Multiple sequence alignment - TraesCS1D01G012300

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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 TraesCS1D01G012300 chr1D 100.000 4010 0 0 1 4010 6474169 6478178 0.000000e+00 7406.0
1 TraesCS1D01G012300 chr1D 91.837 49 3 1 473 521 8232339 8232386 2.590000e-07 67.6
2 TraesCS1D01G012300 chr1B 93.783 3024 148 19 1 2990 8775760 8772743 0.000000e+00 4506.0
3 TraesCS1D01G012300 chr1B 90.566 53 5 0 473 525 40875385 40875437 2.000000e-08 71.3
4 TraesCS1D01G012300 chr1B 93.182 44 3 0 480 523 453340779 453340736 9.300000e-07 65.8
5 TraesCS1D01G012300 chr3D 82.408 1819 246 42 1026 2816 614675446 614677218 0.000000e+00 1519.0
6 TraesCS1D01G012300 chr3D 85.057 87 6 2 840 921 406408173 406408257 9.240000e-12 82.4
7 TraesCS1D01G012300 chrUn 83.728 1647 224 30 992 2615 239739844 239738219 0.000000e+00 1517.0
8 TraesCS1D01G012300 chrUn 82.369 1832 234 50 1032 2820 37812993 37811208 0.000000e+00 1511.0
9 TraesCS1D01G012300 chr5B 96.291 647 22 1 3115 3759 633661205 633661851 0.000000e+00 1061.0
10 TraesCS1D01G012300 chr4B 95.164 641 28 2 3113 3751 58240849 58240210 0.000000e+00 1009.0
11 TraesCS1D01G012300 chr4B 80.702 114 13 5 836 944 396716127 396716236 3.320000e-11 80.5
12 TraesCS1D01G012300 chr2B 95.674 601 24 2 3112 3712 64074058 64074656 0.000000e+00 965.0
13 TraesCS1D01G012300 chr2A 77.656 640 114 20 2210 2845 31696228 31696842 2.950000e-96 363.0
14 TraesCS1D01G012300 chr3A 83.708 178 27 1 762 937 739144460 739144283 2.480000e-37 167.0
15 TraesCS1D01G012300 chr3B 83.140 172 24 5 747 914 532637304 532637474 6.940000e-33 152.0
16 TraesCS1D01G012300 chr3B 91.489 47 4 0 479 525 412556648 412556602 9.300000e-07 65.8
17 TraesCS1D01G012300 chr7A 76.410 195 40 5 762 953 42997437 42997246 2.550000e-17 100.0
18 TraesCS1D01G012300 chr6D 80.451 133 13 8 817 944 3346029 3346153 5.520000e-14 89.8
19 TraesCS1D01G012300 chr6D 89.130 46 5 0 480 525 7414519 7414564 1.560000e-04 58.4
20 TraesCS1D01G012300 chr6D 81.707 82 4 9 497 575 10064005 10063932 1.560000e-04 58.4
21 TraesCS1D01G012300 chr6A 81.579 114 13 6 836 944 87253085 87252975 1.990000e-13 87.9
22 TraesCS1D01G012300 chr7B 81.443 97 10 6 817 912 700788323 700788412 5.560000e-09 73.1
23 TraesCS1D01G012300 chr1A 93.182 44 3 0 480 523 438296519 438296476 9.300000e-07 65.8
24 TraesCS1D01G012300 chr6B 100.000 31 0 0 495 525 14312565 14312535 1.560000e-04 58.4


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 TraesCS1D01G012300 chr1D 6474169 6478178 4009 False 7406 7406 100.000 1 4010 1 chr1D.!!$F1 4009
1 TraesCS1D01G012300 chr1B 8772743 8775760 3017 True 4506 4506 93.783 1 2990 1 chr1B.!!$R1 2989
2 TraesCS1D01G012300 chr3D 614675446 614677218 1772 False 1519 1519 82.408 1026 2816 1 chr3D.!!$F2 1790
3 TraesCS1D01G012300 chrUn 239738219 239739844 1625 True 1517 1517 83.728 992 2615 1 chrUn.!!$R2 1623
4 TraesCS1D01G012300 chrUn 37811208 37812993 1785 True 1511 1511 82.369 1032 2820 1 chrUn.!!$R1 1788
5 TraesCS1D01G012300 chr5B 633661205 633661851 646 False 1061 1061 96.291 3115 3759 1 chr5B.!!$F1 644
6 TraesCS1D01G012300 chr4B 58240210 58240849 639 True 1009 1009 95.164 3113 3751 1 chr4B.!!$R1 638
7 TraesCS1D01G012300 chr2B 64074058 64074656 598 False 965 965 95.674 3112 3712 1 chr2B.!!$F1 600
8 TraesCS1D01G012300 chr2A 31696228 31696842 614 False 363 363 77.656 2210 2845 1 chr2A.!!$F1 635

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
195 197 1.068541 GGAGGGCAAACGTGTCATTTC 60.069 52.381 0.00 0.0 0.00 2.17 F
1186 1225 0.250727 CAAAGGAGAAGGGCGTCCAA 60.251 55.000 9.71 0.0 35.02 3.53 F
1855 1900 0.105964 TAAAGCAGTATGGCGCGGAT 59.894 50.000 8.83 0.0 39.27 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1879 0.105964 TATCCGCGCCATACTGCTTT 59.894 50.0 0.0 0.0 0.0 3.51 R
2230 2293 0.253044 TGGCCAGCTTGTACATCTCC 59.747 55.0 0.0 0.0 0.0 3.71 R
3529 3607 0.318360 GGTTTGTAGTTTGGTGGCGC 60.318 55.0 0.0 0.0 0.0 6.53 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
28 29 2.959507 TTGCTATCTGTTGCTAGCGA 57.040 45.000 10.77 5.12 42.62 4.93
44 45 5.572511 TGCTAGCGAATTAACAATTTTGCTG 59.427 36.000 10.77 10.57 40.64 4.41
45 46 5.004726 GCTAGCGAATTAACAATTTTGCTGG 59.995 40.000 16.26 14.96 40.64 4.85
64 65 4.688879 GCTGGTTTACAAAATTACTTGCCC 59.311 41.667 0.00 0.00 0.00 5.36
87 88 2.868583 CAGGTCCAAGCTATTGATGACG 59.131 50.000 0.00 0.00 38.83 4.35
96 97 5.339008 AGCTATTGATGACGACCAGTAAA 57.661 39.130 0.00 0.00 0.00 2.01
100 101 6.198591 GCTATTGATGACGACCAGTAAACTAC 59.801 42.308 0.00 0.00 0.00 2.73
102 103 5.654603 TGATGACGACCAGTAAACTACAT 57.345 39.130 0.00 0.00 0.00 2.29
135 137 2.176045 TCTCAGTCCGCTGGAAACATA 58.824 47.619 0.00 0.00 42.78 2.29
142 144 3.168773 GCTGGAAACATAAGGGCGA 57.831 52.632 0.00 0.00 41.51 5.54
169 171 5.839063 AGGGCATGCTTAGTACTACTATTCA 59.161 40.000 18.92 0.00 29.64 2.57
195 197 1.068541 GGAGGGCAAACGTGTCATTTC 60.069 52.381 0.00 0.00 0.00 2.17
200 202 2.286772 GGCAAACGTGTCATTTCGTTCT 60.287 45.455 3.60 0.00 46.95 3.01
260 262 9.128107 CTTACAATTTATCCACACAACACATTC 57.872 33.333 0.00 0.00 0.00 2.67
326 328 9.440761 AGTAAGGTTCTATTCTATCATCACCTT 57.559 33.333 5.63 5.63 44.01 3.50
327 329 9.482627 GTAAGGTTCTATTCTATCATCACCTTG 57.517 37.037 9.96 0.00 42.20 3.61
330 332 8.592809 AGGTTCTATTCTATCATCACCTTGATC 58.407 37.037 0.00 0.00 34.28 2.92
430 432 7.646654 TTCTGGGGGAATATTGATCTTATGA 57.353 36.000 0.00 0.00 0.00 2.15
459 461 1.537562 GGTAACAAGATACTCCCGCCG 60.538 57.143 0.00 0.00 0.00 6.46
492 494 6.986904 AAAAAGAAGATACTCCGTCCATTC 57.013 37.500 0.00 0.00 0.00 2.67
493 495 5.941555 AAAGAAGATACTCCGTCCATTCT 57.058 39.130 0.00 0.00 0.00 2.40
579 581 7.229907 GGGAGTAGTTGTTGGATTTAAACTTGA 59.770 37.037 0.00 0.00 34.76 3.02
621 623 1.212688 TGTTCCATGATTGGCGGATCT 59.787 47.619 0.00 0.00 43.29 2.75
682 684 6.839124 AACAATCCTATGTGAATTTGCTGA 57.161 33.333 0.00 0.00 32.81 4.26
683 685 6.199937 ACAATCCTATGTGAATTTGCTGAC 57.800 37.500 0.00 0.00 30.82 3.51
684 686 5.948162 ACAATCCTATGTGAATTTGCTGACT 59.052 36.000 0.00 0.00 30.82 3.41
718 721 5.376625 AGAACAGAAGGACACTTATTTGCA 58.623 37.500 0.00 0.00 36.97 4.08
720 723 5.695851 ACAGAAGGACACTTATTTGCAAG 57.304 39.130 0.00 0.00 36.97 4.01
741 744 7.877612 TGCAAGTGAATAACATACAGAGAAGAA 59.122 33.333 0.00 0.00 0.00 2.52
762 765 7.588497 AGAATCTCAACAAAAATATAGGGCC 57.412 36.000 0.00 0.00 0.00 5.80
777 780 1.819632 GGCCCTGATAAGTGCCACG 60.820 63.158 0.00 0.00 43.46 4.94
792 795 3.230540 ACGCACGTGACATGAACG 58.769 55.556 22.23 19.30 46.32 3.95
805 808 1.794701 CATGAACGCATGGTATCTCCG 59.205 52.381 0.00 0.00 46.45 4.63
808 811 2.102420 TGAACGCATGGTATCTCCGAAT 59.898 45.455 0.00 0.00 39.52 3.34
810 813 1.412710 ACGCATGGTATCTCCGAATGT 59.587 47.619 0.00 0.00 39.52 2.71
926 952 6.986424 AACTTTAGTTGCAATAAAGAACGC 57.014 33.333 28.62 8.44 40.95 4.84
933 959 1.740025 GCAATAAAGAACGCCAGAGCT 59.260 47.619 0.00 0.00 36.60 4.09
934 960 2.476854 GCAATAAAGAACGCCAGAGCTG 60.477 50.000 0.00 0.00 36.60 4.24
945 971 3.140576 CAGAGCTGGAGTGCTTCAG 57.859 57.895 3.17 3.17 44.17 3.02
962 988 6.371548 GTGCTTCAGGTCACACTTATCATTTA 59.628 38.462 0.00 0.00 33.63 1.40
964 990 6.037610 GCTTCAGGTCACACTTATCATTTAGG 59.962 42.308 0.00 0.00 0.00 2.69
1030 1063 1.523938 GATGGCCGCCCAGAACTAC 60.524 63.158 7.03 0.00 46.24 2.73
1186 1225 0.250727 CAAAGGAGAAGGGCGTCCAA 60.251 55.000 9.71 0.00 35.02 3.53
1255 1294 2.508891 GCTCCACGTCGCATTCGAG 61.509 63.158 0.00 0.00 46.46 4.04
1570 1612 2.830104 CTGGACATCATCATCGAGCAA 58.170 47.619 0.00 0.00 0.00 3.91
1753 1795 0.538977 ACTGGCTCAAGTTGCTGCAT 60.539 50.000 17.88 0.00 0.00 3.96
1795 1837 0.809385 CGACCACGGACATAGTGTCT 59.191 55.000 9.66 0.00 46.19 3.41
1855 1900 0.105964 TAAAGCAGTATGGCGCGGAT 59.894 50.000 8.83 0.00 39.27 4.18
1942 1987 3.063704 ATGTCGGTGGCGTACGGA 61.064 61.111 18.39 1.88 36.42 4.69
2006 2051 2.817834 GCGAGTACAATGGCGGCA 60.818 61.111 16.34 16.34 0.00 5.69
2008 2053 1.934463 CGAGTACAATGGCGGCATC 59.066 57.895 25.97 12.57 0.00 3.91
2230 2293 1.746615 CATCCAGAAGCACGGGGTG 60.747 63.158 0.00 0.04 38.47 4.61
2431 2494 0.746659 TCATCGACATCACCTGCGAT 59.253 50.000 0.00 0.00 41.52 4.58
2434 2497 1.389555 TCGACATCACCTGCGATAGT 58.610 50.000 0.00 0.00 39.35 2.12
2503 2578 2.681778 CCGCTGGACCCTGAGAGT 60.682 66.667 0.00 0.00 0.00 3.24
2662 2740 2.202932 GACATCGCCACAGCCGAT 60.203 61.111 0.00 0.00 34.17 4.18
2665 2743 2.029666 ATCGCCACAGCCGATAGC 59.970 61.111 0.00 0.00 44.25 2.97
2855 2933 1.865340 GAACCGCCTAATTCCATCGTC 59.135 52.381 0.00 0.00 0.00 4.20
2874 2952 3.695060 CGTCACTCCTATTCCACACTAGT 59.305 47.826 0.00 0.00 0.00 2.57
2876 2954 5.220815 CGTCACTCCTATTCCACACTAGTAC 60.221 48.000 0.00 0.00 0.00 2.73
2881 2959 5.692928 TCCTATTCCACACTAGTACTCCTC 58.307 45.833 0.00 0.00 0.00 3.71
2887 2965 3.949113 CCACACTAGTACTCCTCTTCTCC 59.051 52.174 0.00 0.00 0.00 3.71
2958 3036 0.389025 GTTGGACAGGCTTTGGGTTG 59.611 55.000 0.00 0.00 0.00 3.77
2970 3048 2.988684 GGGTTGCGCCATTCCACA 60.989 61.111 4.18 0.00 39.65 4.17
2971 3049 2.258286 GGTTGCGCCATTCCACAC 59.742 61.111 4.18 0.00 37.17 3.82
2990 3068 2.548057 CACCGTGCTTTGCTCTTTTCTA 59.452 45.455 0.00 0.00 0.00 2.10
2991 3069 3.189287 CACCGTGCTTTGCTCTTTTCTAT 59.811 43.478 0.00 0.00 0.00 1.98
2992 3070 3.437049 ACCGTGCTTTGCTCTTTTCTATC 59.563 43.478 0.00 0.00 0.00 2.08
2993 3071 3.484229 CCGTGCTTTGCTCTTTTCTATCG 60.484 47.826 0.00 0.00 0.00 2.92
2994 3072 3.367932 CGTGCTTTGCTCTTTTCTATCGA 59.632 43.478 0.00 0.00 0.00 3.59
2995 3073 4.642953 GTGCTTTGCTCTTTTCTATCGAC 58.357 43.478 0.00 0.00 0.00 4.20
2996 3074 3.367932 TGCTTTGCTCTTTTCTATCGACG 59.632 43.478 0.00 0.00 0.00 5.12
2997 3075 3.612860 GCTTTGCTCTTTTCTATCGACGA 59.387 43.478 0.00 0.00 0.00 4.20
2998 3076 4.491120 GCTTTGCTCTTTTCTATCGACGAC 60.491 45.833 0.00 0.00 0.00 4.34
2999 3077 2.782163 TGCTCTTTTCTATCGACGACG 58.218 47.619 0.00 0.00 41.26 5.12
3014 3092 5.688823 TCGACGACGACTAAATAAAGTTCA 58.311 37.500 5.75 0.00 43.81 3.18
3015 3093 6.317088 TCGACGACGACTAAATAAAGTTCAT 58.683 36.000 5.75 0.00 43.81 2.57
3016 3094 6.467047 TCGACGACGACTAAATAAAGTTCATC 59.533 38.462 5.75 0.00 43.81 2.92
3017 3095 6.468319 CGACGACGACTAAATAAAGTTCATCT 59.532 38.462 0.00 0.00 42.66 2.90
3018 3096 7.507672 ACGACGACTAAATAAAGTTCATCTG 57.492 36.000 0.00 0.00 0.00 2.90
3019 3097 6.034683 ACGACGACTAAATAAAGTTCATCTGC 59.965 38.462 0.00 0.00 0.00 4.26
3020 3098 6.508088 CGACGACTAAATAAAGTTCATCTGCC 60.508 42.308 0.00 0.00 0.00 4.85
3021 3099 5.291128 ACGACTAAATAAAGTTCATCTGCCG 59.709 40.000 0.00 0.00 0.00 5.69
3022 3100 5.291128 CGACTAAATAAAGTTCATCTGCCGT 59.709 40.000 0.00 0.00 0.00 5.68
3023 3101 6.183360 CGACTAAATAAAGTTCATCTGCCGTT 60.183 38.462 0.00 0.00 0.00 4.44
3024 3102 7.073342 ACTAAATAAAGTTCATCTGCCGTTC 57.927 36.000 0.00 0.00 0.00 3.95
3025 3103 6.879458 ACTAAATAAAGTTCATCTGCCGTTCT 59.121 34.615 0.00 0.00 0.00 3.01
3026 3104 5.803020 AATAAAGTTCATCTGCCGTTCTC 57.197 39.130 0.00 0.00 0.00 2.87
3027 3105 2.839486 AAGTTCATCTGCCGTTCTCA 57.161 45.000 0.00 0.00 0.00 3.27
3028 3106 3.340814 AAGTTCATCTGCCGTTCTCAT 57.659 42.857 0.00 0.00 0.00 2.90
3029 3107 4.471904 AAGTTCATCTGCCGTTCTCATA 57.528 40.909 0.00 0.00 0.00 2.15
3030 3108 4.679373 AGTTCATCTGCCGTTCTCATAT 57.321 40.909 0.00 0.00 0.00 1.78
3031 3109 5.028549 AGTTCATCTGCCGTTCTCATATT 57.971 39.130 0.00 0.00 0.00 1.28
3032 3110 5.431765 AGTTCATCTGCCGTTCTCATATTT 58.568 37.500 0.00 0.00 0.00 1.40
3033 3111 5.882557 AGTTCATCTGCCGTTCTCATATTTT 59.117 36.000 0.00 0.00 0.00 1.82
3034 3112 6.375455 AGTTCATCTGCCGTTCTCATATTTTT 59.625 34.615 0.00 0.00 0.00 1.94
3035 3113 7.552687 AGTTCATCTGCCGTTCTCATATTTTTA 59.447 33.333 0.00 0.00 0.00 1.52
3036 3114 7.482654 TCATCTGCCGTTCTCATATTTTTAG 57.517 36.000 0.00 0.00 0.00 1.85
3037 3115 7.047891 TCATCTGCCGTTCTCATATTTTTAGT 58.952 34.615 0.00 0.00 0.00 2.24
3038 3116 6.662414 TCTGCCGTTCTCATATTTTTAGTG 57.338 37.500 0.00 0.00 0.00 2.74
3039 3117 5.064707 TCTGCCGTTCTCATATTTTTAGTGC 59.935 40.000 0.00 0.00 0.00 4.40
3040 3118 4.941263 TGCCGTTCTCATATTTTTAGTGCT 59.059 37.500 0.00 0.00 0.00 4.40
3041 3119 6.110033 TGCCGTTCTCATATTTTTAGTGCTA 58.890 36.000 0.00 0.00 0.00 3.49
3042 3120 6.765989 TGCCGTTCTCATATTTTTAGTGCTAT 59.234 34.615 0.00 0.00 0.00 2.97
3043 3121 7.282224 TGCCGTTCTCATATTTTTAGTGCTATT 59.718 33.333 0.00 0.00 0.00 1.73
3044 3122 8.129211 GCCGTTCTCATATTTTTAGTGCTATTT 58.871 33.333 0.00 0.00 0.00 1.40
3097 3175 8.934023 AACAACTAAATAAAGTTCATCTCCCA 57.066 30.769 0.00 0.00 37.61 4.37
3098 3176 8.567285 ACAACTAAATAAAGTTCATCTCCCAG 57.433 34.615 0.00 0.00 37.61 4.45
3099 3177 8.164070 ACAACTAAATAAAGTTCATCTCCCAGT 58.836 33.333 0.00 0.00 37.61 4.00
3100 3178 8.669243 CAACTAAATAAAGTTCATCTCCCAGTC 58.331 37.037 0.00 0.00 37.61 3.51
3101 3179 8.152023 ACTAAATAAAGTTCATCTCCCAGTCT 57.848 34.615 0.00 0.00 0.00 3.24
3102 3180 8.261522 ACTAAATAAAGTTCATCTCCCAGTCTC 58.738 37.037 0.00 0.00 0.00 3.36
3103 3181 6.627087 AATAAAGTTCATCTCCCAGTCTCA 57.373 37.500 0.00 0.00 0.00 3.27
3104 3182 4.982241 AAAGTTCATCTCCCAGTCTCAA 57.018 40.909 0.00 0.00 0.00 3.02
3105 3183 4.982241 AAGTTCATCTCCCAGTCTCAAA 57.018 40.909 0.00 0.00 0.00 2.69
3106 3184 4.550076 AGTTCATCTCCCAGTCTCAAAG 57.450 45.455 0.00 0.00 0.00 2.77
3107 3185 3.906846 AGTTCATCTCCCAGTCTCAAAGT 59.093 43.478 0.00 0.00 0.00 2.66
3108 3186 4.349342 AGTTCATCTCCCAGTCTCAAAGTT 59.651 41.667 0.00 0.00 0.00 2.66
3109 3187 4.277515 TCATCTCCCAGTCTCAAAGTTG 57.722 45.455 0.00 0.00 0.00 3.16
3110 3188 3.648067 TCATCTCCCAGTCTCAAAGTTGT 59.352 43.478 0.00 0.00 0.00 3.32
3111 3189 4.838423 TCATCTCCCAGTCTCAAAGTTGTA 59.162 41.667 0.00 0.00 0.00 2.41
3218 3296 2.036731 TCTGGATCCCGACCACGT 59.963 61.111 9.90 0.00 37.88 4.49
3232 3310 0.593008 CCACGTCGACGAACAGAACA 60.593 55.000 41.52 0.00 43.02 3.18
3477 3555 2.915659 ACGAGCACGGGGAAGACA 60.916 61.111 8.74 0.00 44.46 3.41
3481 3559 3.423154 GCACGGGGAAGACAAGCG 61.423 66.667 0.00 0.00 0.00 4.68
3504 3582 1.648174 GCCGTAGAGCTCCGTAGAC 59.352 63.158 10.93 0.22 0.00 2.59
3542 3620 1.671054 GAGCAGCGCCACCAAACTA 60.671 57.895 2.29 0.00 0.00 2.24
3549 3627 0.040781 CGCCACCAAACTACAAACCG 60.041 55.000 0.00 0.00 0.00 4.44
3611 3689 4.978083 AACAGACCCTACACTATGTACG 57.022 45.455 0.00 0.00 0.00 3.67
3613 3691 2.034305 CAGACCCTACACTATGTACGCC 59.966 54.545 0.00 0.00 0.00 5.68
3712 3790 0.760945 GAGGTGGATCGACTGGGGAT 60.761 60.000 7.84 0.00 0.00 3.85
3714 3792 1.227674 GTGGATCGACTGGGGATGC 60.228 63.158 0.00 0.00 33.40 3.91
3742 3822 1.001760 GCCCCCTCTCCTGTAGACA 59.998 63.158 0.00 0.00 0.00 3.41
3759 3839 1.228429 CAAAGAGGGGAACGGCCAA 60.228 57.895 2.24 0.00 38.95 4.52
3760 3840 1.074951 AAAGAGGGGAACGGCCAAG 59.925 57.895 2.24 0.00 38.95 3.61
3761 3841 2.426305 AAAGAGGGGAACGGCCAAGG 62.426 60.000 2.24 0.00 38.95 3.61
3762 3842 3.647771 GAGGGGAACGGCCAAGGT 61.648 66.667 2.24 0.00 38.95 3.50
3763 3843 3.623703 GAGGGGAACGGCCAAGGTC 62.624 68.421 2.24 0.00 38.95 3.85
3770 3850 2.660802 CGGCCAAGGTCCGTAACT 59.339 61.111 2.24 0.00 41.85 2.24
3771 3851 1.892338 CGGCCAAGGTCCGTAACTA 59.108 57.895 2.24 0.00 41.85 2.24
3772 3852 0.247185 CGGCCAAGGTCCGTAACTAA 59.753 55.000 2.24 0.00 41.85 2.24
3773 3853 1.338011 CGGCCAAGGTCCGTAACTAAA 60.338 52.381 2.24 0.00 41.85 1.85
3774 3854 2.781923 GGCCAAGGTCCGTAACTAAAA 58.218 47.619 0.00 0.00 0.00 1.52
3775 3855 2.745821 GGCCAAGGTCCGTAACTAAAAG 59.254 50.000 0.00 0.00 0.00 2.27
3776 3856 3.405831 GCCAAGGTCCGTAACTAAAAGT 58.594 45.455 0.00 0.00 0.00 2.66
3777 3857 4.563374 GGCCAAGGTCCGTAACTAAAAGTA 60.563 45.833 0.00 0.00 0.00 2.24
3778 3858 4.628766 GCCAAGGTCCGTAACTAAAAGTAG 59.371 45.833 0.00 0.00 0.00 2.57
3779 3859 5.787380 CCAAGGTCCGTAACTAAAAGTAGT 58.213 41.667 0.00 0.00 42.66 2.73
3780 3860 5.866092 CCAAGGTCCGTAACTAAAAGTAGTC 59.134 44.000 0.00 0.00 39.79 2.59
3781 3861 6.294955 CCAAGGTCCGTAACTAAAAGTAGTCT 60.295 42.308 0.00 0.00 39.79 3.24
3782 3862 6.507958 AGGTCCGTAACTAAAAGTAGTCTC 57.492 41.667 0.00 0.00 39.79 3.36
3783 3863 6.006449 AGGTCCGTAACTAAAAGTAGTCTCA 58.994 40.000 0.00 0.00 39.79 3.27
3784 3864 6.491403 AGGTCCGTAACTAAAAGTAGTCTCAA 59.509 38.462 0.00 0.00 39.79 3.02
3785 3865 7.014615 AGGTCCGTAACTAAAAGTAGTCTCAAA 59.985 37.037 0.00 0.00 39.79 2.69
3786 3866 7.328005 GGTCCGTAACTAAAAGTAGTCTCAAAG 59.672 40.741 0.00 0.00 39.79 2.77
3787 3867 7.864882 GTCCGTAACTAAAAGTAGTCTCAAAGT 59.135 37.037 0.00 0.00 39.79 2.66
3788 3868 8.416329 TCCGTAACTAAAAGTAGTCTCAAAGTT 58.584 33.333 0.00 0.00 39.79 2.66
3789 3869 8.485591 CCGTAACTAAAAGTAGTCTCAAAGTTG 58.514 37.037 0.00 0.00 39.79 3.16
3790 3870 9.028185 CGTAACTAAAAGTAGTCTCAAAGTTGT 57.972 33.333 0.00 0.00 39.79 3.32
3798 3878 9.708092 AAAGTAGTCTCAAAGTTGTATCTTACC 57.292 33.333 0.00 0.00 0.00 2.85
3799 3879 8.653036 AGTAGTCTCAAAGTTGTATCTTACCT 57.347 34.615 0.00 0.00 0.00 3.08
3800 3880 9.091220 AGTAGTCTCAAAGTTGTATCTTACCTT 57.909 33.333 0.00 0.00 0.00 3.50
3801 3881 9.708092 GTAGTCTCAAAGTTGTATCTTACCTTT 57.292 33.333 0.00 0.00 0.00 3.11
3802 3882 8.608844 AGTCTCAAAGTTGTATCTTACCTTTG 57.391 34.615 0.00 0.00 38.33 2.77
3803 3883 8.211629 AGTCTCAAAGTTGTATCTTACCTTTGT 58.788 33.333 9.46 0.00 38.24 2.83
3804 3884 9.485206 GTCTCAAAGTTGTATCTTACCTTTGTA 57.515 33.333 9.46 0.00 38.24 2.41
3805 3885 9.485206 TCTCAAAGTTGTATCTTACCTTTGTAC 57.515 33.333 9.46 0.00 38.24 2.90
3806 3886 9.490379 CTCAAAGTTGTATCTTACCTTTGTACT 57.510 33.333 9.46 0.00 38.24 2.73
3807 3887 9.841295 TCAAAGTTGTATCTTACCTTTGTACTT 57.159 29.630 9.46 0.00 38.24 2.24
3903 3983 8.995027 ATCCATCTATCTATCATCCACTCTAC 57.005 38.462 0.00 0.00 0.00 2.59
3904 3984 7.933223 TCCATCTATCTATCATCCACTCTACA 58.067 38.462 0.00 0.00 0.00 2.74
3905 3985 8.052141 TCCATCTATCTATCATCCACTCTACAG 58.948 40.741 0.00 0.00 0.00 2.74
3906 3986 7.833682 CCATCTATCTATCATCCACTCTACAGT 59.166 40.741 0.00 0.00 0.00 3.55
3907 3987 9.241919 CATCTATCTATCATCCACTCTACAGTT 57.758 37.037 0.00 0.00 0.00 3.16
3908 3988 9.821240 ATCTATCTATCATCCACTCTACAGTTT 57.179 33.333 0.00 0.00 0.00 2.66
3909 3989 9.290988 TCTATCTATCATCCACTCTACAGTTTC 57.709 37.037 0.00 0.00 0.00 2.78
3910 3990 9.295825 CTATCTATCATCCACTCTACAGTTTCT 57.704 37.037 0.00 0.00 0.00 2.52
3912 3992 9.821240 ATCTATCATCCACTCTACAGTTTCTAT 57.179 33.333 0.00 0.00 0.00 1.98
3913 3993 9.072375 TCTATCATCCACTCTACAGTTTCTATG 57.928 37.037 0.00 0.00 0.00 2.23
3914 3994 5.907207 TCATCCACTCTACAGTTTCTATGC 58.093 41.667 0.00 0.00 0.00 3.14
3915 3995 4.737855 TCCACTCTACAGTTTCTATGCC 57.262 45.455 0.00 0.00 0.00 4.40
3916 3996 3.130516 TCCACTCTACAGTTTCTATGCCG 59.869 47.826 0.00 0.00 0.00 5.69
3917 3997 2.860735 CACTCTACAGTTTCTATGCCGC 59.139 50.000 0.00 0.00 0.00 6.53
3918 3998 2.159085 ACTCTACAGTTTCTATGCCGCC 60.159 50.000 0.00 0.00 0.00 6.13
3919 3999 2.101582 CTCTACAGTTTCTATGCCGCCT 59.898 50.000 0.00 0.00 0.00 5.52
3920 4000 2.100916 TCTACAGTTTCTATGCCGCCTC 59.899 50.000 0.00 0.00 0.00 4.70
3921 4001 0.460284 ACAGTTTCTATGCCGCCTCG 60.460 55.000 0.00 0.00 0.00 4.63
3922 4002 0.179111 CAGTTTCTATGCCGCCTCGA 60.179 55.000 0.00 0.00 0.00 4.04
3923 4003 0.103208 AGTTTCTATGCCGCCTCGAG 59.897 55.000 5.13 5.13 0.00 4.04
3924 4004 1.227263 TTTCTATGCCGCCTCGAGC 60.227 57.895 6.99 1.53 38.52 5.03
3925 4005 2.644555 TTTCTATGCCGCCTCGAGCC 62.645 60.000 6.99 0.00 38.78 4.70
3926 4006 3.610669 CTATGCCGCCTCGAGCCT 61.611 66.667 6.99 0.00 38.78 4.58
3927 4007 3.565910 CTATGCCGCCTCGAGCCTC 62.566 68.421 6.99 0.00 38.78 4.70
3937 4017 3.741029 TCGAGCCTCGAATTTCAGG 57.259 52.632 15.58 9.32 46.90 3.86
3942 4022 2.101700 CCTCGAATTTCAGGCCTGC 58.898 57.895 28.91 12.59 0.00 4.85
3943 4023 1.709147 CCTCGAATTTCAGGCCTGCG 61.709 60.000 28.91 23.76 0.00 5.18
3944 4024 1.709147 CTCGAATTTCAGGCCTGCGG 61.709 60.000 28.91 14.27 0.00 5.69
3945 4025 2.040544 CGAATTTCAGGCCTGCGGT 61.041 57.895 28.91 12.70 0.00 5.68
3946 4026 1.508088 GAATTTCAGGCCTGCGGTG 59.492 57.895 28.91 5.03 0.00 4.94
3947 4027 1.937546 GAATTTCAGGCCTGCGGTGG 61.938 60.000 28.91 3.05 0.00 4.61
3969 4049 4.489771 GGGCTGGGGGTGATCGTG 62.490 72.222 0.00 0.00 0.00 4.35
3970 4050 4.489771 GGCTGGGGGTGATCGTGG 62.490 72.222 0.00 0.00 0.00 4.94
3971 4051 4.489771 GCTGGGGGTGATCGTGGG 62.490 72.222 0.00 0.00 0.00 4.61
3972 4052 4.489771 CTGGGGGTGATCGTGGGC 62.490 72.222 0.00 0.00 0.00 5.36
3976 4056 4.041762 GGGTGATCGTGGGCCCAA 62.042 66.667 30.64 13.71 40.76 4.12
3977 4057 2.750237 GGTGATCGTGGGCCCAAC 60.750 66.667 30.64 21.21 0.00 3.77
3978 4058 2.351276 GTGATCGTGGGCCCAACT 59.649 61.111 30.64 14.65 0.00 3.16
3979 4059 2.040544 GTGATCGTGGGCCCAACTG 61.041 63.158 30.64 20.05 0.00 3.16
3980 4060 2.351276 GATCGTGGGCCCAACTGT 59.649 61.111 30.64 13.50 0.00 3.55
3981 4061 1.195442 TGATCGTGGGCCCAACTGTA 61.195 55.000 30.64 10.95 0.00 2.74
3982 4062 0.035820 GATCGTGGGCCCAACTGTAA 60.036 55.000 30.64 8.86 0.00 2.41
3983 4063 0.035439 ATCGTGGGCCCAACTGTAAG 60.035 55.000 30.64 12.03 42.29 2.34
3984 4064 1.122632 TCGTGGGCCCAACTGTAAGA 61.123 55.000 30.64 14.24 37.43 2.10
3985 4065 0.035439 CGTGGGCCCAACTGTAAGAT 60.035 55.000 30.64 0.00 37.43 2.40
3986 4066 1.463674 GTGGGCCCAACTGTAAGATG 58.536 55.000 30.64 0.00 36.36 2.90
3987 4067 1.072266 TGGGCCCAACTGTAAGATGT 58.928 50.000 26.33 0.00 34.53 3.06
3988 4068 1.271871 TGGGCCCAACTGTAAGATGTG 60.272 52.381 26.33 0.00 34.53 3.21
3989 4069 1.271926 GGGCCCAACTGTAAGATGTGT 60.272 52.381 19.95 0.00 34.53 3.72
3990 4070 1.812571 GGCCCAACTGTAAGATGTGTG 59.187 52.381 0.00 0.00 34.53 3.82
3991 4071 1.200020 GCCCAACTGTAAGATGTGTGC 59.800 52.381 0.00 0.00 34.53 4.57
3992 4072 2.783135 CCCAACTGTAAGATGTGTGCT 58.217 47.619 0.00 0.00 34.53 4.40
3993 4073 3.149196 CCCAACTGTAAGATGTGTGCTT 58.851 45.455 0.00 0.00 34.53 3.91
3994 4074 3.189287 CCCAACTGTAAGATGTGTGCTTC 59.811 47.826 0.00 0.00 34.53 3.86
3995 4075 3.120546 CCAACTGTAAGATGTGTGCTTCG 60.121 47.826 0.00 0.00 34.53 3.79
3996 4076 3.660501 ACTGTAAGATGTGTGCTTCGA 57.339 42.857 0.00 0.00 37.43 3.71
3997 4077 4.193826 ACTGTAAGATGTGTGCTTCGAT 57.806 40.909 0.00 0.00 37.43 3.59
3998 4078 5.324784 ACTGTAAGATGTGTGCTTCGATA 57.675 39.130 0.00 0.00 37.43 2.92
3999 4079 5.103000 ACTGTAAGATGTGTGCTTCGATAC 58.897 41.667 0.00 0.00 37.43 2.24
4000 4080 5.105716 ACTGTAAGATGTGTGCTTCGATACT 60.106 40.000 0.00 0.00 37.43 2.12
4001 4081 5.720202 TGTAAGATGTGTGCTTCGATACTT 58.280 37.500 0.00 0.00 0.00 2.24
4002 4082 5.805486 TGTAAGATGTGTGCTTCGATACTTC 59.195 40.000 0.00 0.00 0.00 3.01
4003 4083 4.727507 AGATGTGTGCTTCGATACTTCT 57.272 40.909 0.00 0.00 0.00 2.85
4004 4084 5.836821 AGATGTGTGCTTCGATACTTCTA 57.163 39.130 0.00 0.00 0.00 2.10
4005 4085 6.398234 AGATGTGTGCTTCGATACTTCTAT 57.602 37.500 0.00 0.00 0.00 1.98
4006 4086 7.511959 AGATGTGTGCTTCGATACTTCTATA 57.488 36.000 0.00 0.00 0.00 1.31
4007 4087 8.116651 AGATGTGTGCTTCGATACTTCTATAT 57.883 34.615 0.00 0.00 0.00 0.86
4008 4088 8.026026 AGATGTGTGCTTCGATACTTCTATATG 58.974 37.037 0.00 0.00 0.00 1.78
4009 4089 6.447162 TGTGTGCTTCGATACTTCTATATGG 58.553 40.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.190079 TCGCTAGCAACAGATAGCAAAG 58.810 45.455 16.45 0.00 45.12 2.77
11 12 5.234329 TGTTAATTCGCTAGCAACAGATAGC 59.766 40.000 16.45 2.88 42.31 2.97
44 45 3.676172 GCGGGCAAGTAATTTTGTAAACC 59.324 43.478 0.00 0.00 0.00 3.27
45 46 4.299978 TGCGGGCAAGTAATTTTGTAAAC 58.700 39.130 0.00 0.00 0.00 2.01
58 59 3.058160 CTTGGACCTGCGGGCAAG 61.058 66.667 12.89 14.26 35.63 4.01
64 65 1.600957 CATCAATAGCTTGGACCTGCG 59.399 52.381 0.00 0.00 32.95 5.18
87 88 7.668525 AAGCACTTAATGTAGTTTACTGGTC 57.331 36.000 0.00 0.00 0.00 4.02
96 97 6.992715 ACTGAGAACAAAGCACTTAATGTAGT 59.007 34.615 0.00 0.00 0.00 2.73
100 101 5.615544 CGGACTGAGAACAAAGCACTTAATG 60.616 44.000 0.00 0.00 0.00 1.90
102 103 3.807622 CGGACTGAGAACAAAGCACTTAA 59.192 43.478 0.00 0.00 0.00 1.85
135 137 4.473520 CATGCCCTCGTCGCCCTT 62.474 66.667 0.00 0.00 0.00 3.95
142 144 1.486211 AGTACTAAGCATGCCCTCGT 58.514 50.000 15.66 9.30 0.00 4.18
169 171 2.752903 GACACGTTTGCCCTCCATATTT 59.247 45.455 0.00 0.00 0.00 1.40
176 178 1.399727 CGAAATGACACGTTTGCCCTC 60.400 52.381 0.00 0.00 0.00 4.30
195 197 6.978659 TGTTATATAGAGGTCTGCAAAGAACG 59.021 38.462 0.00 0.00 0.00 3.95
260 262 3.486841 GCTTGCATATATTTGGTTGTGCG 59.513 43.478 0.00 0.00 35.46 5.34
318 320 7.914346 GCAAAAGAGAAATAGATCAAGGTGATG 59.086 37.037 0.00 0.00 37.20 3.07
321 323 7.120285 TCTGCAAAAGAGAAATAGATCAAGGTG 59.880 37.037 0.00 0.00 0.00 4.00
407 409 7.835728 ATCATAAGATCAATATTCCCCCAGA 57.164 36.000 0.00 0.00 0.00 3.86
408 410 9.979897 TTAATCATAAGATCAATATTCCCCCAG 57.020 33.333 0.00 0.00 31.90 4.45
430 432 7.497909 CGGGAGTATCTTGTTACCACAATTAAT 59.502 37.037 0.00 0.00 42.21 1.40
540 542 5.769162 ACAACTACTCCCTCCGTTCTATATC 59.231 44.000 0.00 0.00 0.00 1.63
541 543 5.703310 ACAACTACTCCCTCCGTTCTATAT 58.297 41.667 0.00 0.00 0.00 0.86
544 546 3.446442 ACAACTACTCCCTCCGTTCTA 57.554 47.619 0.00 0.00 0.00 2.10
545 547 2.299297 CAACAACTACTCCCTCCGTTCT 59.701 50.000 0.00 0.00 0.00 3.01
613 615 2.222027 CCAAATCTACCAAGATCCGCC 58.778 52.381 0.00 0.00 41.81 6.13
621 623 3.709653 AGATCCTACGCCAAATCTACCAA 59.290 43.478 0.00 0.00 0.00 3.67
692 695 7.665559 TGCAAATAAGTGTCCTTCTGTTCTTAT 59.334 33.333 0.00 0.00 32.02 1.73
741 744 5.835280 CAGGGCCCTATATTTTTGTTGAGAT 59.165 40.000 28.13 0.00 0.00 2.75
762 765 4.615901 TGCGTGGCACTTATCAGG 57.384 55.556 16.72 0.00 31.71 3.86
777 780 0.790495 CATGCGTTCATGTCACGTGC 60.790 55.000 11.67 6.86 43.85 5.34
792 795 4.900635 AAAACATTCGGAGATACCATGC 57.099 40.909 0.00 0.00 38.90 4.06
818 821 6.473455 GCCATGCTTATGTCACTAAATTTGTC 59.527 38.462 0.00 0.00 0.00 3.18
819 822 6.071447 TGCCATGCTTATGTCACTAAATTTGT 60.071 34.615 0.00 0.00 0.00 2.83
823 826 5.653769 AGTTGCCATGCTTATGTCACTAAAT 59.346 36.000 0.00 0.00 0.00 1.40
879 904 8.885722 GTTGTCATCCGAAATATAAGTAAACCA 58.114 33.333 0.00 0.00 0.00 3.67
885 910 9.886132 ACTAAAGTTGTCATCCGAAATATAAGT 57.114 29.630 0.00 0.00 0.00 2.24
914 940 2.096496 CCAGCTCTGGCGTTCTTTATTG 59.904 50.000 2.59 0.00 44.73 1.90
933 959 0.106708 GTGTGACCTGAAGCACTCCA 59.893 55.000 0.00 0.00 36.05 3.86
934 960 0.394565 AGTGTGACCTGAAGCACTCC 59.605 55.000 0.00 0.00 37.62 3.85
935 961 2.246719 AAGTGTGACCTGAAGCACTC 57.753 50.000 0.00 0.00 40.79 3.51
936 962 3.324846 TGATAAGTGTGACCTGAAGCACT 59.675 43.478 0.00 0.00 43.13 4.40
1022 1055 5.464057 TGTTGTACAATTCACCGTAGTTCTG 59.536 40.000 12.26 0.00 0.00 3.02
1030 1063 3.062099 CGAGGATGTTGTACAATTCACCG 59.938 47.826 12.26 13.54 0.00 4.94
1186 1225 0.833834 AGCGGAGGATCATCGGGAAT 60.834 55.000 15.49 0.00 36.25 3.01
1255 1294 1.885871 GGTGTGCTTGATGGCCTTC 59.114 57.895 11.69 11.69 0.00 3.46
1454 1496 1.977594 GCGTCCTTGTACCCATTGCG 61.978 60.000 0.00 0.00 0.00 4.85
1507 1549 2.832643 TGATGACATTCAGGCCCATT 57.167 45.000 0.00 0.00 0.00 3.16
1684 1726 1.534175 GCCACCTCGTAGATCTTGTCG 60.534 57.143 0.00 4.45 33.89 4.35
1753 1795 0.617935 TCATGGAGCCGATGTGGAAA 59.382 50.000 0.00 0.00 42.00 3.13
1837 1879 0.105964 TATCCGCGCCATACTGCTTT 59.894 50.000 0.00 0.00 0.00 3.51
1855 1900 1.218047 GCAGTCCAGCGTGGTCATA 59.782 57.895 4.33 0.00 39.03 2.15
1909 1954 1.145598 CATGTCGGAGCTGCCTGAT 59.854 57.895 0.00 0.00 0.00 2.90
1942 1987 2.045131 GGACGCGTACTCCTCCAGT 61.045 63.158 15.95 0.00 39.41 4.00
2006 2051 1.778383 ACAACACAGGGTGGGGGAT 60.778 57.895 1.07 0.00 37.94 3.85
2008 2053 2.203480 CACAACACAGGGTGGGGG 60.203 66.667 1.07 0.00 37.94 5.40
2230 2293 0.253044 TGGCCAGCTTGTACATCTCC 59.747 55.000 0.00 0.00 0.00 3.71
2431 2494 3.244078 ACTTGTCAATCTTGCCGTCACTA 60.244 43.478 0.00 0.00 0.00 2.74
2434 2497 2.254546 ACTTGTCAATCTTGCCGTCA 57.745 45.000 0.00 0.00 0.00 4.35
2503 2578 4.137872 GCCACGTAGTAGCCGCCA 62.138 66.667 0.00 0.00 39.78 5.69
2794 2872 1.009675 AGGTAGGGCATGGAGGTAAGT 59.990 52.381 0.00 0.00 0.00 2.24
2855 2933 5.299782 GGAGTACTAGTGTGGAATAGGAGTG 59.700 48.000 5.39 0.00 0.00 3.51
2874 2952 3.544698 AAGGTGTGGAGAAGAGGAGTA 57.455 47.619 0.00 0.00 0.00 2.59
2876 2954 3.778954 AAAAGGTGTGGAGAAGAGGAG 57.221 47.619 0.00 0.00 0.00 3.69
2958 3036 4.101790 CACGGTGTGGAATGGCGC 62.102 66.667 0.00 0.00 0.00 6.53
2970 3048 1.680338 AGAAAAGAGCAAAGCACGGT 58.320 45.000 0.00 0.00 0.00 4.83
2971 3049 3.484229 CGATAGAAAAGAGCAAAGCACGG 60.484 47.826 0.00 0.00 39.76 4.94
2991 3069 5.688823 TGAACTTTATTTAGTCGTCGTCGA 58.311 37.500 0.00 0.00 44.12 4.20
2992 3070 5.980324 TGAACTTTATTTAGTCGTCGTCG 57.020 39.130 0.00 0.00 38.55 5.12
2993 3071 7.601775 CAGATGAACTTTATTTAGTCGTCGTC 58.398 38.462 0.00 0.00 0.00 4.20
2994 3072 6.034683 GCAGATGAACTTTATTTAGTCGTCGT 59.965 38.462 0.00 0.00 0.00 4.34
2995 3073 6.403615 GCAGATGAACTTTATTTAGTCGTCG 58.596 40.000 0.00 0.00 0.00 5.12
2996 3074 6.508088 CGGCAGATGAACTTTATTTAGTCGTC 60.508 42.308 0.00 0.00 0.00 4.20
2997 3075 5.291128 CGGCAGATGAACTTTATTTAGTCGT 59.709 40.000 0.00 0.00 0.00 4.34
2998 3076 5.291128 ACGGCAGATGAACTTTATTTAGTCG 59.709 40.000 0.00 0.00 0.00 4.18
2999 3077 6.663944 ACGGCAGATGAACTTTATTTAGTC 57.336 37.500 0.00 0.00 0.00 2.59
3000 3078 6.879458 AGAACGGCAGATGAACTTTATTTAGT 59.121 34.615 0.00 0.00 0.00 2.24
3001 3079 7.064609 TGAGAACGGCAGATGAACTTTATTTAG 59.935 37.037 0.00 0.00 0.00 1.85
3002 3080 6.876789 TGAGAACGGCAGATGAACTTTATTTA 59.123 34.615 0.00 0.00 0.00 1.40
3003 3081 5.705441 TGAGAACGGCAGATGAACTTTATTT 59.295 36.000 0.00 0.00 0.00 1.40
3004 3082 5.245531 TGAGAACGGCAGATGAACTTTATT 58.754 37.500 0.00 0.00 0.00 1.40
3005 3083 4.832248 TGAGAACGGCAGATGAACTTTAT 58.168 39.130 0.00 0.00 0.00 1.40
3006 3084 4.265904 TGAGAACGGCAGATGAACTTTA 57.734 40.909 0.00 0.00 0.00 1.85
3007 3085 3.126001 TGAGAACGGCAGATGAACTTT 57.874 42.857 0.00 0.00 0.00 2.66
3008 3086 2.839486 TGAGAACGGCAGATGAACTT 57.161 45.000 0.00 0.00 0.00 2.66
3009 3087 4.679373 ATATGAGAACGGCAGATGAACT 57.321 40.909 0.00 0.00 0.00 3.01
3010 3088 5.741388 AAATATGAGAACGGCAGATGAAC 57.259 39.130 0.00 0.00 0.00 3.18
3011 3089 6.757897 AAAAATATGAGAACGGCAGATGAA 57.242 33.333 0.00 0.00 0.00 2.57
3012 3090 7.011389 CACTAAAAATATGAGAACGGCAGATGA 59.989 37.037 0.00 0.00 0.00 2.92
3013 3091 7.128331 CACTAAAAATATGAGAACGGCAGATG 58.872 38.462 0.00 0.00 0.00 2.90
3014 3092 6.238484 GCACTAAAAATATGAGAACGGCAGAT 60.238 38.462 0.00 0.00 0.00 2.90
3015 3093 5.064707 GCACTAAAAATATGAGAACGGCAGA 59.935 40.000 0.00 0.00 0.00 4.26
3016 3094 5.065218 AGCACTAAAAATATGAGAACGGCAG 59.935 40.000 0.00 0.00 0.00 4.85
3017 3095 4.941263 AGCACTAAAAATATGAGAACGGCA 59.059 37.500 0.00 0.00 0.00 5.69
3018 3096 5.485662 AGCACTAAAAATATGAGAACGGC 57.514 39.130 0.00 0.00 0.00 5.68
3072 3150 8.934023 TGGGAGATGAACTTTATTTAGTTGTT 57.066 30.769 0.00 0.00 38.43 2.83
3073 3151 8.164070 ACTGGGAGATGAACTTTATTTAGTTGT 58.836 33.333 0.00 0.00 38.43 3.32
3074 3152 8.567285 ACTGGGAGATGAACTTTATTTAGTTG 57.433 34.615 0.00 0.00 38.43 3.16
3075 3153 8.606830 AGACTGGGAGATGAACTTTATTTAGTT 58.393 33.333 0.00 0.00 40.92 2.24
3076 3154 8.152023 AGACTGGGAGATGAACTTTATTTAGT 57.848 34.615 0.00 0.00 0.00 2.24
3077 3155 8.260818 TGAGACTGGGAGATGAACTTTATTTAG 58.739 37.037 0.00 0.00 0.00 1.85
3078 3156 8.146053 TGAGACTGGGAGATGAACTTTATTTA 57.854 34.615 0.00 0.00 0.00 1.40
3079 3157 7.020827 TGAGACTGGGAGATGAACTTTATTT 57.979 36.000 0.00 0.00 0.00 1.40
3080 3158 6.627087 TGAGACTGGGAGATGAACTTTATT 57.373 37.500 0.00 0.00 0.00 1.40
3081 3159 6.627087 TTGAGACTGGGAGATGAACTTTAT 57.373 37.500 0.00 0.00 0.00 1.40
3082 3160 6.043243 ACTTTGAGACTGGGAGATGAACTTTA 59.957 38.462 0.00 0.00 0.00 1.85
3083 3161 4.982241 TTGAGACTGGGAGATGAACTTT 57.018 40.909 0.00 0.00 0.00 2.66
3084 3162 4.349342 ACTTTGAGACTGGGAGATGAACTT 59.651 41.667 0.00 0.00 0.00 2.66
3085 3163 3.906846 ACTTTGAGACTGGGAGATGAACT 59.093 43.478 0.00 0.00 0.00 3.01
3086 3164 4.278975 ACTTTGAGACTGGGAGATGAAC 57.721 45.455 0.00 0.00 0.00 3.18
3087 3165 4.103153 ACAACTTTGAGACTGGGAGATGAA 59.897 41.667 0.00 0.00 0.00 2.57
3088 3166 3.648067 ACAACTTTGAGACTGGGAGATGA 59.352 43.478 0.00 0.00 0.00 2.92
3089 3167 4.013267 ACAACTTTGAGACTGGGAGATG 57.987 45.455 0.00 0.00 0.00 2.90
3090 3168 5.723887 AGATACAACTTTGAGACTGGGAGAT 59.276 40.000 0.00 0.00 0.00 2.75
3091 3169 5.087323 AGATACAACTTTGAGACTGGGAGA 58.913 41.667 0.00 0.00 0.00 3.71
3092 3170 5.413309 AGATACAACTTTGAGACTGGGAG 57.587 43.478 0.00 0.00 0.00 4.30
3093 3171 5.825593 AAGATACAACTTTGAGACTGGGA 57.174 39.130 0.00 0.00 0.00 4.37
3094 3172 6.884280 AAAAGATACAACTTTGAGACTGGG 57.116 37.500 0.00 0.00 39.57 4.45
3179 3257 2.227149 GGGACCCGTGTGTAATTTTCAC 59.773 50.000 0.00 0.00 36.48 3.18
3218 3296 0.937699 CGGCTTGTTCTGTTCGTCGA 60.938 55.000 0.00 0.00 0.00 4.20
3490 3568 0.622136 TGGTGGTCTACGGAGCTCTA 59.378 55.000 14.64 0.00 40.29 2.43
3529 3607 0.318360 GGTTTGTAGTTTGGTGGCGC 60.318 55.000 0.00 0.00 0.00 6.53
3535 3613 1.070175 CGCAGTCGGTTTGTAGTTTGG 60.070 52.381 0.00 0.00 0.00 3.28
3585 3663 1.064825 AGTGTAGGGTCTGTTTGGGG 58.935 55.000 0.00 0.00 0.00 4.96
3712 3790 2.361104 GGGGGCGATTTGTGAGCA 60.361 61.111 0.00 0.00 0.00 4.26
3714 3792 0.462759 GAGAGGGGGCGATTTGTGAG 60.463 60.000 0.00 0.00 0.00 3.51
3742 3822 1.074951 CTTGGCCGTTCCCCTCTTT 59.925 57.895 0.00 0.00 0.00 2.52
3759 3839 6.006449 TGAGACTACTTTTAGTTACGGACCT 58.994 40.000 0.00 0.00 38.77 3.85
3760 3840 6.259550 TGAGACTACTTTTAGTTACGGACC 57.740 41.667 0.00 0.00 38.77 4.46
3761 3841 7.864882 ACTTTGAGACTACTTTTAGTTACGGAC 59.135 37.037 0.00 0.00 38.77 4.79
3762 3842 7.945134 ACTTTGAGACTACTTTTAGTTACGGA 58.055 34.615 0.00 0.00 38.77 4.69
3763 3843 8.485591 CAACTTTGAGACTACTTTTAGTTACGG 58.514 37.037 0.00 0.00 38.77 4.02
3764 3844 9.028185 ACAACTTTGAGACTACTTTTAGTTACG 57.972 33.333 0.00 0.00 38.77 3.18
3772 3852 9.708092 GGTAAGATACAACTTTGAGACTACTTT 57.292 33.333 0.00 0.00 0.00 2.66
3773 3853 9.091220 AGGTAAGATACAACTTTGAGACTACTT 57.909 33.333 0.00 0.00 0.00 2.24
3774 3854 8.653036 AGGTAAGATACAACTTTGAGACTACT 57.347 34.615 0.00 0.00 0.00 2.57
3775 3855 9.708092 AAAGGTAAGATACAACTTTGAGACTAC 57.292 33.333 0.00 0.00 30.86 2.73
3776 3856 9.706691 CAAAGGTAAGATACAACTTTGAGACTA 57.293 33.333 6.98 0.00 46.58 2.59
3777 3857 8.211629 ACAAAGGTAAGATACAACTTTGAGACT 58.788 33.333 17.22 0.00 46.58 3.24
3778 3858 8.379457 ACAAAGGTAAGATACAACTTTGAGAC 57.621 34.615 17.22 0.00 46.58 3.36
3779 3859 9.485206 GTACAAAGGTAAGATACAACTTTGAGA 57.515 33.333 17.22 4.59 46.58 3.27
3780 3860 9.490379 AGTACAAAGGTAAGATACAACTTTGAG 57.510 33.333 17.22 0.00 46.58 3.02
3781 3861 9.841295 AAGTACAAAGGTAAGATACAACTTTGA 57.159 29.630 17.22 1.75 46.58 2.69
3878 3958 8.564370 TGTAGAGTGGATGATAGATAGATGGAT 58.436 37.037 0.00 0.00 0.00 3.41
3879 3959 7.933223 TGTAGAGTGGATGATAGATAGATGGA 58.067 38.462 0.00 0.00 0.00 3.41
3880 3960 7.833682 ACTGTAGAGTGGATGATAGATAGATGG 59.166 40.741 0.00 0.00 0.00 3.51
3881 3961 8.806429 ACTGTAGAGTGGATGATAGATAGATG 57.194 38.462 0.00 0.00 0.00 2.90
3882 3962 9.821240 AAACTGTAGAGTGGATGATAGATAGAT 57.179 33.333 0.00 0.00 30.61 1.98
3883 3963 9.290988 GAAACTGTAGAGTGGATGATAGATAGA 57.709 37.037 0.00 0.00 30.61 1.98
3884 3964 9.295825 AGAAACTGTAGAGTGGATGATAGATAG 57.704 37.037 0.00 0.00 30.61 2.08
3886 3966 9.821240 ATAGAAACTGTAGAGTGGATGATAGAT 57.179 33.333 0.00 0.00 30.61 1.98
3887 3967 9.072375 CATAGAAACTGTAGAGTGGATGATAGA 57.928 37.037 0.00 0.00 30.61 1.98
3888 3968 7.812191 GCATAGAAACTGTAGAGTGGATGATAG 59.188 40.741 0.00 0.00 30.61 2.08
3889 3969 7.255977 GGCATAGAAACTGTAGAGTGGATGATA 60.256 40.741 0.00 0.00 30.61 2.15
3890 3970 6.463614 GGCATAGAAACTGTAGAGTGGATGAT 60.464 42.308 0.00 0.00 30.61 2.45
3891 3971 5.163405 GGCATAGAAACTGTAGAGTGGATGA 60.163 44.000 0.00 0.00 30.61 2.92
3892 3972 5.053145 GGCATAGAAACTGTAGAGTGGATG 58.947 45.833 0.00 0.00 30.61 3.51
3893 3973 4.202161 CGGCATAGAAACTGTAGAGTGGAT 60.202 45.833 0.00 0.00 30.61 3.41
3894 3974 3.130516 CGGCATAGAAACTGTAGAGTGGA 59.869 47.826 0.00 0.00 30.61 4.02
3895 3975 3.448686 CGGCATAGAAACTGTAGAGTGG 58.551 50.000 0.00 0.00 30.61 4.00
3896 3976 2.860735 GCGGCATAGAAACTGTAGAGTG 59.139 50.000 0.00 0.00 30.61 3.51
3897 3977 2.159085 GGCGGCATAGAAACTGTAGAGT 60.159 50.000 3.07 0.00 0.00 3.24
3898 3978 2.101582 AGGCGGCATAGAAACTGTAGAG 59.898 50.000 13.08 0.00 0.00 2.43
3899 3979 2.100916 GAGGCGGCATAGAAACTGTAGA 59.899 50.000 13.08 0.00 0.00 2.59
3900 3980 2.474816 GAGGCGGCATAGAAACTGTAG 58.525 52.381 13.08 0.00 0.00 2.74
3901 3981 1.202371 CGAGGCGGCATAGAAACTGTA 60.202 52.381 13.08 0.00 0.00 2.74
3902 3982 0.460284 CGAGGCGGCATAGAAACTGT 60.460 55.000 13.08 0.00 0.00 3.55
3903 3983 0.179111 TCGAGGCGGCATAGAAACTG 60.179 55.000 13.08 0.00 0.00 3.16
3904 3984 0.103208 CTCGAGGCGGCATAGAAACT 59.897 55.000 13.08 0.00 0.00 2.66
3905 3985 1.491505 GCTCGAGGCGGCATAGAAAC 61.492 60.000 15.58 0.00 0.00 2.78
3906 3986 1.227263 GCTCGAGGCGGCATAGAAA 60.227 57.895 15.58 0.00 0.00 2.52
3907 3987 2.417516 GCTCGAGGCGGCATAGAA 59.582 61.111 15.58 0.00 0.00 2.10
3908 3988 3.606662 GGCTCGAGGCGGCATAGA 61.607 66.667 24.18 6.31 42.94 1.98
3909 3989 3.565910 GAGGCTCGAGGCGGCATAG 62.566 68.421 30.50 6.30 46.23 2.23
3910 3990 3.606662 GAGGCTCGAGGCGGCATA 61.607 66.667 30.50 0.00 46.23 3.14
3924 4004 1.709147 CGCAGGCCTGAAATTCGAGG 61.709 60.000 37.21 5.92 0.00 4.63
3925 4005 1.709147 CCGCAGGCCTGAAATTCGAG 61.709 60.000 37.21 17.86 46.14 4.04
3926 4006 1.745115 CCGCAGGCCTGAAATTCGA 60.745 57.895 37.21 0.00 46.14 3.71
3927 4007 2.793946 CCGCAGGCCTGAAATTCG 59.206 61.111 37.21 27.08 46.14 3.34
3952 4032 4.489771 CACGATCACCCCCAGCCC 62.490 72.222 0.00 0.00 0.00 5.19
3953 4033 4.489771 CCACGATCACCCCCAGCC 62.490 72.222 0.00 0.00 0.00 4.85
3954 4034 4.489771 CCCACGATCACCCCCAGC 62.490 72.222 0.00 0.00 0.00 4.85
3955 4035 4.489771 GCCCACGATCACCCCCAG 62.490 72.222 0.00 0.00 0.00 4.45
3959 4039 4.041762 TTGGGCCCACGATCACCC 62.042 66.667 28.70 0.00 43.14 4.61
3960 4040 2.750237 GTTGGGCCCACGATCACC 60.750 66.667 28.70 2.33 0.00 4.02
3961 4041 2.040544 CAGTTGGGCCCACGATCAC 61.041 63.158 28.70 20.58 0.00 3.06
3962 4042 1.195442 TACAGTTGGGCCCACGATCA 61.195 55.000 28.70 6.45 0.00 2.92
3963 4043 0.035820 TTACAGTTGGGCCCACGATC 60.036 55.000 28.70 15.50 0.00 3.69
3964 4044 0.035439 CTTACAGTTGGGCCCACGAT 60.035 55.000 28.70 13.41 0.00 3.73
3965 4045 1.122632 TCTTACAGTTGGGCCCACGA 61.123 55.000 28.70 8.46 0.00 4.35
3966 4046 0.035439 ATCTTACAGTTGGGCCCACG 60.035 55.000 28.70 19.07 0.00 4.94
3967 4047 1.271926 ACATCTTACAGTTGGGCCCAC 60.272 52.381 28.70 20.08 0.00 4.61
3968 4048 1.072266 ACATCTTACAGTTGGGCCCA 58.928 50.000 24.45 24.45 0.00 5.36
3969 4049 1.271926 ACACATCTTACAGTTGGGCCC 60.272 52.381 17.59 17.59 0.00 5.80
3970 4050 1.812571 CACACATCTTACAGTTGGGCC 59.187 52.381 0.00 0.00 0.00 5.80
3971 4051 1.200020 GCACACATCTTACAGTTGGGC 59.800 52.381 0.00 0.00 0.00 5.36
3972 4052 2.783135 AGCACACATCTTACAGTTGGG 58.217 47.619 0.00 0.00 0.00 4.12
3973 4053 3.120546 CGAAGCACACATCTTACAGTTGG 60.121 47.826 0.00 0.00 0.00 3.77
3974 4054 3.740832 TCGAAGCACACATCTTACAGTTG 59.259 43.478 0.00 0.00 0.00 3.16
3975 4055 3.990092 TCGAAGCACACATCTTACAGTT 58.010 40.909 0.00 0.00 0.00 3.16
3976 4056 3.660501 TCGAAGCACACATCTTACAGT 57.339 42.857 0.00 0.00 0.00 3.55
3977 4057 5.344066 AGTATCGAAGCACACATCTTACAG 58.656 41.667 0.00 0.00 0.00 2.74
3978 4058 5.324784 AGTATCGAAGCACACATCTTACA 57.675 39.130 0.00 0.00 0.00 2.41
3979 4059 6.037098 AGAAGTATCGAAGCACACATCTTAC 58.963 40.000 0.00 0.00 0.00 2.34
3980 4060 6.208988 AGAAGTATCGAAGCACACATCTTA 57.791 37.500 0.00 0.00 0.00 2.10
3981 4061 5.078411 AGAAGTATCGAAGCACACATCTT 57.922 39.130 0.00 0.00 0.00 2.40
3982 4062 4.727507 AGAAGTATCGAAGCACACATCT 57.272 40.909 0.00 0.00 0.00 2.90
3983 4063 7.274468 CCATATAGAAGTATCGAAGCACACATC 59.726 40.741 0.00 0.00 0.00 3.06
3984 4064 7.093354 CCATATAGAAGTATCGAAGCACACAT 58.907 38.462 0.00 0.00 0.00 3.21
3985 4065 6.447162 CCATATAGAAGTATCGAAGCACACA 58.553 40.000 0.00 0.00 0.00 3.72
3986 4066 6.936222 CCATATAGAAGTATCGAAGCACAC 57.064 41.667 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.