 3201 4.590850 ACAAACAAGATCCAAAAGAGCC 57.409 40.909 0.00 0.00 0.00 4.70
3092 3202 6.560253 TCTACAAACAAGATCCAAAAGAGC 57.440 37.500 0.00 0.00 0.00 4.09
3093 3203 8.788409 GTTTCTACAAACAAGATCCAAAAGAG 57.212 34.615 0.00 0.00 41.53 2.85
3107 3217 3.955771 TTCGCAGGTGTTTCTACAAAC 57.044 42.857 0.00 0.00 42.16 2.93
3123 3233 8.063038 CCAGTATGTAGATCTACGTATATTCGC 58.937 40.741 28.97 18.56 39.08 4.70
3138 3248 6.884836 AGCGTGTCATATATCCAGTATGTAGA 59.115 38.462 0.00 0.00 32.63 2.59
3145 3255 6.040504 TCAGTTTAGCGTGTCATATATCCAGT 59.959 38.462 0.00 0.00 0.00 4.00
3188 3298 9.974980 TTCATCAAATTACTCAAAAACCCTAAC 57.025 29.630 0.00 0.00 0.00 2.34
3191 3301 8.250143 ACTTCATCAAATTACTCAAAAACCCT 57.750 30.769 0.00 0.00 0.00 4.34
3205 3315 9.520204 CTGACAAAACACTTTACTTCATCAAAT 57.480 29.630 0.00 0.00 0.00 2.32
3207 3317 7.479980 CCTGACAAAACACTTTACTTCATCAA 58.520 34.615 0.00 0.00 0.00 2.57
3213 3323 5.407502 GTTGCCTGACAAAACACTTTACTT 58.592 37.500 0.00 0.00 40.82 2.24
3214 3324 4.142249 GGTTGCCTGACAAAACACTTTACT 60.142 41.667 0.00 0.00 40.82 2.24
3215 3325 4.109766 GGTTGCCTGACAAAACACTTTAC 58.890 43.478 0.00 0.00 40.82 2.01
3216 3326 3.131400 GGGTTGCCTGACAAAACACTTTA 59.869 43.478 0.00 0.00 40.82 1.85
3217 3327 2.093711 GGGTTGCCTGACAAAACACTTT 60.094 45.455 0.00 0.00 40.82 2.66
3222 3332 1.269723 GCTAGGGTTGCCTGACAAAAC 59.730 52.381 0.00 0.00 40.82 2.43
3231 3341 0.960861 GTGTGGAAGCTAGGGTTGCC 60.961 60.000 0.00 0.00 30.64 4.52
3237 3347 1.625818 AGAGGTTGTGTGGAAGCTAGG 59.374 52.381 0.00 0.00 33.83 3.02
3242 3352 2.304180 AGGATGAGAGGTTGTGTGGAAG 59.696 50.000 0.00 0.00 0.00 3.46
3245 3355 2.430465 CAAGGATGAGAGGTTGTGTGG 58.570 52.381 0.00 0.00 0.00 4.17
3246 3356 1.808945 GCAAGGATGAGAGGTTGTGTG 59.191 52.381 0.00 0.00 0.00 3.82
3248 3358 1.457346 GGCAAGGATGAGAGGTTGTG 58.543 55.000 0.00 0.00 0.00 3.33
3249 3359 0.036010 CGGCAAGGATGAGAGGTTGT 60.036 55.000 0.00 0.00 0.00 3.32
3252 3362 3.036429 GCCGGCAAGGATGAGAGGT 62.036 63.158 24.80 0.00 45.00 3.85
3253 3363 2.203126 GCCGGCAAGGATGAGAGG 60.203 66.667 24.80 0.00 45.00 3.69
3254 3364 2.906458 AGCCGGCAAGGATGAGAG 59.094 61.111 31.54 0.00 45.00 3.20
3259 3369 0.465097 CAGAATCAGCCGGCAAGGAT 60.465 55.000 31.54 24.12 45.00 3.24
3260 3370 1.078214 CAGAATCAGCCGGCAAGGA 60.078 57.895 31.54 22.91 45.00 3.36
3261 3371 1.372087 GACAGAATCAGCCGGCAAGG 61.372 60.000 31.54 17.97 44.97 3.61
3262 3372 1.699656 CGACAGAATCAGCCGGCAAG 61.700 60.000 31.54 21.15 0.00 4.01
3263 3373 1.741401 CGACAGAATCAGCCGGCAA 60.741 57.895 31.54 17.44 0.00 4.52
3265 3375 1.218230 GATCGACAGAATCAGCCGGC 61.218 60.000 21.89 21.89 0.00 6.13
3266 3376 0.387202 AGATCGACAGAATCAGCCGG 59.613 55.000 0.00 0.00 0.00 6.13
3267 3377 2.123342 GAAGATCGACAGAATCAGCCG 58.877 52.381 0.00 0.00 0.00 5.52
3269 3379 3.380142 GAGGAAGATCGACAGAATCAGC 58.620 50.000 0.00 0.00 0.00 4.26
3270 3380 3.549827 CCGAGGAAGATCGACAGAATCAG 60.550 52.174 0.00 0.00 45.56 2.90
3272 3382 2.860582 GCCGAGGAAGATCGACAGAATC 60.861 54.545 0.00 0.00 45.56 2.52
3273 3383 1.067821 GCCGAGGAAGATCGACAGAAT 59.932 52.381 0.00 0.00 45.56 2.40
3274 3384 0.456221 GCCGAGGAAGATCGACAGAA 59.544 55.000 0.00 0.00 45.56 3.02
3275 3385 0.394488 AGCCGAGGAAGATCGACAGA 60.394 55.000 0.00 0.00 45.56 3.41
3276 3386 0.030101 GAGCCGAGGAAGATCGACAG 59.970 60.000 0.00 0.00 45.56 3.51
3277 3387 1.384989 GGAGCCGAGGAAGATCGACA 61.385 60.000 0.00 0.00 45.56 4.35
3278 3388 1.360911 GGAGCCGAGGAAGATCGAC 59.639 63.158 0.00 0.00 45.56 4.20
3279 3389 2.187493 CGGAGCCGAGGAAGATCGA 61.187 63.158 2.00 0.00 45.56 3.59
3280 3390 2.333225 CGGAGCCGAGGAAGATCG 59.667 66.667 2.00 0.00 42.83 3.69
3281 3391 2.731374 CCGGAGCCGAGGAAGATC 59.269 66.667 11.05 0.00 42.83 2.75
3282 3392 3.541713 GCCGGAGCCGAGGAAGAT 61.542 66.667 5.05 0.00 42.83 2.40
3283 3393 4.761058 AGCCGGAGCCGAGGAAGA 62.761 66.667 5.05 0.00 42.83 2.87
3284 3394 4.521062 CAGCCGGAGCCGAGGAAG 62.521 72.222 5.05 0.00 42.83 3.46
3297 3407 3.723348 GTGTCGAAACCGGCAGCC 61.723 66.667 0.00 0.00 42.74 4.85
3304 3414 2.047560 CCTCCCGGTGTCGAAACC 60.048 66.667 15.38 15.38 39.00 3.27
3332 3442 1.068588 CCAACGAGCCGAAGATCCATA 59.931 52.381 1.50 0.00 0.00 2.74
3343 3453 0.667184 CACCAAAATGCCAACGAGCC 60.667 55.000 0.00 0.00 0.00 4.70
3347 3458 0.673437 AGGACACCAAAATGCCAACG 59.327 50.000 0.00 0.00 0.00 4.10
3367 3478 8.820933 AGATTGTTTGTATATGAACGAGACATG 58.179 33.333 0.00 0.00 0.00 3.21
3368 3479 8.820933 CAGATTGTTTGTATATGAACGAGACAT 58.179 33.333 0.00 0.00 0.00 3.06
3377 3488 9.671279 ACATGAGTTCAGATTGTTTGTATATGA 57.329 29.630 0.00 0.00 0.00 2.15
3381 3492 7.596248 GCAAACATGAGTTCAGATTGTTTGTAT 59.404 33.333 25.30 3.87 45.99 2.29
3382 3493 6.917477 GCAAACATGAGTTCAGATTGTTTGTA 59.083 34.615 25.30 0.00 45.99 2.41
3383 3494 5.750067 GCAAACATGAGTTCAGATTGTTTGT 59.250 36.000 25.30 8.31 45.99 2.83
3418 3529 4.744631 CACGCAACCTTAAAAGCTTGATTT 59.255 37.500 0.00 0.00 0.00 2.17
3419 3530 4.298332 CACGCAACCTTAAAAGCTTGATT 58.702 39.130 0.00 0.00 0.00 2.57
3420 3531 3.857010 GCACGCAACCTTAAAAGCTTGAT 60.857 43.478 0.00 0.00 0.00 2.57
3433 3544 0.871722 TTGACTGTATGCACGCAACC 59.128 50.000 0.00 0.00 0.00 3.77
3434 3545 1.262950 TGTTGACTGTATGCACGCAAC 59.737 47.619 13.60 13.60 36.92 4.17
3437 3548 1.148310 AGTGTTGACTGTATGCACGC 58.852 50.000 0.00 0.00 35.46 5.34
3439 3550 5.924475 AAACTAGTGTTGACTGTATGCAC 57.076 39.130 0.00 0.00 36.39 4.57
3440 3551 8.615878 ATTAAAACTAGTGTTGACTGTATGCA 57.384 30.769 8.66 0.00 36.39 3.96
3441 3552 8.175716 GGATTAAAACTAGTGTTGACTGTATGC 58.824 37.037 8.66 0.00 36.39 3.14
3448 3559 9.744468 AAAATGTGGATTAAAACTAGTGTTGAC 57.256 29.630 8.66 0.15 36.39 3.18
3530 3643 6.500684 TGAGCATTTTAGATCACTTTGTCC 57.499 37.500 0.00 0.00 0.00 4.02
3531 3644 7.862372 TGTTTGAGCATTTTAGATCACTTTGTC 59.138 33.333 0.00 0.00 33.03 3.18
3558 3671 0.184692 TGGTGGTGTTTGATGCTCCA 59.815 50.000 0.00 0.00 0.00 3.86
3583 3696 4.136796 CCAAGATGGACAAGTTTGAGTGA 58.863 43.478 0.00 0.00 40.96 3.41
3604 3717 6.842676 AGTCTTATTAGTCCCATCCAATTCC 58.157 40.000 0.00 0.00 0.00 3.01
3615 3728 7.439655 CACTATGGCTCAAAGTCTTATTAGTCC 59.560 40.741 0.00 0.00 0.00 3.85
3630 3743 3.640498 CAGAATCTCTCCACTATGGCTCA 59.360 47.826 0.00 0.00 37.47 4.26
3647 3760 5.239306 TCTCAAACGCAATTCAACTCAGAAT 59.761 36.000 0.00 0.00 39.81 2.40
3657 3770 9.554724 TTATATTCAAAGTCTCAAACGCAATTC 57.445 29.630 0.00 0.00 0.00 2.17
3696 3884 3.431207 CCCGTCGGGCTTTTCTAGATAAA 60.431 47.826 19.48 0.00 35.35 1.40
3712 3900 0.530650 CCTTGATGATCACCCCGTCG 60.531 60.000 0.00 0.00 0.00 5.12
3713 3901 0.541863 ACCTTGATGATCACCCCGTC 59.458 55.000 0.00 0.00 0.00 4.79
3714 3902 1.762957 CTACCTTGATGATCACCCCGT 59.237 52.381 0.00 0.00 0.00 5.28
3715 3903 2.039418 TCTACCTTGATGATCACCCCG 58.961 52.381 0.00 0.00 0.00 5.73
3716 3904 3.041946 AGTCTACCTTGATGATCACCCC 58.958 50.000 0.00 0.00 0.00 4.95
3761 3950 3.199880 AGGATAGGTGGCAAAGAATCG 57.800 47.619 0.00 0.00 0.00 3.34
3790 3979 4.362279 GGCAACCAACATATATGCAACTG 58.638 43.478 12.79 5.39 38.73 3.16
3815 4004 5.922544 CCATTTTCTTTCTCGATTTGCACTT 59.077 36.000 0.00 0.00 0.00 3.16
3817 4006 5.222631 ACCATTTTCTTTCTCGATTTGCAC 58.777 37.500 0.00 0.00 0.00 4.57
3868 4057 6.183360 TGCAATACTAACACATTGACATCGAC 60.183 38.462 0.00 0.00 34.69 4.20
3878 4067 9.955208 CATCAACATAATGCAATACTAACACAT 57.045 29.630 0.00 0.00 0.00 3.21
3905 4094 6.669125 AATGTTCCAAGAAAATGATGGTGA 57.331 33.333 0.00 0.00 35.66 4.02
3913 4102 9.933723 CTTTTCCAGATAATGTTCCAAGAAAAT 57.066 29.630 0.00 0.00 32.22 1.82


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

AutoCloner maintained by Alex Coulton.