Multiple sequence alignment - TraesCS4D01G100300

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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 TraesCS4D01G100300 chr4D 100.000 4371 0 0 1 4371 77275028 77279398 0.000000e+00 8072.0
1 TraesCS4D01G100300 chr4B 95.514 1694 48 10 1 1671 109400356 109402044 0.000000e+00 2682.0
2 TraesCS4D01G100300 chr4B 92.766 1023 56 8 2722 3733 109403153 109404168 0.000000e+00 1463.0
3 TraesCS4D01G100300 chr4B 94.551 936 37 6 1724 2645 109402204 109403139 0.000000e+00 1434.0
4 TraesCS4D01G100300 chr4B 86.239 654 46 23 3718 4345 109404123 109404758 0.000000e+00 669.0
5 TraesCS4D01G100300 chr1A 86.165 412 33 11 273 665 21081752 21081346 1.450000e-114 424.0
6 TraesCS4D01G100300 chr1A 90.217 92 7 2 724 815 21081358 21081269 7.680000e-23 119.0
7 TraesCS4D01G100300 chr3A 90.698 172 13 3 276 446 13208115 13207946 4.400000e-55 226.0
8 TraesCS4D01G100300 chr3A 87.586 145 7 3 491 627 13202937 13202796 1.630000e-34 158.0
9 TraesCS4D01G100300 chr3B 82.520 246 33 3 1 237 74537031 74537275 1.590000e-49 207.0
10 TraesCS4D01G100300 chr2D 81.410 156 19 4 47 193 576288325 576288479 7.680000e-23 119.0
11 TraesCS4D01G100300 chr2A 81.410 156 19 4 47 193 714337269 714337423 7.680000e-23 119.0
12 TraesCS4D01G100300 chr2A 90.909 55 5 0 2387 2441 39694900 39694846 1.690000e-09 75.0
13 TraesCS4D01G100300 chr1B 90.217 92 7 1 724 815 31468009 31467920 7.680000e-23 119.0
14 TraesCS4D01G100300 chr1B 86.408 103 14 0 823 925 31467861 31467759 3.570000e-21 113.0
15 TraesCS4D01G100300 chr2B 78.231 147 13 13 47 193 692469516 692469643 4.690000e-10 76.8
16 TraesCS4D01G100300 chr5B 90.741 54 5 0 2387 2440 38363421 38363368 6.060000e-09 73.1
17 TraesCS4D01G100300 chr7D 100.000 29 0 0 2387 2415 457226597 457226569 2.000000e-03 54.7
18 TraesCS4D01G100300 chr6D 100.000 29 0 0 2387 2415 97570986 97570958 2.000000e-03 54.7
19 TraesCS4D01G100300 chrUn 88.372 43 5 0 2399 2441 277981897 277981855 8.000000e-03 52.8


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 TraesCS4D01G100300 chr4D 77275028 77279398 4370 False 8072 8072 100.0000 1 4371 1 chr4D.!!$F1 4370
1 TraesCS4D01G100300 chr4B 109400356 109404758 4402 False 1562 2682 92.2675 1 4345 4 chr4B.!!$F1 4344

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
757 767 1.077357 TTGGTCTTGTGTGCCGGTT 60.077 52.632 1.9 0.0 0.00 4.44 F
2120 2256 0.109781 ATGATTCGGTTGTTGCGTGC 60.110 50.000 0.0 0.0 0.00 5.34 F
2175 2319 0.608582 CAAGAGGCAGGCAAGAAGCT 60.609 55.000 0.0 0.0 44.79 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2459 2603 0.320683 GGTTGGGTGCCATGAAAAGC 60.321 55.0 0.0 0.0 31.53 3.51 R
3075 3220 0.040425 CACTTTCCCGGTTTTCTGCG 60.040 55.0 0.0 0.0 0.00 5.18 R
3859 4015 0.665835 TCACACATCCGGTTTGCAAC 59.334 50.0 0.0 0.0 0.00 4.17 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
81 82 1.992557 AGTTTCTCAGGTGGGCCATTA 59.007 47.619 10.70 0.00 37.19 1.90
130 131 5.784750 TCGATTTGAGTTGATACAAGCAG 57.215 39.130 0.00 0.00 0.00 4.24
133 134 6.595326 TCGATTTGAGTTGATACAAGCAGAAT 59.405 34.615 0.00 0.00 0.00 2.40
142 143 8.076178 AGTTGATACAAGCAGAATTGTACAAAC 58.924 33.333 13.23 9.93 45.68 2.93
408 410 7.589958 ATTGTTGATGTACTTTTACCAACCA 57.410 32.000 0.00 0.00 34.64 3.67
454 456 8.849168 TCCATCCTGCTAATATTTGTTGTATTG 58.151 33.333 0.00 0.00 0.00 1.90
488 490 5.426689 AGCAGATTGTTCTCCTGTTATCA 57.573 39.130 0.00 0.00 0.00 2.15
624 626 8.017946 CCTAAGTTTTTCTCTATTCACTTGTGC 58.982 37.037 0.00 0.00 0.00 4.57
696 699 1.270550 GCTAATGCAATGGAATCGGGG 59.729 52.381 0.00 0.00 39.41 5.73
723 726 5.708736 TTGCCCTCCTGATTGTCTAAATA 57.291 39.130 0.00 0.00 0.00 1.40
757 767 1.077357 TTGGTCTTGTGTGCCGGTT 60.077 52.632 1.90 0.00 0.00 4.44
773 783 2.545952 CCGGTTCCCAGATCGAGTAATG 60.546 54.545 0.00 0.00 0.00 1.90
793 803 8.141909 AGTAATGATGATGCAATTCTTGATTGG 58.858 33.333 0.00 0.00 44.34 3.16
898 908 5.886960 AGAGATTTCCTCACCAAATTTCG 57.113 39.130 0.00 0.00 44.40 3.46
925 935 1.153823 CGGAGCGTACCTGTTCCAG 60.154 63.158 4.90 0.00 39.02 3.86
982 993 6.036953 CCATAAGAGACAGAGAAATTGACAGC 59.963 42.308 0.00 0.00 0.00 4.40
985 996 3.062763 AGACAGAGAAATTGACAGCACG 58.937 45.455 0.00 0.00 0.00 5.34
1000 1011 1.591703 CACGGCTCTTCCACAGCTA 59.408 57.895 0.00 0.00 37.05 3.32
1001 1012 0.176680 CACGGCTCTTCCACAGCTAT 59.823 55.000 0.00 0.00 37.05 2.97
1002 1013 0.176680 ACGGCTCTTCCACAGCTATG 59.823 55.000 0.00 0.00 37.05 2.23
1003 1014 0.176680 CGGCTCTTCCACAGCTATGT 59.823 55.000 0.00 0.00 41.57 2.29
1011 1030 3.895232 TCCACAGCTATGTCTTCTTCC 57.105 47.619 0.00 0.00 37.65 3.46
1063 1082 3.589288 GGCCATTATCCACCTCCTTCTAT 59.411 47.826 0.00 0.00 0.00 1.98
1146 1165 2.988010 ACGCAATCTCCTGCATCTTA 57.012 45.000 0.00 0.00 42.77 2.10
1148 1167 2.093500 ACGCAATCTCCTGCATCTTACA 60.093 45.455 0.00 0.00 42.77 2.41
1317 1340 4.838423 TGACATGACCTCCTTTCAGTCTTA 59.162 41.667 0.00 0.00 0.00 2.10
1318 1341 5.306937 TGACATGACCTCCTTTCAGTCTTAA 59.693 40.000 0.00 0.00 0.00 1.85
1366 1389 3.316029 TGCATGCCTTCCTCAATATTTCG 59.684 43.478 16.68 0.00 0.00 3.46
1377 1400 9.098355 CTTCCTCAATATTTCGTGATCTTGTAA 57.902 33.333 0.00 0.00 0.00 2.41
1429 1453 4.217767 ACTTATTTTCCCAACTTCTTCCGC 59.782 41.667 0.00 0.00 0.00 5.54
1476 1500 4.268405 CACATTTTGTGCTTCAACTTCCAC 59.732 41.667 0.00 0.00 41.89 4.02
1480 1504 2.479837 TGTGCTTCAACTTCCACTACG 58.520 47.619 0.00 0.00 0.00 3.51
1482 1506 1.414919 TGCTTCAACTTCCACTACGGT 59.585 47.619 0.00 0.00 35.57 4.83
1540 1564 1.794437 CGTACGTGCAGCCTCTTCTAC 60.794 57.143 7.22 0.00 0.00 2.59
1589 1613 1.012486 GCCCTACAACCTTGACGTCG 61.012 60.000 11.62 0.00 0.00 5.12
1625 1649 2.734723 CGTGGCTGGAGTGTGACG 60.735 66.667 0.00 0.00 0.00 4.35
1709 1804 8.147244 ACCTTAATTAGACTTGTATCACCTGT 57.853 34.615 0.00 0.00 0.00 4.00
1711 1806 8.883731 CCTTAATTAGACTTGTATCACCTGTTG 58.116 37.037 0.00 0.00 0.00 3.33
1766 1897 4.714632 CCTTCCAAGTTCCAACTCAACTA 58.285 43.478 0.00 0.00 38.57 2.24
1775 1906 6.951971 AGTTCCAACTCAACTATAGCTTCAT 58.048 36.000 0.00 0.00 32.86 2.57
1844 1975 2.130821 TATTGCAGGGGCCACACGAA 62.131 55.000 8.31 0.00 40.13 3.85
1883 2014 1.243342 CCAACGTGGTGCCATGTGAT 61.243 55.000 15.92 0.00 44.45 3.06
1892 2023 1.281960 GCCATGTGATGATGAGCGC 59.718 57.895 0.00 0.00 0.00 5.92
1967 2098 3.436704 CAGACCAATGCGACTATGTGTTT 59.563 43.478 0.00 0.00 0.00 2.83
1972 2103 4.155099 CCAATGCGACTATGTGTTTGGTTA 59.845 41.667 0.00 0.00 31.52 2.85
2007 2138 2.826777 ATCCTTGGGCGTGCTCTTGG 62.827 60.000 0.00 0.00 0.00 3.61
2045 2176 1.544537 CCCACCAACAATGAGAACCGA 60.545 52.381 0.00 0.00 0.00 4.69
2057 2188 1.228154 GAACCGACCCAACCTTGCT 60.228 57.895 0.00 0.00 0.00 3.91
2072 2203 1.231958 TTGCTTTCGGGTAGGCGTTG 61.232 55.000 0.00 0.00 0.00 4.10
2082 2213 1.197036 GGTAGGCGTTGCTGAAACTTC 59.803 52.381 0.00 0.00 36.56 3.01
2120 2256 0.109781 ATGATTCGGTTGTTGCGTGC 60.110 50.000 0.00 0.00 0.00 5.34
2172 2316 4.085876 GCAAGAGGCAGGCAAGAA 57.914 55.556 0.00 0.00 43.97 2.52
2173 2317 1.881602 GCAAGAGGCAGGCAAGAAG 59.118 57.895 0.00 0.00 43.97 2.85
2175 2319 0.608582 CAAGAGGCAGGCAAGAAGCT 60.609 55.000 0.00 0.00 44.79 3.74
2185 2329 2.037136 CAAGAAGCTGGTGGAGGCG 61.037 63.158 0.00 0.00 0.00 5.52
2188 2332 3.011517 AAGCTGGTGGAGGCGGAT 61.012 61.111 0.00 0.00 0.00 4.18
2208 2352 4.271816 CGTCCTCGGGATCGGCAG 62.272 72.222 0.00 0.00 32.73 4.85
2255 2399 4.706476 AGCTAAAGCAACAAGGCATAATCA 59.294 37.500 4.54 0.00 45.16 2.57
2256 2400 4.800471 GCTAAAGCAACAAGGCATAATCAC 59.200 41.667 0.00 0.00 41.59 3.06
2275 2419 4.009675 TCACTGACAATATCTTTGGCCAC 58.990 43.478 3.88 0.00 0.00 5.01
2377 2521 2.614057 GGCTCAGAATGTCGGGTAATTG 59.386 50.000 0.00 0.00 37.40 2.32
2379 2523 2.614057 CTCAGAATGTCGGGTAATTGCC 59.386 50.000 3.57 3.57 37.40 4.52
2427 2571 1.871080 CTATAGCGGTTTGAGCAGGG 58.129 55.000 0.00 0.00 37.01 4.45
2442 2586 3.658757 GCAGGGTGCTGTTAAATGAAA 57.341 42.857 0.00 0.00 40.96 2.69
2446 2590 5.576774 GCAGGGTGCTGTTAAATGAAATAAC 59.423 40.000 0.00 0.00 40.96 1.89
2607 2752 1.139058 GGGAGCACCTACACCTATGTG 59.861 57.143 0.00 0.00 40.16 3.21
2635 2780 4.134563 GGACACATATGGTCGCCTTATTT 58.865 43.478 7.80 0.00 36.12 1.40
2649 2794 6.274001 CGCCTTATTTCAGCGGTATATATG 57.726 41.667 0.00 0.00 45.88 1.78
2650 2795 5.810587 CGCCTTATTTCAGCGGTATATATGT 59.189 40.000 0.00 0.00 45.88 2.29
2651 2796 6.312918 CGCCTTATTTCAGCGGTATATATGTT 59.687 38.462 0.00 0.00 45.88 2.71
2652 2797 7.148474 CGCCTTATTTCAGCGGTATATATGTTT 60.148 37.037 0.00 0.00 45.88 2.83
2656 2801 9.549078 TTATTTCAGCGGTATATATGTTTCACA 57.451 29.630 0.00 0.00 0.00 3.58
2657 2802 8.621532 ATTTCAGCGGTATATATGTTTCACAT 57.378 30.769 0.00 0.00 42.35 3.21
2658 2803 7.652300 TTCAGCGGTATATATGTTTCACATC 57.348 36.000 0.00 0.00 39.88 3.06
2659 2804 6.754193 TCAGCGGTATATATGTTTCACATCA 58.246 36.000 0.00 0.00 39.88 3.07
2660 2805 6.645003 TCAGCGGTATATATGTTTCACATCAC 59.355 38.462 0.00 0.00 39.88 3.06
2661 2806 6.423604 CAGCGGTATATATGTTTCACATCACA 59.576 38.462 0.00 0.00 39.88 3.58
2662 2807 6.646653 AGCGGTATATATGTTTCACATCACAG 59.353 38.462 0.00 0.00 39.88 3.66
2663 2808 6.618592 GCGGTATATATGTTTCACATCACAGC 60.619 42.308 0.00 0.00 39.88 4.40
2664 2809 6.646653 CGGTATATATGTTTCACATCACAGCT 59.353 38.462 0.00 0.00 39.88 4.24
2665 2810 7.812669 CGGTATATATGTTTCACATCACAGCTA 59.187 37.037 0.00 0.00 39.88 3.32
2666 2811 9.144747 GGTATATATGTTTCACATCACAGCTAG 57.855 37.037 0.00 0.00 39.88 3.42
2667 2812 9.914131 GTATATATGTTTCACATCACAGCTAGA 57.086 33.333 0.00 0.00 39.88 2.43
2669 2814 3.329386 TGTTTCACATCACAGCTAGAGC 58.671 45.455 0.00 0.00 42.49 4.09
2670 2815 4.323333 ATGTTTCACATCACAGCTAGAGCT 60.323 41.667 0.00 0.00 43.55 4.09
2671 2816 5.105187 ATGTTTCACATCACAGCTAGAGCTA 60.105 40.000 3.17 0.00 41.71 3.32
2672 2817 6.903901 ATGTTTCACATCACAGCTAGAGCTAG 60.904 42.308 3.17 0.34 41.71 3.42
2684 2829 4.497473 CTAGAGCTAGCCACTCACATAC 57.503 50.000 12.13 0.00 36.58 2.39
2685 2830 2.739943 AGAGCTAGCCACTCACATACA 58.260 47.619 12.13 0.00 36.58 2.29
2686 2831 3.303938 AGAGCTAGCCACTCACATACAT 58.696 45.455 12.13 0.00 36.58 2.29
2687 2832 3.708631 AGAGCTAGCCACTCACATACATT 59.291 43.478 12.13 0.00 36.58 2.71
2688 2833 4.895889 AGAGCTAGCCACTCACATACATTA 59.104 41.667 12.13 0.00 36.58 1.90
2689 2834 5.010516 AGAGCTAGCCACTCACATACATTAG 59.989 44.000 12.13 0.00 36.58 1.73
2690 2835 4.895889 AGCTAGCCACTCACATACATTAGA 59.104 41.667 12.13 0.00 0.00 2.10
2691 2836 5.541868 AGCTAGCCACTCACATACATTAGAT 59.458 40.000 12.13 0.00 0.00 1.98
2692 2837 5.866633 GCTAGCCACTCACATACATTAGATC 59.133 44.000 2.29 0.00 0.00 2.75
2693 2838 5.876651 AGCCACTCACATACATTAGATCA 57.123 39.130 0.00 0.00 0.00 2.92
2694 2839 5.851720 AGCCACTCACATACATTAGATCAG 58.148 41.667 0.00 0.00 0.00 2.90
2695 2840 5.365025 AGCCACTCACATACATTAGATCAGT 59.635 40.000 0.00 0.00 0.00 3.41
2696 2841 5.464722 GCCACTCACATACATTAGATCAGTG 59.535 44.000 0.00 0.00 0.00 3.66
2697 2842 6.577103 CCACTCACATACATTAGATCAGTGT 58.423 40.000 0.00 0.00 0.00 3.55
2698 2843 7.684428 GCCACTCACATACATTAGATCAGTGTA 60.684 40.741 0.00 1.47 33.35 2.90
2699 2844 8.197439 CCACTCACATACATTAGATCAGTGTAA 58.803 37.037 8.35 0.00 32.65 2.41
2700 2845 9.025020 CACTCACATACATTAGATCAGTGTAAC 57.975 37.037 8.35 0.00 32.65 2.50
2715 2860 4.510038 GTGTAACTACTCCCTTCGTTCA 57.490 45.455 0.00 0.00 0.00 3.18
2716 2861 5.069501 GTGTAACTACTCCCTTCGTTCAT 57.930 43.478 0.00 0.00 0.00 2.57
2717 2862 6.199937 GTGTAACTACTCCCTTCGTTCATA 57.800 41.667 0.00 0.00 0.00 2.15
2718 2863 6.032717 GTGTAACTACTCCCTTCGTTCATAC 58.967 44.000 0.00 0.00 0.00 2.39
2719 2864 5.711506 TGTAACTACTCCCTTCGTTCATACA 59.288 40.000 0.00 0.00 0.00 2.29
2720 2865 5.934402 AACTACTCCCTTCGTTCATACAT 57.066 39.130 0.00 0.00 0.00 2.29
2727 2872 8.833231 ACTCCCTTCGTTCATACATATATTTG 57.167 34.615 0.00 0.00 0.00 2.32
2794 2939 1.180456 TTGCATTGCAGGTGGGAGTG 61.180 55.000 11.76 0.00 40.61 3.51
2840 2985 2.202919 TGGACGATGATGCGCTGG 60.203 61.111 9.73 0.00 33.86 4.85
2859 3004 1.895131 GGCTGAATGCTGGGAAGAAAA 59.105 47.619 0.00 0.00 42.39 2.29
2874 3019 5.230182 GGAAGAAAACGAGCCAATTCAATT 58.770 37.500 0.00 0.00 0.00 2.32
2985 3130 7.760794 TGAAAACTATATCGTTGTCACGGTAAT 59.239 33.333 8.53 0.00 45.09 1.89
2987 3132 9.585099 AAAACTATATCGTTGTCACGGTAATTA 57.415 29.630 0.00 0.00 45.09 1.40
2988 3133 9.585099 AAACTATATCGTTGTCACGGTAATTAA 57.415 29.630 0.00 0.00 45.09 1.40
2989 3134 8.792831 ACTATATCGTTGTCACGGTAATTAAG 57.207 34.615 0.00 0.00 45.09 1.85
2990 3135 8.408601 ACTATATCGTTGTCACGGTAATTAAGT 58.591 33.333 0.00 0.00 45.09 2.24
2991 3136 9.882996 CTATATCGTTGTCACGGTAATTAAGTA 57.117 33.333 0.00 0.00 45.09 2.24
3004 3149 7.884354 ACGGTAATTAAGTAAACCTTGGATTGA 59.116 33.333 0.00 0.00 34.46 2.57
3016 3161 3.340928 CTTGGATTGATCACTGCACTGA 58.659 45.455 6.76 0.00 0.00 3.41
3033 3178 0.684535 TGACTGCCTGAAACGGATCA 59.315 50.000 0.00 0.00 0.00 2.92
3097 3244 1.029681 AGAAAACCGGGAAAGTGTGC 58.970 50.000 6.32 0.00 0.00 4.57
3175 3322 5.099575 GGTGTGAAATTCAGTCAAACGTTT 58.900 37.500 7.96 7.96 34.53 3.60
3178 3325 5.106118 TGTGAAATTCAGTCAAACGTTTCCA 60.106 36.000 11.37 0.00 0.00 3.53
3197 3344 5.255397 TCCACTTTGGGAAACTATGACAT 57.745 39.130 0.00 0.00 38.32 3.06
3243 3390 6.916440 TGATCATTTCCACACTGATTTTCTG 58.084 36.000 0.00 0.00 30.00 3.02
3258 3405 9.220767 ACTGATTTTCTGTTCTTCAGGTAATAC 57.779 33.333 0.00 0.00 43.76 1.89
3301 3448 0.377554 ACGATAACGAGAGAGCACGG 59.622 55.000 0.00 0.00 42.66 4.94
3342 3489 3.117776 TCATGCTATGAAATGCCAGGTCT 60.118 43.478 0.00 0.00 36.11 3.85
3369 3523 2.278206 CATCGGGTCGCGTCTCTG 60.278 66.667 5.77 2.17 0.00 3.35
3375 3529 0.802607 GGGTCGCGTCTCTGAATGAC 60.803 60.000 5.77 0.00 0.00 3.06
3398 3552 0.321919 TCTTCTGACATGCTGTGGGC 60.322 55.000 0.00 0.00 42.22 5.36
3400 3554 0.983467 TTCTGACATGCTGTGGGCTA 59.017 50.000 0.00 0.00 42.39 3.93
3405 3559 0.911769 ACATGCTGTGGGCTAAGCTA 59.088 50.000 0.00 0.00 42.39 3.32
3437 3591 2.930682 GGAGGTGTCATCGCTTTAGAAC 59.069 50.000 0.00 0.00 0.00 3.01
3472 3626 5.701290 ACCTTAACAAGAATGAAGGACTTCG 59.299 40.000 6.52 0.00 40.88 3.79
3473 3627 5.932303 CCTTAACAAGAATGAAGGACTTCGA 59.068 40.000 7.49 0.00 40.88 3.71
3541 3696 3.146618 CTGATTGCAGCATTCTGTTCC 57.853 47.619 16.38 0.00 42.29 3.62
3547 3702 4.520846 GCATTCTGTTCCGCCGCG 62.521 66.667 5.59 5.59 0.00 6.46
3565 3720 2.125552 CGCTGCACCTTCCGATCA 60.126 61.111 0.00 0.00 0.00 2.92
3574 3729 1.561730 CTTCCGATCATCGCTTGCG 59.438 57.895 8.87 8.87 38.82 4.85
3577 3732 0.664466 TCCGATCATCGCTTGCGATC 60.664 55.000 24.87 15.40 38.82 3.69
3580 3735 2.319472 CGATCATCGCTTGCGATCTTA 58.681 47.619 24.87 14.91 34.63 2.10
3585 3740 0.800683 TCGCTTGCGATCTTACGGTG 60.801 55.000 13.93 0.00 0.00 4.94
3596 3751 2.219458 TCTTACGGTGATAGAGAGCGG 58.781 52.381 0.00 0.00 38.62 5.52
3617 3772 3.068691 CATGCAGCCTGCCTTGCT 61.069 61.111 15.29 0.00 44.23 3.91
3624 3779 1.404391 CAGCCTGCCTTGCTTTATCTG 59.596 52.381 0.00 0.00 36.81 2.90
3628 3783 3.490419 GCCTGCCTTGCTTTATCTGATTG 60.490 47.826 0.00 0.00 0.00 2.67
3706 3862 6.431198 TTGTCTAAAGAATGTATTTCCCGC 57.569 37.500 0.00 0.00 34.67 6.13
3709 3865 6.601613 TGTCTAAAGAATGTATTTCCCGCAAT 59.398 34.615 0.00 0.00 34.67 3.56
3710 3866 7.771361 TGTCTAAAGAATGTATTTCCCGCAATA 59.229 33.333 0.00 0.00 34.67 1.90
3711 3867 8.617809 GTCTAAAGAATGTATTTCCCGCAATAA 58.382 33.333 0.00 0.00 34.67 1.40
3712 3868 9.179909 TCTAAAGAATGTATTTCCCGCAATAAA 57.820 29.630 0.00 0.00 34.67 1.40
3713 3869 9.796120 CTAAAGAATGTATTTCCCGCAATAAAA 57.204 29.630 0.00 0.00 34.67 1.52
3737 3893 8.926715 AAAAATCTAAAGAATGTATTTCCCGC 57.073 30.769 0.00 0.00 34.67 6.13
3738 3894 7.639113 AAATCTAAAGAATGTATTTCCCGCA 57.361 32.000 0.00 0.00 34.67 5.69
3739 3895 7.639113 AATCTAAAGAATGTATTTCCCGCAA 57.361 32.000 0.00 0.00 34.67 4.85
3740 3896 7.639113 ATCTAAAGAATGTATTTCCCGCAAA 57.361 32.000 0.00 0.00 34.67 3.68
3741 3897 7.455641 TCTAAAGAATGTATTTCCCGCAAAA 57.544 32.000 0.00 0.00 34.67 2.44
3742 3898 7.887381 TCTAAAGAATGTATTTCCCGCAAAAA 58.113 30.769 0.00 0.00 34.67 1.94
3828 3984 1.299850 TGCTTCTGTGGTCGTCGTG 60.300 57.895 0.00 0.00 0.00 4.35
3829 3985 1.299926 GCTTCTGTGGTCGTCGTGT 60.300 57.895 0.00 0.00 0.00 4.49
3835 3991 4.016629 TGGTCGTCGTGTCGGTCG 62.017 66.667 0.00 0.00 0.00 4.79
3859 4015 1.446792 AGTGCCATTGAGTCGCTCG 60.447 57.895 3.08 0.00 32.35 5.03
3869 4025 2.127758 GTCGCTCGTTGCAAACCG 60.128 61.111 0.00 1.03 46.28 4.44
3872 4028 2.677003 CGCTCGTTGCAAACCGGAT 61.677 57.895 9.46 0.00 46.28 4.18
3895 4051 2.364647 TGTGATGTTGCAAAGCCATTCA 59.635 40.909 0.00 2.48 0.00 2.57
3898 4054 1.117994 TGTTGCAAAGCCATTCACCA 58.882 45.000 0.00 0.00 0.00 4.17
3899 4055 1.202510 TGTTGCAAAGCCATTCACCAC 60.203 47.619 0.00 0.00 0.00 4.16
3914 4070 1.027357 ACCACTGTCTTTTGCTGCTG 58.973 50.000 0.00 0.00 0.00 4.41
3928 4084 4.065281 GCTGCAAAGCCTGGCCAG 62.065 66.667 26.87 26.87 0.00 4.85
3953 4109 1.153353 TACAAAGCTAGCCACGCAAC 58.847 50.000 12.13 0.00 0.00 4.17
3986 4142 2.050985 GACGCCACTGTTGCAAGC 60.051 61.111 0.00 0.00 0.00 4.01
3988 4144 4.688419 CGCCACTGTTGCAAGCCG 62.688 66.667 0.00 0.00 0.00 5.52
4056 4212 3.485743 GCCGCTGTTTCTTTTTGTTGTAG 59.514 43.478 0.00 0.00 0.00 2.74
4061 4217 4.915704 TGTTTCTTTTTGTTGTAGAGCCG 58.084 39.130 0.00 0.00 0.00 5.52
4073 4229 1.337384 TAGAGCCGGCCACATGACAT 61.337 55.000 26.15 0.00 0.00 3.06
4094 4250 5.663106 ACATTGCAGGGTAGAGAGAAATAGA 59.337 40.000 0.00 0.00 0.00 1.98
4095 4251 5.860941 TTGCAGGGTAGAGAGAAATAGAG 57.139 43.478 0.00 0.00 0.00 2.43
4100 4256 6.127310 GCAGGGTAGAGAGAAATAGAGTGAAA 60.127 42.308 0.00 0.00 0.00 2.69
4104 4260 8.968969 GGGTAGAGAGAAATAGAGTGAAAAGTA 58.031 37.037 0.00 0.00 0.00 2.24
4112 4268 9.965902 AGAAATAGAGTGAAAAGTACATTGGAT 57.034 29.630 0.00 0.00 0.00 3.41
4123 4279 8.477419 AAAAGTACATTGGATTTCTCAAAGGA 57.523 30.769 0.00 0.00 0.00 3.36
4148 4304 5.568685 TTTGAGTTCACGTTGAAATTCCA 57.431 34.783 0.00 0.00 38.22 3.53
4149 4305 5.568685 TTGAGTTCACGTTGAAATTCCAA 57.431 34.783 0.00 0.00 38.22 3.53
4196 4378 4.151883 TTCCATAGGAATTTGGCTATGCC 58.848 43.478 1.01 1.01 42.29 4.40
4217 4399 3.119101 CCAATCGTAGGAATCGATAGGGG 60.119 52.174 0.00 1.51 45.33 4.79
4288 4470 6.362248 TCCTACAAAAATCCTACAATAGGCC 58.638 40.000 0.00 0.00 45.82 5.19
4305 4487 3.816994 AGGCCGTAAATCCTTCCATAAC 58.183 45.455 0.00 0.00 0.00 1.89
4337 4519 2.425668 CTGAATCAACATGCATGGCTGA 59.574 45.455 29.41 27.74 0.00 4.26
4339 4521 1.842052 ATCAACATGCATGGCTGACA 58.158 45.000 29.41 12.12 30.08 3.58
4345 4527 0.885879 ATGCATGGCTGACACACAAG 59.114 50.000 0.00 0.00 0.00 3.16
4346 4528 1.174078 TGCATGGCTGACACACAAGG 61.174 55.000 0.00 0.00 0.00 3.61
4347 4529 0.890542 GCATGGCTGACACACAAGGA 60.891 55.000 0.00 0.00 0.00 3.36
4348 4530 1.830279 CATGGCTGACACACAAGGAT 58.170 50.000 0.00 0.00 0.00 3.24
4349 4531 2.940971 GCATGGCTGACACACAAGGATA 60.941 50.000 0.00 0.00 0.00 2.59
4350 4532 3.346315 CATGGCTGACACACAAGGATAA 58.654 45.455 0.00 0.00 0.00 1.75
4351 4533 3.500448 TGGCTGACACACAAGGATAAA 57.500 42.857 0.00 0.00 0.00 1.40
4352 4534 4.032960 TGGCTGACACACAAGGATAAAT 57.967 40.909 0.00 0.00 0.00 1.40
4353 4535 5.172687 TGGCTGACACACAAGGATAAATA 57.827 39.130 0.00 0.00 0.00 1.40
4354 4536 5.565509 TGGCTGACACACAAGGATAAATAA 58.434 37.500 0.00 0.00 0.00 1.40
4355 4537 5.647658 TGGCTGACACACAAGGATAAATAAG 59.352 40.000 0.00 0.00 0.00 1.73
4356 4538 5.648092 GGCTGACACACAAGGATAAATAAGT 59.352 40.000 0.00 0.00 0.00 2.24
4357 4539 6.183360 GGCTGACACACAAGGATAAATAAGTC 60.183 42.308 0.00 0.00 0.00 3.01
4358 4540 6.595716 GCTGACACACAAGGATAAATAAGTCT 59.404 38.462 0.00 0.00 0.00 3.24
4359 4541 7.201565 GCTGACACACAAGGATAAATAAGTCTC 60.202 40.741 0.00 0.00 0.00 3.36
4360 4542 6.811665 TGACACACAAGGATAAATAAGTCTCG 59.188 38.462 0.00 0.00 0.00 4.04
4361 4543 6.931838 ACACACAAGGATAAATAAGTCTCGA 58.068 36.000 0.00 0.00 0.00 4.04
4362 4544 7.036220 ACACACAAGGATAAATAAGTCTCGAG 58.964 38.462 5.93 5.93 0.00 4.04
4363 4545 6.477033 CACACAAGGATAAATAAGTCTCGAGG 59.523 42.308 13.56 0.00 0.00 4.63
4364 4546 5.986135 CACAAGGATAAATAAGTCTCGAGGG 59.014 44.000 13.56 0.00 0.00 4.30
4365 4547 5.897824 ACAAGGATAAATAAGTCTCGAGGGA 59.102 40.000 13.56 0.00 0.00 4.20
4366 4548 6.183360 ACAAGGATAAATAAGTCTCGAGGGAC 60.183 42.308 13.56 4.49 36.56 4.46
4367 4549 5.455872 AGGATAAATAAGTCTCGAGGGACA 58.544 41.667 13.56 0.00 38.57 4.02
4368 4550 6.078664 AGGATAAATAAGTCTCGAGGGACAT 58.921 40.000 13.56 0.00 38.57 3.06
4369 4551 6.015010 AGGATAAATAAGTCTCGAGGGACATG 60.015 42.308 13.56 0.00 38.57 3.21
4370 4552 4.408182 AAATAAGTCTCGAGGGACATGG 57.592 45.455 13.56 0.00 38.57 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.691219 GGCCTGGAGGGTTTGATGA 59.309 57.895 0.00 0.00 37.43 2.92
25 26 0.405585 TTCTTCTTTGGGCCTGGAGG 59.594 55.000 4.53 0.91 38.53 4.30
81 82 7.507616 TCCACTTGAACCCTTAATACAAACAAT 59.492 33.333 0.00 0.00 0.00 2.71
130 131 8.726988 TCTAACTAAGGCATGTTTGTACAATTC 58.273 33.333 9.56 6.73 37.91 2.17
133 134 8.453238 TTTCTAACTAAGGCATGTTTGTACAA 57.547 30.769 3.59 3.59 37.91 2.41
142 143 7.639113 TTGGGTAATTTCTAACTAAGGCATG 57.361 36.000 0.00 0.00 0.00 4.06
263 264 6.024552 AGGCAAATCAAAAGCGATAGAAAA 57.975 33.333 0.00 0.00 39.76 2.29
264 265 5.643379 AGGCAAATCAAAAGCGATAGAAA 57.357 34.783 0.00 0.00 39.76 2.52
265 266 5.643379 AAGGCAAATCAAAAGCGATAGAA 57.357 34.783 0.00 0.00 39.76 2.10
266 267 5.643379 AAAGGCAAATCAAAAGCGATAGA 57.357 34.783 0.00 0.00 39.76 1.98
267 268 5.634859 ACAAAAGGCAAATCAAAAGCGATAG 59.365 36.000 0.00 0.00 0.00 2.08
396 398 8.028938 CCAAGAGTGAATATTGGTTGGTAAAAG 58.971 37.037 0.00 0.00 43.96 2.27
408 410 4.536090 TGGACCTGACCAAGAGTGAATATT 59.464 41.667 0.00 0.00 36.96 1.28
488 490 3.881688 GCTCAATGTGGAATCTGCTACAT 59.118 43.478 0.00 0.00 41.02 2.29
624 626 6.823689 AGTAGTACATTGGTTGAATGCCTTAG 59.176 38.462 2.52 0.00 44.85 2.18
723 726 6.493458 ACAAGACCAACAACCAGCTATAAAAT 59.507 34.615 0.00 0.00 0.00 1.82
757 767 4.322273 GCATCATCATTACTCGATCTGGGA 60.322 45.833 0.00 0.00 0.00 4.37
849 859 2.354821 GACTGTTCTCTTGGCGTTGTTT 59.645 45.455 0.00 0.00 0.00 2.83
1000 1011 1.630878 GGTGGTGGAGGAAGAAGACAT 59.369 52.381 0.00 0.00 0.00 3.06
1001 1012 1.056660 GGTGGTGGAGGAAGAAGACA 58.943 55.000 0.00 0.00 0.00 3.41
1002 1013 1.056660 TGGTGGTGGAGGAAGAAGAC 58.943 55.000 0.00 0.00 0.00 3.01
1003 1014 1.630369 CATGGTGGTGGAGGAAGAAGA 59.370 52.381 0.00 0.00 0.00 2.87
1011 1030 2.753043 GCAGCCATGGTGGTGGAG 60.753 66.667 14.67 0.00 42.02 3.86
1043 1062 5.006386 GCAATAGAAGGAGGTGGATAATGG 58.994 45.833 0.00 0.00 0.00 3.16
1178 1197 8.438373 AGTATCATGGAATTCAATGACTGAGAT 58.562 33.333 24.75 12.35 34.81 2.75
1187 1206 6.483307 CCGTGTGTAGTATCATGGAATTCAAT 59.517 38.462 7.93 0.00 41.65 2.57
1317 1340 8.301730 GCAATTGCAATATAATGTACTGCATT 57.698 30.769 25.36 0.00 42.22 3.56
1318 1341 7.878477 GCAATTGCAATATAATGTACTGCAT 57.122 32.000 25.36 0.00 42.22 3.96
1350 1373 6.540189 ACAAGATCACGAAATATTGAGGAAGG 59.460 38.462 13.35 0.00 33.23 3.46
1366 1389 6.144724 GCGATAAGATCTGGTTACAAGATCAC 59.855 42.308 26.16 15.26 40.46 3.06
1429 1453 6.581919 TGCATGAACAACTGAAATGTAATTCG 59.418 34.615 0.00 0.00 33.67 3.34
1473 1497 3.247006 ACTCAAATGCTACCGTAGTGG 57.753 47.619 7.40 0.00 46.41 4.00
1476 1500 5.178623 TGTCAAAACTCAAATGCTACCGTAG 59.821 40.000 0.76 0.76 0.00 3.51
1480 1504 4.622740 GCATGTCAAAACTCAAATGCTACC 59.377 41.667 0.00 0.00 37.89 3.18
1482 1506 5.710513 AGCATGTCAAAACTCAAATGCTA 57.289 34.783 6.18 0.00 46.53 3.49
1540 1564 2.717390 TCCCCAATGTTCATGGTAACG 58.283 47.619 0.00 0.00 42.51 3.18
1567 1591 1.270678 ACGTCAAGGTTGTAGGGCTTC 60.271 52.381 0.00 0.00 0.00 3.86
1582 1606 4.337060 CTGCCCGTGTCGACGTCA 62.337 66.667 17.16 0.00 44.54 4.35
1610 1634 4.314440 GGCGTCACACTCCAGCCA 62.314 66.667 0.00 0.00 46.48 4.75
1682 1777 8.883731 CAGGTGATACAAGTCTAATTAAGGTTG 58.116 37.037 0.00 0.00 0.00 3.77
1709 1804 2.628178 AGGAGCTAGCATATACGCACAA 59.372 45.455 18.83 0.00 0.00 3.33
1711 1806 2.989840 CAAGGAGCTAGCATATACGCAC 59.010 50.000 18.83 0.00 0.00 5.34
1766 1897 6.721208 TGGAAACTGAAGGAAAATGAAGCTAT 59.279 34.615 0.00 0.00 0.00 2.97
1775 1906 4.080015 TCAGGACTGGAAACTGAAGGAAAA 60.080 41.667 0.00 0.00 38.22 2.29
1819 1950 1.812571 GTGGCCCCTGCAATAATATCG 59.187 52.381 0.00 0.00 40.13 2.92
1844 1975 1.006571 CGGTGTTGGTCTGTACGCT 60.007 57.895 0.00 0.00 0.00 5.07
1939 2070 1.002624 TCGCATTGGTCTGGGTTCC 60.003 57.895 0.00 0.00 0.00 3.62
1967 2098 1.290955 CTCGCCGTCCTTGTAACCA 59.709 57.895 0.00 0.00 0.00 3.67
1972 2103 1.215647 GATGACTCGCCGTCCTTGT 59.784 57.895 2.86 0.00 42.13 3.16
1988 2119 1.377725 CAAGAGCACGCCCAAGGAT 60.378 57.895 0.00 0.00 0.00 3.24
2007 2138 2.579738 GAGGGAGAACTGGTCGGC 59.420 66.667 0.00 0.00 0.00 5.54
2045 2176 1.530655 CCCGAAAGCAAGGTTGGGT 60.531 57.895 0.00 0.00 31.82 4.51
2057 2188 1.669760 CAGCAACGCCTACCCGAAA 60.670 57.895 0.00 0.00 0.00 3.46
2072 2203 1.856265 CGGTGCAGGGAAGTTTCAGC 61.856 60.000 0.00 0.00 0.00 4.26
2156 2300 0.608582 AGCTTCTTGCCTGCCTCTTG 60.609 55.000 0.00 0.00 44.23 3.02
2172 2316 3.790437 CATCCGCCTCCACCAGCT 61.790 66.667 0.00 0.00 0.00 4.24
2173 2317 4.864334 CCATCCGCCTCCACCAGC 62.864 72.222 0.00 0.00 0.00 4.85
2224 2368 1.079503 GTTGCTTTAGCTGGGAGACG 58.920 55.000 0.00 0.00 42.66 4.18
2255 2399 4.012374 CAGTGGCCAAAGATATTGTCAGT 58.988 43.478 7.24 0.00 0.00 3.41
2256 2400 3.181493 GCAGTGGCCAAAGATATTGTCAG 60.181 47.826 7.24 0.00 0.00 3.51
2377 2521 2.486918 ACCGGCTATTTATGTAACGGC 58.513 47.619 0.00 0.00 43.28 5.68
2379 2523 6.810182 AGCTATAACCGGCTATTTATGTAACG 59.190 38.462 0.00 0.00 37.00 3.18
2427 2571 8.512138 ACACCTAGTTATTTCATTTAACAGCAC 58.488 33.333 0.00 0.00 33.02 4.40
2438 2582 5.302360 AGCGTGAAACACCTAGTTATTTCA 58.698 37.500 7.91 7.91 40.26 2.69
2442 2586 5.761234 TGAAAAGCGTGAAACACCTAGTTAT 59.239 36.000 0.00 0.00 40.26 1.89
2446 2590 4.466828 CATGAAAAGCGTGAAACACCTAG 58.533 43.478 0.00 0.00 35.74 3.02
2459 2603 0.320683 GGTTGGGTGCCATGAAAAGC 60.321 55.000 0.00 0.00 31.53 3.51
2607 2752 2.480419 GCGACCATATGTGTCCTTATGC 59.520 50.000 14.80 10.12 30.88 3.14
2663 2808 3.885901 TGTATGTGAGTGGCTAGCTCTAG 59.114 47.826 15.72 0.00 34.30 2.43
2664 2809 3.898482 TGTATGTGAGTGGCTAGCTCTA 58.102 45.455 15.72 0.00 34.30 2.43
2665 2810 2.739943 TGTATGTGAGTGGCTAGCTCT 58.260 47.619 15.72 13.25 34.30 4.09
2666 2811 3.742433 ATGTATGTGAGTGGCTAGCTC 57.258 47.619 15.72 5.01 0.00 4.09
2667 2812 4.895889 TCTAATGTATGTGAGTGGCTAGCT 59.104 41.667 15.72 0.00 0.00 3.32
2668 2813 5.201713 TCTAATGTATGTGAGTGGCTAGC 57.798 43.478 6.04 6.04 0.00 3.42
2669 2814 6.986250 TGATCTAATGTATGTGAGTGGCTAG 58.014 40.000 0.00 0.00 0.00 3.42
2670 2815 6.551227 ACTGATCTAATGTATGTGAGTGGCTA 59.449 38.462 0.00 0.00 0.00 3.93
2671 2816 5.365025 ACTGATCTAATGTATGTGAGTGGCT 59.635 40.000 0.00 0.00 0.00 4.75
2672 2817 5.464722 CACTGATCTAATGTATGTGAGTGGC 59.535 44.000 0.00 0.00 0.00 5.01
2673 2818 6.577103 ACACTGATCTAATGTATGTGAGTGG 58.423 40.000 0.00 0.00 34.02 4.00
2674 2819 9.025020 GTTACACTGATCTAATGTATGTGAGTG 57.975 37.037 0.00 0.00 35.50 3.51
2675 2820 8.972127 AGTTACACTGATCTAATGTATGTGAGT 58.028 33.333 0.00 0.00 0.00 3.41
2680 2825 9.900710 GGAGTAGTTACACTGATCTAATGTATG 57.099 37.037 0.00 0.00 0.00 2.39
2681 2826 9.080097 GGGAGTAGTTACACTGATCTAATGTAT 57.920 37.037 0.00 0.00 0.00 2.29
2682 2827 8.280084 AGGGAGTAGTTACACTGATCTAATGTA 58.720 37.037 0.00 0.00 0.00 2.29
2683 2828 7.126733 AGGGAGTAGTTACACTGATCTAATGT 58.873 38.462 0.00 0.00 0.00 2.71
2684 2829 7.589958 AGGGAGTAGTTACACTGATCTAATG 57.410 40.000 0.00 0.00 0.00 1.90
2685 2830 7.013464 CGAAGGGAGTAGTTACACTGATCTAAT 59.987 40.741 0.00 0.00 0.00 1.73
2686 2831 6.318144 CGAAGGGAGTAGTTACACTGATCTAA 59.682 42.308 0.00 0.00 0.00 2.10
2687 2832 5.821470 CGAAGGGAGTAGTTACACTGATCTA 59.179 44.000 0.00 0.00 0.00 1.98
2688 2833 4.641094 CGAAGGGAGTAGTTACACTGATCT 59.359 45.833 0.00 0.00 0.00 2.75
2689 2834 4.398673 ACGAAGGGAGTAGTTACACTGATC 59.601 45.833 0.00 0.00 0.00 2.92
2690 2835 4.342359 ACGAAGGGAGTAGTTACACTGAT 58.658 43.478 0.00 0.00 0.00 2.90
2691 2836 3.759581 ACGAAGGGAGTAGTTACACTGA 58.240 45.455 0.00 0.00 0.00 3.41
2692 2837 4.022589 TGAACGAAGGGAGTAGTTACACTG 60.023 45.833 0.00 0.00 0.00 3.66
2693 2838 4.147321 TGAACGAAGGGAGTAGTTACACT 58.853 43.478 0.00 0.00 0.00 3.55
2694 2839 4.510038 TGAACGAAGGGAGTAGTTACAC 57.490 45.455 0.00 0.00 0.00 2.90
2695 2840 5.711506 TGTATGAACGAAGGGAGTAGTTACA 59.288 40.000 0.00 0.00 0.00 2.41
2696 2841 6.199937 TGTATGAACGAAGGGAGTAGTTAC 57.800 41.667 0.00 0.00 0.00 2.50
2697 2842 8.701908 ATATGTATGAACGAAGGGAGTAGTTA 57.298 34.615 0.00 0.00 0.00 2.24
2698 2843 5.934402 ATGTATGAACGAAGGGAGTAGTT 57.066 39.130 0.00 0.00 0.00 2.24
2699 2844 8.880991 ATATATGTATGAACGAAGGGAGTAGT 57.119 34.615 0.00 0.00 0.00 2.73
2701 2846 9.923143 CAAATATATGTATGAACGAAGGGAGTA 57.077 33.333 0.00 0.00 0.00 2.59
2702 2847 8.647796 TCAAATATATGTATGAACGAAGGGAGT 58.352 33.333 0.00 0.00 0.00 3.85
2703 2848 8.926710 GTCAAATATATGTATGAACGAAGGGAG 58.073 37.037 0.00 0.00 0.00 4.30
2704 2849 7.876068 GGTCAAATATATGTATGAACGAAGGGA 59.124 37.037 0.00 0.00 0.00 4.20
2705 2850 8.029642 GGTCAAATATATGTATGAACGAAGGG 57.970 38.462 0.00 0.00 0.00 3.95
2711 2856 9.701098 TTACTCCGGTCAAATATATGTATGAAC 57.299 33.333 0.00 2.77 0.00 3.18
2712 2857 9.701098 GTTACTCCGGTCAAATATATGTATGAA 57.299 33.333 0.00 0.00 0.00 2.57
2713 2858 9.085645 AGTTACTCCGGTCAAATATATGTATGA 57.914 33.333 0.00 0.00 0.00 2.15
2716 2861 8.517878 GCTAGTTACTCCGGTCAAATATATGTA 58.482 37.037 0.00 0.00 0.00 2.29
2717 2862 7.232941 AGCTAGTTACTCCGGTCAAATATATGT 59.767 37.037 0.00 0.00 0.00 2.29
2718 2863 7.603651 AGCTAGTTACTCCGGTCAAATATATG 58.396 38.462 0.00 0.00 0.00 1.78
2719 2864 7.778185 AGCTAGTTACTCCGGTCAAATATAT 57.222 36.000 0.00 0.00 0.00 0.86
2720 2865 8.571336 GTTAGCTAGTTACTCCGGTCAAATATA 58.429 37.037 0.00 0.00 0.00 0.86
2727 2872 5.236263 GTCTAGTTAGCTAGTTACTCCGGTC 59.764 48.000 12.72 0.00 43.86 4.79
2794 2939 2.096248 AGTGATGAACCCTCGAGAGTC 58.904 52.381 15.71 8.44 0.00 3.36
2840 2985 2.669391 CGTTTTCTTCCCAGCATTCAGC 60.669 50.000 0.00 0.00 46.19 4.26
2859 3004 4.298332 GTCAACAAATTGAATTGGCTCGT 58.702 39.130 0.00 0.00 46.40 4.18
2874 3019 2.572191 ACTCTTGACGTCGTCAACAA 57.428 45.000 31.49 22.11 45.88 2.83
2971 3116 7.307337 AAGGTTTACTTAATTACCGTGACAACG 60.307 37.037 0.00 0.00 42.98 4.10
2985 3130 7.094377 GCAGTGATCAATCCAAGGTTTACTTAA 60.094 37.037 0.00 0.00 37.29 1.85
2987 3132 5.183904 GCAGTGATCAATCCAAGGTTTACTT 59.816 40.000 0.00 0.00 41.00 2.24
2988 3133 4.702131 GCAGTGATCAATCCAAGGTTTACT 59.298 41.667 0.00 0.00 0.00 2.24
2989 3134 4.458989 TGCAGTGATCAATCCAAGGTTTAC 59.541 41.667 0.00 0.00 0.00 2.01
2990 3135 4.458989 GTGCAGTGATCAATCCAAGGTTTA 59.541 41.667 0.00 0.00 0.00 2.01
2991 3136 3.256631 GTGCAGTGATCAATCCAAGGTTT 59.743 43.478 0.00 0.00 0.00 3.27
3016 3161 1.523758 GTTGATCCGTTTCAGGCAGT 58.476 50.000 0.00 0.00 0.00 4.40
3073 3218 1.165270 CTTTCCCGGTTTTCTGCGAT 58.835 50.000 0.00 0.00 0.00 4.58
3075 3220 0.040425 CACTTTCCCGGTTTTCTGCG 60.040 55.000 0.00 0.00 0.00 5.18
3076 3221 1.029681 ACACTTTCCCGGTTTTCTGC 58.970 50.000 0.00 0.00 0.00 4.26
3097 3244 1.925120 TCCATTGAGGATGCCCAGG 59.075 57.895 0.00 0.00 43.07 4.45
3175 3322 4.715534 TGTCATAGTTTCCCAAAGTGGA 57.284 40.909 0.00 0.00 40.96 4.02
3178 3325 4.406456 TGCATGTCATAGTTTCCCAAAGT 58.594 39.130 0.00 0.00 0.00 2.66
3220 3367 6.917533 ACAGAAAATCAGTGTGGAAATGATC 58.082 36.000 0.00 0.00 32.59 2.92
3223 3370 6.742109 AGAACAGAAAATCAGTGTGGAAATG 58.258 36.000 0.00 0.00 0.00 2.32
3243 3390 6.985188 TCTGCATTGTATTACCTGAAGAAC 57.015 37.500 0.00 0.00 0.00 3.01
3280 3427 2.223611 CCGTGCTCTCTCGTTATCGTAT 59.776 50.000 0.00 0.00 38.33 3.06
3321 3468 3.220110 AGACCTGGCATTTCATAGCATG 58.780 45.455 0.00 0.00 0.00 4.06
3322 3469 3.484407 GAGACCTGGCATTTCATAGCAT 58.516 45.455 0.00 0.00 0.00 3.79
3325 3472 3.459232 TCGAGACCTGGCATTTCATAG 57.541 47.619 0.00 0.00 0.00 2.23
3326 3473 3.531538 GTTCGAGACCTGGCATTTCATA 58.468 45.455 0.00 0.00 0.00 2.15
3342 3489 1.374343 CGACCCGATGAGAGGTTCGA 61.374 60.000 0.00 0.00 36.17 3.71
3369 3523 3.484886 GCATGTCAGAAGAAGCGTCATTC 60.485 47.826 1.61 3.42 0.00 2.67
3398 3552 6.719370 ACACCTCCATCTATCTTCTAGCTTAG 59.281 42.308 0.00 0.00 0.00 2.18
3400 3554 5.463154 ACACCTCCATCTATCTTCTAGCTT 58.537 41.667 0.00 0.00 0.00 3.74
3405 3559 4.522405 CGATGACACCTCCATCTATCTTCT 59.478 45.833 0.00 0.00 38.53 2.85
3437 3591 0.834612 TGTTAAGGTATGAGCCCCGG 59.165 55.000 0.00 0.00 0.00 5.73
3501 3655 3.006430 CAGCCGGTGGGAAAAATAGTTTT 59.994 43.478 1.90 0.00 39.70 2.43
3547 3702 3.567797 GATCGGAAGGTGCAGCGC 61.568 66.667 10.78 0.00 0.00 5.92
3550 3705 1.493950 GCGATGATCGGAAGGTGCAG 61.494 60.000 17.27 0.00 40.84 4.41
3554 3709 0.811616 GCAAGCGATGATCGGAAGGT 60.812 55.000 17.27 0.00 40.84 3.50
3574 3729 3.120130 CCGCTCTCTATCACCGTAAGATC 60.120 52.174 0.00 0.00 43.02 2.75
3577 3732 1.335142 GCCGCTCTCTATCACCGTAAG 60.335 57.143 0.00 0.00 0.00 2.34
3580 3735 2.491022 GGCCGCTCTCTATCACCGT 61.491 63.158 0.00 0.00 0.00 4.83
3585 3740 1.735920 CATGCGGCCGCTCTCTATC 60.736 63.158 45.79 19.46 42.51 2.08
3617 3772 6.647334 TGTTTCAGTTGGCAATCAGATAAA 57.353 33.333 1.92 0.00 0.00 1.40
3624 3779 4.232221 CTGTGATGTTTCAGTTGGCAATC 58.768 43.478 1.92 0.00 30.85 2.67
3628 3783 1.610522 AGCTGTGATGTTTCAGTTGGC 59.389 47.619 0.00 0.00 34.57 4.52
3683 3839 5.941058 TGCGGGAAATACATTCTTTAGACAA 59.059 36.000 0.00 0.00 38.18 3.18
3712 3868 8.527810 TGCGGGAAATACATTCTTTAGATTTTT 58.472 29.630 0.00 0.00 38.18 1.94
3713 3869 8.062065 TGCGGGAAATACATTCTTTAGATTTT 57.938 30.769 0.00 0.00 38.18 1.82
3714 3870 7.639113 TGCGGGAAATACATTCTTTAGATTT 57.361 32.000 0.00 0.00 38.18 2.17
3715 3871 7.639113 TTGCGGGAAATACATTCTTTAGATT 57.361 32.000 0.00 0.00 38.18 2.40
3716 3872 7.639113 TTTGCGGGAAATACATTCTTTAGAT 57.361 32.000 0.00 0.00 38.18 1.98
3717 3873 7.455641 TTTTGCGGGAAATACATTCTTTAGA 57.544 32.000 0.00 0.00 38.18 2.10
3768 3924 6.433847 TGTTCTTTGGGTTCATAGAAGAGA 57.566 37.500 0.00 0.00 40.07 3.10
3769 3925 6.404074 GCATGTTCTTTGGGTTCATAGAAGAG 60.404 42.308 0.00 0.00 40.07 2.85
3783 3939 9.499585 CACTCTATAAAGATTGCATGTTCTTTG 57.500 33.333 21.10 11.76 41.15 2.77
3784 3940 9.236006 ACACTCTATAAAGATTGCATGTTCTTT 57.764 29.630 18.22 18.22 42.96 2.52
3786 3942 7.201679 GCACACTCTATAAAGATTGCATGTTCT 60.202 37.037 0.00 0.00 36.19 3.01
3787 3943 6.909357 GCACACTCTATAAAGATTGCATGTTC 59.091 38.462 0.00 0.00 36.19 3.18
3835 3991 4.824166 CTCAATGGCACTGCGCGC 62.824 66.667 27.26 27.26 43.84 6.86
3841 3997 1.446792 CGAGCGACTCAATGGCACT 60.447 57.895 0.00 0.00 33.70 4.40
3859 4015 0.665835 TCACACATCCGGTTTGCAAC 59.334 50.000 0.00 0.00 0.00 4.17
3869 4025 2.331194 GCTTTGCAACATCACACATCC 58.669 47.619 0.00 0.00 0.00 3.51
3872 4028 1.109609 TGGCTTTGCAACATCACACA 58.890 45.000 0.00 0.00 0.00 3.72
3895 4051 1.027357 CAGCAGCAAAAGACAGTGGT 58.973 50.000 0.00 0.00 0.00 4.16
3928 4084 1.136057 GTGGCTAGCTTTGTAACACGC 60.136 52.381 15.72 0.00 0.00 5.34
3970 4126 3.595758 GGCTTGCAACAGTGGCGT 61.596 61.111 0.00 0.00 0.00 5.68
3971 4127 4.688419 CGGCTTGCAACAGTGGCG 62.688 66.667 15.94 15.94 41.56 5.69
3973 4129 1.973281 ATCCGGCTTGCAACAGTGG 60.973 57.895 0.00 0.00 0.00 4.00
3994 4150 3.142162 CCGGCCATGCAGCATCAA 61.142 61.111 4.38 0.00 0.00 2.57
4056 4212 1.750399 AATGTCATGTGGCCGGCTC 60.750 57.895 28.56 19.88 0.00 4.70
4061 4217 1.514087 CCTGCAATGTCATGTGGCC 59.486 57.895 0.00 0.00 0.00 5.36
4073 4229 5.127845 CACTCTATTTCTCTCTACCCTGCAA 59.872 44.000 0.00 0.00 0.00 4.08
4094 4250 8.463930 TTGAGAAATCCAATGTACTTTTCACT 57.536 30.769 0.00 0.00 0.00 3.41
4095 4251 9.185192 CTTTGAGAAATCCAATGTACTTTTCAC 57.815 33.333 0.00 0.00 0.00 3.18
4100 4256 8.477419 TTTCCTTTGAGAAATCCAATGTACTT 57.523 30.769 0.00 0.00 30.87 2.24
4104 4260 8.431222 TCAAATTTCCTTTGAGAAATCCAATGT 58.569 29.630 0.36 0.00 46.45 2.71
4123 4279 7.038659 TGGAATTTCAACGTGAACTCAAATTT 58.961 30.769 0.00 0.00 35.89 1.82
4188 4370 6.643055 TCGATTCCTACGATTGGCATAGCC 62.643 50.000 0.00 0.00 40.96 3.93
4190 4372 4.174411 TCGATTCCTACGATTGGCATAG 57.826 45.455 0.00 0.00 34.85 2.23
4196 4378 3.510360 ACCCCTATCGATTCCTACGATTG 59.490 47.826 1.71 6.48 46.06 2.67
4239 4421 9.813446 GAATTTTAGAGCATTTGATTGAATCCT 57.187 29.630 2.26 0.00 0.00 3.24
4241 4423 9.813446 AGGAATTTTAGAGCATTTGATTGAATC 57.187 29.630 0.00 0.00 0.00 2.52
4244 4426 9.241919 TGTAGGAATTTTAGAGCATTTGATTGA 57.758 29.630 0.00 0.00 0.00 2.57
4245 4427 9.859427 TTGTAGGAATTTTAGAGCATTTGATTG 57.141 29.630 0.00 0.00 0.00 2.67
4288 4470 3.881089 GTGGGGTTATGGAAGGATTTACG 59.119 47.826 0.00 0.00 0.00 3.18
4337 4519 6.931838 TCGAGACTTATTTATCCTTGTGTGT 58.068 36.000 0.00 0.00 0.00 3.72
4339 4521 6.407074 CCCTCGAGACTTATTTATCCTTGTGT 60.407 42.308 15.71 0.00 0.00 3.72
4345 4527 5.786264 TGTCCCTCGAGACTTATTTATCC 57.214 43.478 15.71 0.00 37.66 2.59
4346 4528 6.159988 CCATGTCCCTCGAGACTTATTTATC 58.840 44.000 15.71 0.00 37.66 1.75
4347 4529 6.102897 CCATGTCCCTCGAGACTTATTTAT 57.897 41.667 15.71 0.00 37.66 1.40
4348 4530 5.531122 CCATGTCCCTCGAGACTTATTTA 57.469 43.478 15.71 0.00 37.66 1.40
4349 4531 4.408182 CCATGTCCCTCGAGACTTATTT 57.592 45.455 15.71 0.00 37.66 1.40


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

AutoCloner maintained by Alex Coulton.