Multiple sequence alignment - TraesCS4D01G316300

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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 TraesCS4D01G316300 chr4D 100.000 3009 0 0 1 3009 481449355 481446347 0.000000e+00 5557.0
1 TraesCS4D01G316300 chr4D 84.000 100 14 2 2719 2817 430839782 430839684 8.880000e-16 95.3
2 TraesCS4D01G316300 chr4B 89.449 2360 119 53 460 2716 610435927 610433595 0.000000e+00 2859.0
3 TraesCS4D01G316300 chr4B 90.465 430 15 9 1 419 610436349 610435935 7.340000e-151 544.0
4 TraesCS4D01G316300 chr4B 78.800 250 46 4 2720 2965 578034259 578034013 8.630000e-36 161.0
5 TraesCS4D01G316300 chr4B 75.648 193 37 10 1492 1679 531094096 531094283 1.490000e-13 87.9
6 TraesCS4D01G316300 chr5A 88.314 1797 95 47 145 1875 661220828 661222575 0.000000e+00 2049.0
7 TraesCS4D01G316300 chr5A 85.286 734 35 34 2039 2716 661222805 661223521 0.000000e+00 689.0
8 TraesCS4D01G316300 chr5B 94.198 293 13 3 2719 3009 106813351 106813061 7.650000e-121 444.0
9 TraesCS4D01G316300 chr5B 88.889 72 8 0 2894 2965 31144533 31144604 4.130000e-14 89.8
10 TraesCS4D01G316300 chr3B 94.178 292 15 2 2719 3009 818886554 818886264 7.650000e-121 444.0
11 TraesCS4D01G316300 chr2D 93.471 291 18 1 2720 3009 570155466 570155176 5.960000e-117 431.0
12 TraesCS4D01G316300 chr2D 77.689 251 47 7 2720 2965 300431134 300431380 8.690000e-31 145.0
13 TraesCS4D01G316300 chr4A 93.151 292 17 2 2720 3009 691295269 691295559 2.770000e-115 425.0
14 TraesCS4D01G316300 chr4A 76.289 194 34 12 1492 1679 34294938 34295125 3.190000e-15 93.5
15 TraesCS4D01G316300 chr7B 86.000 100 12 2 2719 2817 60478820 60478722 4.100000e-19 106.0
16 TraesCS4D01G316300 chr7B 77.160 162 33 4 2720 2879 65320148 65320307 1.150000e-14 91.6
17 TraesCS4D01G316300 chr7B 87.500 72 7 2 2894 2964 32344587 32344517 6.910000e-12 82.4


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 TraesCS4D01G316300 chr4D 481446347 481449355 3008 True 5557.0 5557 100.000 1 3009 1 chr4D.!!$R2 3008
1 TraesCS4D01G316300 chr4B 610433595 610436349 2754 True 1701.5 2859 89.957 1 2716 2 chr4B.!!$R2 2715
2 TraesCS4D01G316300 chr5A 661220828 661223521 2693 False 1369.0 2049 86.800 145 2716 2 chr5A.!!$F1 2571

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
682 721 0.101579 TGCGTCTCACTGTCGTTTCA 59.898 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2384 0.84203 TCCTCTCCCACCAAGCATGT 60.842 55.0 0.0 0.0 0.0 3.21 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 5.050499 GTCGAGCAAATGAGGTATGATGAAG 60.050 44.000 0.00 0.00 0.00 3.02
129 130 4.521075 CGGAGTGCATCAACGGAT 57.479 55.556 0.00 0.00 0.00 4.18
209 210 4.980805 GTCCGGTTCCAGCACGCA 62.981 66.667 0.00 0.00 0.00 5.24
210 211 4.680237 TCCGGTTCCAGCACGCAG 62.680 66.667 0.00 0.00 0.00 5.18
241 244 5.131642 TCTTCCAAGGCATCTCAACTCATAT 59.868 40.000 0.00 0.00 0.00 1.78
242 245 6.327365 TCTTCCAAGGCATCTCAACTCATATA 59.673 38.462 0.00 0.00 0.00 0.86
243 246 6.692849 TCCAAGGCATCTCAACTCATATAT 57.307 37.500 0.00 0.00 0.00 0.86
244 247 7.797121 TCCAAGGCATCTCAACTCATATATA 57.203 36.000 0.00 0.00 0.00 0.86
245 248 7.845037 TCCAAGGCATCTCAACTCATATATAG 58.155 38.462 0.00 0.00 0.00 1.31
246 249 7.455953 TCCAAGGCATCTCAACTCATATATAGT 59.544 37.037 0.00 0.00 0.00 2.12
247 250 8.753133 CCAAGGCATCTCAACTCATATATAGTA 58.247 37.037 0.00 0.00 0.00 1.82
248 251 9.579768 CAAGGCATCTCAACTCATATATAGTAC 57.420 37.037 0.00 0.00 0.00 2.73
249 252 9.540538 AAGGCATCTCAACTCATATATAGTACT 57.459 33.333 0.00 0.00 0.00 2.73
316 328 7.229506 CCCTCTGATCCAAATCAAATAGGTTAC 59.770 40.741 0.00 0.00 41.33 2.50
317 329 7.229506 CCTCTGATCCAAATCAAATAGGTTACC 59.770 40.741 0.00 0.00 41.33 2.85
318 330 7.060421 TCTGATCCAAATCAAATAGGTTACCC 58.940 38.462 0.00 0.00 41.33 3.69
337 349 1.548582 CCATAATCAGGCCCATCCCAC 60.549 57.143 0.00 0.00 34.51 4.61
338 350 0.779997 ATAATCAGGCCCATCCCACC 59.220 55.000 0.00 0.00 34.51 4.61
476 495 1.153686 GGTTTCCCGGTCGTAGCTC 60.154 63.158 0.00 0.00 0.00 4.09
496 515 3.969995 CTAGCCTAGCTCCGTTTCC 57.030 57.895 0.00 0.00 40.44 3.13
600 619 0.729140 CATCACCGCAAGAAAACGCC 60.729 55.000 0.00 0.00 43.02 5.68
648 687 1.239296 ACTCGATCGTCCGGAACACA 61.239 55.000 15.94 0.00 0.00 3.72
673 712 1.607801 TAGCCTGCATGCGTCTCACT 61.608 55.000 14.09 6.93 36.02 3.41
682 721 0.101579 TGCGTCTCACTGTCGTTTCA 59.898 50.000 0.00 0.00 0.00 2.69
733 787 6.362283 ACACTGTTCTTTTGTTTTTCAGTTCG 59.638 34.615 0.00 0.00 33.35 3.95
736 790 5.566016 TGTTCTTTTGTTTTTCAGTTCGTCG 59.434 36.000 0.00 0.00 0.00 5.12
745 799 1.008194 CAGTTCGTCGGGTTCGTGA 60.008 57.895 0.00 0.00 37.69 4.35
752 806 3.694734 TCGTCGGGTTCGTGATAATTAC 58.305 45.455 0.00 0.00 37.69 1.89
763 817 6.947644 TCGTGATAATTACTACTGCTGGTA 57.052 37.500 0.00 0.00 0.00 3.25
799 861 1.270305 ACCAGACAGTGACATTGACCG 60.270 52.381 4.78 0.00 0.00 4.79
836 898 7.147776 GGTGCCCTGATACTACTAGTTTTTAGA 60.148 40.741 0.00 0.00 0.00 2.10
905 968 2.048222 TGCACACGCCACTAGAGC 60.048 61.111 0.00 0.00 37.32 4.09
940 1003 4.032786 GCAACAAAAGAATTGTGTGACACC 59.967 41.667 13.85 0.00 32.73 4.16
950 1013 1.148949 TGTGACACCAGTGCTGCAT 59.851 52.632 5.27 0.00 0.00 3.96
976 1041 3.827784 CGCGCTCGGTTTCACTCG 61.828 66.667 5.56 0.00 0.00 4.18
977 1042 4.135493 GCGCTCGGTTTCACTCGC 62.135 66.667 0.00 0.00 35.82 5.03
978 1043 3.479269 CGCTCGGTTTCACTCGCC 61.479 66.667 0.00 0.00 0.00 5.54
1051 1116 1.068250 CTCGCTAGCCAAGTAGCCC 59.932 63.158 9.66 0.00 42.21 5.19
1054 1119 2.822399 CTAGCCAAGTAGCCCGGG 59.178 66.667 19.09 19.09 0.00 5.73
1152 1217 1.634702 CGAAGAAGAGGAAGAAGGCG 58.365 55.000 0.00 0.00 0.00 5.52
1709 1798 2.657237 CGACCCCACGAAGAAGCT 59.343 61.111 0.00 0.00 35.09 3.74
1746 1835 3.415087 GTCTCCCCTGCAGGCCAT 61.415 66.667 28.39 0.00 0.00 4.40
1747 1836 3.414193 TCTCCCCTGCAGGCCATG 61.414 66.667 28.39 13.54 0.00 3.66
1821 1910 7.267857 ACAAGTTAACTACAGTCCGTAAACTT 58.732 34.615 8.92 0.00 38.39 2.66
1876 1973 1.327460 CGATCCGATGAAAACATGCGT 59.673 47.619 0.00 0.00 0.00 5.24
1919 2016 0.538584 TGATGAGAAGGAGCGTGCAT 59.461 50.000 0.00 0.00 0.00 3.96
1920 2017 0.935898 GATGAGAAGGAGCGTGCATG 59.064 55.000 0.09 0.09 0.00 4.06
1921 2018 0.251354 ATGAGAAGGAGCGTGCATGT 59.749 50.000 7.93 0.00 0.00 3.21
1922 2019 0.671472 TGAGAAGGAGCGTGCATGTG 60.671 55.000 7.93 0.00 0.00 3.21
1923 2020 1.364626 GAGAAGGAGCGTGCATGTGG 61.365 60.000 7.93 0.00 0.00 4.17
1924 2021 3.044059 GAAGGAGCGTGCATGTGGC 62.044 63.158 7.93 0.74 45.13 5.01
1964 2061 2.426738 CGAGCCTGAATCAGTTCTCTCT 59.573 50.000 19.87 5.59 35.33 3.10
2132 2360 0.954449 GCTGATCGCCATGGATCCAG 60.954 60.000 21.33 16.35 41.71 3.86
2156 2384 1.123077 ATCATGAGGCCGAGTTGCTA 58.877 50.000 0.09 0.00 0.00 3.49
2175 2403 0.842030 ACATGCTTGGTGGGAGAGGA 60.842 55.000 4.44 0.00 0.00 3.71
2182 2410 1.613630 GGTGGGAGAGGAAGGCAGA 60.614 63.158 0.00 0.00 0.00 4.26
2300 2536 4.882671 AAACGGGATCGAATTGATTGAG 57.117 40.909 0.00 0.00 37.47 3.02
2308 2552 5.006165 GGATCGAATTGATTGAGTGACTGAC 59.994 44.000 0.00 0.00 37.47 3.51
2312 2556 5.164012 CGAATTGATTGAGTGACTGACTGAC 60.164 44.000 0.00 0.00 33.83 3.51
2321 2565 3.638627 AGTGACTGACTGACTGATGTGAA 59.361 43.478 0.00 0.00 31.75 3.18
2340 2584 4.829518 TGCGTCGGTGCGAGATCG 62.830 66.667 0.00 0.00 36.23 3.69
2341 2585 4.531912 GCGTCGGTGCGAGATCGA 62.532 66.667 6.39 0.00 43.02 3.59
2342 2586 2.328289 CGTCGGTGCGAGATCGAT 59.672 61.111 6.39 0.00 43.02 3.59
2343 2587 1.722852 CGTCGGTGCGAGATCGATC 60.723 63.158 17.91 17.91 43.02 3.69
2388 2632 3.431725 GACTGAAAAGGCCGGCCG 61.432 66.667 38.88 25.78 41.95 6.13
2452 2696 4.620567 CGATCGCAAGGAACATATATCCCA 60.621 45.833 0.26 0.00 37.71 4.37
2467 2711 2.653702 CCATCGATCGCCCCTCTC 59.346 66.667 11.09 0.00 0.00 3.20
2515 2786 0.322187 GTGGTTCGTACCCATGCCTT 60.322 55.000 8.91 0.00 44.35 4.35
2516 2787 0.035820 TGGTTCGTACCCATGCCTTC 60.036 55.000 8.91 0.00 44.35 3.46
2522 2793 0.743345 GTACCCATGCCTTCGTGTCC 60.743 60.000 0.00 0.00 0.00 4.02
2526 2797 0.179084 CCATGCCTTCGTGTCCGTAT 60.179 55.000 0.00 0.00 35.01 3.06
2527 2798 1.067974 CCATGCCTTCGTGTCCGTATA 59.932 52.381 0.00 0.00 35.01 1.47
2716 3005 3.794690 GCAGGATCATGCATGCATC 57.205 52.632 30.07 19.79 44.30 3.91
2717 3006 0.243907 GCAGGATCATGCATGCATCC 59.756 55.000 30.85 30.85 44.30 3.51
2718 3007 0.888619 CAGGATCATGCATGCATCCC 59.111 55.000 32.45 26.93 36.24 3.85
2719 3008 0.481128 AGGATCATGCATGCATCCCA 59.519 50.000 32.45 17.00 36.24 4.37
2720 3009 1.077169 AGGATCATGCATGCATCCCAT 59.923 47.619 32.45 20.73 36.24 4.00
2721 3010 1.476891 GGATCATGCATGCATCCCATC 59.523 52.381 30.07 26.20 33.90 3.51
2722 3011 1.476891 GATCATGCATGCATCCCATCC 59.523 52.381 30.07 12.24 33.90 3.51
2723 3012 0.541063 TCATGCATGCATCCCATCCC 60.541 55.000 30.07 0.00 33.90 3.85
2724 3013 0.830023 CATGCATGCATCCCATCCCA 60.830 55.000 30.07 0.00 33.90 4.37
2725 3014 0.116342 ATGCATGCATCCCATCCCAT 59.884 50.000 27.46 1.89 29.42 4.00
2726 3015 0.105401 TGCATGCATCCCATCCCATT 60.105 50.000 18.46 0.00 29.71 3.16
2727 3016 0.320374 GCATGCATCCCATCCCATTG 59.680 55.000 14.21 0.00 29.71 2.82
2728 3017 1.712056 CATGCATCCCATCCCATTGT 58.288 50.000 0.00 0.00 29.71 2.71
2729 3018 2.043992 CATGCATCCCATCCCATTGTT 58.956 47.619 0.00 0.00 29.71 2.83
2730 3019 3.232662 CATGCATCCCATCCCATTGTTA 58.767 45.455 0.00 0.00 29.71 2.41
2731 3020 2.948115 TGCATCCCATCCCATTGTTAG 58.052 47.619 0.00 0.00 0.00 2.34
2732 3021 2.513317 TGCATCCCATCCCATTGTTAGA 59.487 45.455 0.00 0.00 0.00 2.10
2733 3022 3.152341 GCATCCCATCCCATTGTTAGAG 58.848 50.000 0.00 0.00 0.00 2.43
2734 3023 3.435601 GCATCCCATCCCATTGTTAGAGT 60.436 47.826 0.00 0.00 0.00 3.24
2735 3024 4.392940 CATCCCATCCCATTGTTAGAGTC 58.607 47.826 0.00 0.00 0.00 3.36
2736 3025 3.736094 TCCCATCCCATTGTTAGAGTCT 58.264 45.455 0.00 0.00 0.00 3.24
2737 3026 3.711704 TCCCATCCCATTGTTAGAGTCTC 59.288 47.826 0.00 0.00 0.00 3.36
2738 3027 3.493350 CCCATCCCATTGTTAGAGTCTCG 60.493 52.174 0.00 0.00 0.00 4.04
2739 3028 3.384789 CCATCCCATTGTTAGAGTCTCGA 59.615 47.826 0.00 0.00 0.00 4.04
2740 3029 4.141937 CCATCCCATTGTTAGAGTCTCGAA 60.142 45.833 0.00 0.00 0.00 3.71
2741 3030 4.451629 TCCCATTGTTAGAGTCTCGAAC 57.548 45.455 16.46 16.46 33.45 3.95
2742 3031 3.830178 TCCCATTGTTAGAGTCTCGAACA 59.170 43.478 20.66 20.66 39.59 3.18
2749 3038 7.780008 TTGTTAGAGTCTCGAACAAAATGAA 57.220 32.000 28.48 12.90 44.74 2.57
2750 3039 7.408132 TGTTAGAGTCTCGAACAAAATGAAG 57.592 36.000 21.83 0.00 38.66 3.02
2751 3040 4.999751 AGAGTCTCGAACAAAATGAAGC 57.000 40.909 0.00 0.00 0.00 3.86
2752 3041 3.748568 AGAGTCTCGAACAAAATGAAGCC 59.251 43.478 0.00 0.00 0.00 4.35
2753 3042 3.744660 AGTCTCGAACAAAATGAAGCCT 58.255 40.909 0.00 0.00 0.00 4.58
2754 3043 3.748568 AGTCTCGAACAAAATGAAGCCTC 59.251 43.478 0.00 0.00 0.00 4.70
2755 3044 3.074412 TCTCGAACAAAATGAAGCCTCC 58.926 45.455 0.00 0.00 0.00 4.30
2756 3045 2.159382 TCGAACAAAATGAAGCCTCCC 58.841 47.619 0.00 0.00 0.00 4.30
2757 3046 1.202348 CGAACAAAATGAAGCCTCCCC 59.798 52.381 0.00 0.00 0.00 4.81
2758 3047 1.202348 GAACAAAATGAAGCCTCCCCG 59.798 52.381 0.00 0.00 0.00 5.73
2759 3048 0.112412 ACAAAATGAAGCCTCCCCGT 59.888 50.000 0.00 0.00 0.00 5.28
2760 3049 0.527565 CAAAATGAAGCCTCCCCGTG 59.472 55.000 0.00 0.00 0.00 4.94
2761 3050 1.250840 AAAATGAAGCCTCCCCGTGC 61.251 55.000 0.00 0.00 0.00 5.34
2762 3051 3.976701 AATGAAGCCTCCCCGTGCG 62.977 63.158 0.00 0.00 0.00 5.34
2764 3053 4.699522 GAAGCCTCCCCGTGCGTT 62.700 66.667 0.00 0.00 0.00 4.84
2765 3054 4.265056 AAGCCTCCCCGTGCGTTT 62.265 61.111 0.00 0.00 0.00 3.60
2768 3057 4.323477 CCTCCCCGTGCGTTTGGA 62.323 66.667 0.00 0.00 0.00 3.53
2769 3058 2.046314 CTCCCCGTGCGTTTGGAT 60.046 61.111 0.00 0.00 0.00 3.41
2770 3059 1.674322 CTCCCCGTGCGTTTGGATT 60.674 57.895 0.00 0.00 0.00 3.01
2771 3060 1.228306 TCCCCGTGCGTTTGGATTT 60.228 52.632 0.00 0.00 0.00 2.17
2772 3061 0.824182 TCCCCGTGCGTTTGGATTTT 60.824 50.000 0.00 0.00 0.00 1.82
2773 3062 0.388006 CCCCGTGCGTTTGGATTTTC 60.388 55.000 0.00 0.00 0.00 2.29
2774 3063 0.727793 CCCGTGCGTTTGGATTTTCG 60.728 55.000 0.00 0.00 0.00 3.46
2775 3064 0.236187 CCGTGCGTTTGGATTTTCGA 59.764 50.000 0.00 0.00 0.00 3.71
2776 3065 1.314581 CGTGCGTTTGGATTTTCGAC 58.685 50.000 0.00 0.00 0.00 4.20
2777 3066 1.681825 GTGCGTTTGGATTTTCGACC 58.318 50.000 0.00 0.00 0.00 4.79
2778 3067 0.236187 TGCGTTTGGATTTTCGACCG 59.764 50.000 0.00 0.00 0.00 4.79
2779 3068 0.236449 GCGTTTGGATTTTCGACCGT 59.764 50.000 0.00 0.00 0.00 4.83
2780 3069 1.723701 GCGTTTGGATTTTCGACCGTC 60.724 52.381 0.00 0.00 0.00 4.79
2781 3070 1.136169 CGTTTGGATTTTCGACCGTCC 60.136 52.381 2.92 2.92 0.00 4.79
2782 3071 1.136169 GTTTGGATTTTCGACCGTCCG 60.136 52.381 0.00 0.00 33.39 4.79
2783 3072 0.317799 TTGGATTTTCGACCGTCCGA 59.682 50.000 0.00 0.00 36.70 4.55
2784 3073 0.533491 TGGATTTTCGACCGTCCGAT 59.467 50.000 0.00 0.00 38.45 4.18
2785 3074 1.206523 GGATTTTCGACCGTCCGATC 58.793 55.000 0.00 0.00 38.45 3.69
2786 3075 0.844503 GATTTTCGACCGTCCGATCG 59.155 55.000 8.51 8.51 38.45 3.69
2787 3076 0.452987 ATTTTCGACCGTCCGATCGA 59.547 50.000 18.66 1.30 45.17 3.59
2789 3078 3.570638 TCGACCGTCCGATCGAGC 61.571 66.667 18.66 7.75 42.18 5.03
2790 3079 3.574445 CGACCGTCCGATCGAGCT 61.574 66.667 18.66 0.00 40.86 4.09
2791 3080 2.328639 GACCGTCCGATCGAGCTC 59.671 66.667 18.66 2.73 0.00 4.09
2792 3081 3.183776 GACCGTCCGATCGAGCTCC 62.184 68.421 18.66 0.00 0.00 4.70
2793 3082 3.967335 CCGTCCGATCGAGCTCCC 61.967 72.222 18.66 0.00 0.00 4.30
2794 3083 4.315122 CGTCCGATCGAGCTCCCG 62.315 72.222 18.66 9.34 0.00 5.14
2795 3084 3.967335 GTCCGATCGAGCTCCCGG 61.967 72.222 23.17 23.17 43.02 5.73
2797 3086 3.967335 CCGATCGAGCTCCCGGAC 61.967 72.222 24.23 6.12 44.29 4.79
2798 3087 4.315122 CGATCGAGCTCCCGGACG 62.315 72.222 10.26 3.75 0.00 4.79
2799 3088 4.632458 GATCGAGCTCCCGGACGC 62.632 72.222 8.47 4.61 0.00 5.19
2816 3105 4.570663 CGTCCTGGCCGTCGGATC 62.571 72.222 17.49 6.79 0.00 3.36
2817 3106 4.570663 GTCCTGGCCGTCGGATCG 62.571 72.222 17.49 1.00 0.00 3.69
2824 3113 3.274586 CCGTCGGATCGCGAGGTA 61.275 66.667 16.66 0.00 0.00 3.08
2825 3114 2.248724 CGTCGGATCGCGAGGTAG 59.751 66.667 16.66 6.13 0.00 3.18
2826 3115 2.242572 CGTCGGATCGCGAGGTAGA 61.243 63.158 16.66 8.61 0.00 2.59
2827 3116 1.570475 GTCGGATCGCGAGGTAGAG 59.430 63.158 16.66 2.67 0.00 2.43
2828 3117 2.252346 TCGGATCGCGAGGTAGAGC 61.252 63.158 16.66 0.00 0.00 4.09
2829 3118 2.543802 CGGATCGCGAGGTAGAGCA 61.544 63.158 16.66 0.00 0.00 4.26
2830 3119 1.734137 GGATCGCGAGGTAGAGCAA 59.266 57.895 16.66 0.00 0.00 3.91
2831 3120 0.315568 GGATCGCGAGGTAGAGCAAT 59.684 55.000 16.66 0.00 0.00 3.56
2832 3121 1.667467 GGATCGCGAGGTAGAGCAATC 60.667 57.143 16.66 2.37 0.00 2.67
2833 3122 0.315568 ATCGCGAGGTAGAGCAATCC 59.684 55.000 16.66 0.00 0.00 3.01
2834 3123 1.658717 CGCGAGGTAGAGCAATCCG 60.659 63.158 0.00 0.00 0.00 4.18
2835 3124 1.300233 GCGAGGTAGAGCAATCCGG 60.300 63.158 0.00 0.00 0.00 5.14
2836 3125 1.364171 CGAGGTAGAGCAATCCGGG 59.636 63.158 0.00 0.00 0.00 5.73
2837 3126 1.069935 GAGGTAGAGCAATCCGGGC 59.930 63.158 0.00 0.00 0.00 6.13
2838 3127 2.111251 GGTAGAGCAATCCGGGCC 59.889 66.667 0.00 0.00 0.00 5.80
2839 3128 2.280186 GTAGAGCAATCCGGGCCG 60.280 66.667 21.46 21.46 0.00 6.13
2840 3129 2.762459 TAGAGCAATCCGGGCCGT 60.762 61.111 26.32 4.29 0.00 5.68
2841 3130 2.792947 TAGAGCAATCCGGGCCGTC 61.793 63.158 26.32 14.57 0.00 4.79
2864 3153 3.698382 GCGAGATGGAGCGTTCTG 58.302 61.111 0.00 0.00 0.00 3.02
2865 3154 1.880340 GCGAGATGGAGCGTTCTGG 60.880 63.158 0.00 0.00 0.00 3.86
2866 3155 1.880340 CGAGATGGAGCGTTCTGGC 60.880 63.158 0.00 0.00 0.00 4.85
2867 3156 1.522580 GAGATGGAGCGTTCTGGCC 60.523 63.158 0.00 0.00 0.00 5.36
2868 3157 2.892425 GATGGAGCGTTCTGGCCG 60.892 66.667 0.00 0.00 0.00 6.13
2869 3158 3.665675 GATGGAGCGTTCTGGCCGT 62.666 63.158 0.00 0.00 0.00 5.68
2870 3159 3.665675 ATGGAGCGTTCTGGCCGTC 62.666 63.158 0.00 0.00 0.00 4.79
2874 3163 4.814294 GCGTTCTGGCCGTCGGAT 62.814 66.667 17.49 0.00 0.00 4.18
2875 3164 2.582498 CGTTCTGGCCGTCGGATC 60.582 66.667 17.49 6.79 0.00 3.36
2876 3165 2.582498 GTTCTGGCCGTCGGATCG 60.582 66.667 17.49 1.30 0.00 3.69
2877 3166 2.752640 TTCTGGCCGTCGGATCGA 60.753 61.111 17.49 3.99 0.00 3.59
2878 3167 2.771639 TTCTGGCCGTCGGATCGAG 61.772 63.158 17.49 4.97 36.23 4.04
2879 3168 4.933064 CTGGCCGTCGGATCGAGC 62.933 72.222 17.49 0.00 36.23 5.03
2883 3172 2.593725 CCGTCGGATCGAGCCCTA 60.594 66.667 15.35 0.00 36.23 3.53
2884 3173 1.972223 CCGTCGGATCGAGCCCTAT 60.972 63.158 15.35 0.00 36.23 2.57
2885 3174 1.210413 CGTCGGATCGAGCCCTATG 59.790 63.158 15.35 4.25 36.23 2.23
2886 3175 1.080434 GTCGGATCGAGCCCTATGC 60.080 63.158 15.35 0.00 36.23 3.14
2895 3184 4.445699 GCCCTATGCTCAGGTTCG 57.554 61.111 3.85 0.00 36.87 3.95
2896 3185 1.522569 GCCCTATGCTCAGGTTCGT 59.477 57.895 3.85 0.00 36.87 3.85
2897 3186 0.811616 GCCCTATGCTCAGGTTCGTG 60.812 60.000 3.85 0.00 36.87 4.35
2898 3187 0.811616 CCCTATGCTCAGGTTCGTGC 60.812 60.000 3.85 0.00 33.44 5.34
2899 3188 0.811616 CCTATGCTCAGGTTCGTGCC 60.812 60.000 0.00 0.00 0.00 5.01
2900 3189 0.108186 CTATGCTCAGGTTCGTGCCA 60.108 55.000 1.38 0.00 0.00 4.92
2901 3190 0.391130 TATGCTCAGGTTCGTGCCAC 60.391 55.000 1.38 0.00 0.00 5.01
2902 3191 3.050275 GCTCAGGTTCGTGCCACC 61.050 66.667 0.00 0.00 34.06 4.61
2903 3192 2.738521 CTCAGGTTCGTGCCACCG 60.739 66.667 0.00 0.00 39.56 4.94
2904 3193 4.980805 TCAGGTTCGTGCCACCGC 62.981 66.667 0.00 0.00 39.56 5.68
2909 3198 3.617735 TTCGTGCCACCGCCTGTA 61.618 61.111 0.00 0.00 0.00 2.74
2910 3199 3.166490 TTCGTGCCACCGCCTGTAA 62.166 57.895 0.00 0.00 0.00 2.41
2911 3200 2.661840 TTCGTGCCACCGCCTGTAAA 62.662 55.000 0.00 0.00 0.00 2.01
2912 3201 2.038269 CGTGCCACCGCCTGTAAAT 61.038 57.895 0.00 0.00 0.00 1.40
2913 3202 1.800681 GTGCCACCGCCTGTAAATC 59.199 57.895 0.00 0.00 0.00 2.17
2914 3203 0.676782 GTGCCACCGCCTGTAAATCT 60.677 55.000 0.00 0.00 0.00 2.40
2915 3204 0.392461 TGCCACCGCCTGTAAATCTC 60.392 55.000 0.00 0.00 0.00 2.75
2916 3205 1.429148 GCCACCGCCTGTAAATCTCG 61.429 60.000 0.00 0.00 0.00 4.04
2917 3206 0.108329 CCACCGCCTGTAAATCTCGT 60.108 55.000 0.00 0.00 0.00 4.18
2918 3207 0.999406 CACCGCCTGTAAATCTCGTG 59.001 55.000 0.00 0.00 0.00 4.35
2919 3208 0.739813 ACCGCCTGTAAATCTCGTGC 60.740 55.000 0.00 0.00 0.00 5.34
2920 3209 1.429148 CCGCCTGTAAATCTCGTGCC 61.429 60.000 0.00 0.00 0.00 5.01
2921 3210 1.429148 CGCCTGTAAATCTCGTGCCC 61.429 60.000 0.00 0.00 0.00 5.36
2922 3211 1.095807 GCCTGTAAATCTCGTGCCCC 61.096 60.000 0.00 0.00 0.00 5.80
2923 3212 0.251916 CCTGTAAATCTCGTGCCCCA 59.748 55.000 0.00 0.00 0.00 4.96
2924 3213 1.134098 CCTGTAAATCTCGTGCCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
2925 3214 1.942657 CTGTAAATCTCGTGCCCCATG 59.057 52.381 0.00 0.00 0.00 3.66
2926 3215 1.308998 GTAAATCTCGTGCCCCATGG 58.691 55.000 4.14 4.14 0.00 3.66
2927 3216 1.134220 GTAAATCTCGTGCCCCATGGA 60.134 52.381 15.22 0.00 0.00 3.41
2928 3217 0.107017 AAATCTCGTGCCCCATGGAG 60.107 55.000 15.22 0.00 0.00 3.86
2929 3218 1.987807 AATCTCGTGCCCCATGGAGG 61.988 60.000 15.22 14.13 37.03 4.30
2939 3228 3.909587 CCATGGAGGGCATTCTTGA 57.090 52.632 5.56 0.00 0.00 3.02
2940 3229 1.396653 CCATGGAGGGCATTCTTGAC 58.603 55.000 5.56 0.00 0.00 3.18
2941 3230 1.064166 CCATGGAGGGCATTCTTGACT 60.064 52.381 5.56 0.00 0.00 3.41
2942 3231 2.622452 CCATGGAGGGCATTCTTGACTT 60.622 50.000 5.56 0.00 0.00 3.01
2943 3232 2.978156 TGGAGGGCATTCTTGACTTT 57.022 45.000 0.00 0.00 0.00 2.66
2944 3233 3.243359 TGGAGGGCATTCTTGACTTTT 57.757 42.857 0.00 0.00 0.00 2.27
2945 3234 3.157087 TGGAGGGCATTCTTGACTTTTC 58.843 45.455 0.00 0.00 0.00 2.29
2946 3235 3.157087 GGAGGGCATTCTTGACTTTTCA 58.843 45.455 0.00 0.00 0.00 2.69
2947 3236 3.057245 GGAGGGCATTCTTGACTTTTCAC 60.057 47.826 0.00 0.00 0.00 3.18
2948 3237 3.565307 AGGGCATTCTTGACTTTTCACA 58.435 40.909 0.00 0.00 0.00 3.58
2949 3238 3.319122 AGGGCATTCTTGACTTTTCACAC 59.681 43.478 0.00 0.00 0.00 3.82
2950 3239 3.300009 GGCATTCTTGACTTTTCACACG 58.700 45.455 0.00 0.00 0.00 4.49
2951 3240 3.243068 GGCATTCTTGACTTTTCACACGT 60.243 43.478 0.00 0.00 0.00 4.49
2952 3241 3.968724 GCATTCTTGACTTTTCACACGTC 59.031 43.478 0.00 0.00 0.00 4.34
2953 3242 3.918258 TTCTTGACTTTTCACACGTCG 57.082 42.857 0.00 0.00 0.00 5.12
2954 3243 2.198406 TCTTGACTTTTCACACGTCGG 58.802 47.619 0.00 0.00 0.00 4.79
2955 3244 0.653636 TTGACTTTTCACACGTCGGC 59.346 50.000 0.00 0.00 0.00 5.54
2956 3245 1.200839 GACTTTTCACACGTCGGCG 59.799 57.895 8.42 8.42 44.93 6.46
2968 3257 2.984879 CGTCGGCGTATAAAAGGAAC 57.015 50.000 6.85 0.00 0.00 3.62
2970 3259 2.533129 CGTCGGCGTATAAAAGGAACTC 59.467 50.000 6.85 0.00 38.49 3.01
2971 3260 2.533129 GTCGGCGTATAAAAGGAACTCG 59.467 50.000 6.85 0.00 38.49 4.18
2972 3261 1.257155 CGGCGTATAAAAGGAACTCGC 59.743 52.381 0.00 0.00 42.20 5.03
2974 3263 1.596260 GCGTATAAAAGGAACTCGCCC 59.404 52.381 0.00 0.00 38.49 6.13
2975 3264 2.740904 GCGTATAAAAGGAACTCGCCCT 60.741 50.000 0.00 0.00 38.49 5.19
2976 3265 3.121544 CGTATAAAAGGAACTCGCCCTC 58.878 50.000 0.00 0.00 38.49 4.30
2977 3266 2.711978 ATAAAAGGAACTCGCCCTCC 57.288 50.000 0.00 0.00 38.49 4.30
2978 3267 0.248289 TAAAAGGAACTCGCCCTCCG 59.752 55.000 0.00 0.00 38.49 4.63
2979 3268 1.765597 AAAAGGAACTCGCCCTCCGT 61.766 55.000 0.00 0.00 38.49 4.69
2980 3269 1.765597 AAAGGAACTCGCCCTCCGTT 61.766 55.000 0.00 0.00 38.49 4.44
2981 3270 2.434359 GGAACTCGCCCTCCGTTG 60.434 66.667 0.00 0.00 38.35 4.10
2982 3271 3.119096 GAACTCGCCCTCCGTTGC 61.119 66.667 0.00 0.00 38.35 4.17
3000 3289 4.704833 GCCCGCTGCTTCACTCCA 62.705 66.667 0.00 0.00 36.87 3.86
3001 3290 2.435586 CCCGCTGCTTCACTCCAG 60.436 66.667 0.00 0.00 0.00 3.86
3004 3293 3.123620 GCTGCTTCACTCCAGCCG 61.124 66.667 1.38 0.00 46.59 5.52
3005 3294 3.123620 CTGCTTCACTCCAGCCGC 61.124 66.667 0.00 0.00 36.33 6.53
3006 3295 4.704833 TGCTTCACTCCAGCCGCC 62.705 66.667 0.00 0.00 36.33 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 3.521560 TCATACCTCATTTGCTCGACAC 58.478 45.455 0.00 0.00 0.00 3.67
81 82 2.591133 GTCTCTCTCTCGTTGCTTCAC 58.409 52.381 0.00 0.00 0.00 3.18
128 129 2.558359 TCTCATCCGCATGTGTCGATAT 59.442 45.455 5.38 0.00 0.00 1.63
129 130 1.953686 TCTCATCCGCATGTGTCGATA 59.046 47.619 5.38 0.00 0.00 2.92
207 208 1.441016 CTTGGAAGAAACGCGCTGC 60.441 57.895 5.73 0.00 0.00 5.25
208 209 1.207593 CCTTGGAAGAAACGCGCTG 59.792 57.895 5.73 1.02 0.00 5.18
209 210 2.617274 GCCTTGGAAGAAACGCGCT 61.617 57.895 5.73 0.00 0.00 5.92
210 211 2.126850 GCCTTGGAAGAAACGCGC 60.127 61.111 5.73 0.00 0.00 6.86
244 247 9.240734 ACAAACTAATACAGTGCTAGTAGTACT 57.759 33.333 14.50 14.50 41.96 2.73
247 250 8.189460 GCTACAAACTAATACAGTGCTAGTAGT 58.811 37.037 0.00 6.90 37.63 2.73
248 251 7.376336 CGCTACAAACTAATACAGTGCTAGTAG 59.624 40.741 0.00 0.00 37.63 2.57
249 252 7.066163 TCGCTACAAACTAATACAGTGCTAGTA 59.934 37.037 0.00 0.00 37.63 1.82
250 253 6.034591 CGCTACAAACTAATACAGTGCTAGT 58.965 40.000 0.00 0.00 37.63 2.57
251 254 6.196724 GTCGCTACAAACTAATACAGTGCTAG 59.803 42.308 0.00 0.00 37.63 3.42
252 255 6.032094 GTCGCTACAAACTAATACAGTGCTA 58.968 40.000 0.00 0.00 37.63 3.49
253 256 4.863131 GTCGCTACAAACTAATACAGTGCT 59.137 41.667 0.00 0.00 37.63 4.40
254 257 4.624024 TGTCGCTACAAACTAATACAGTGC 59.376 41.667 0.00 0.00 37.63 4.40
255 258 5.862323 ACTGTCGCTACAAACTAATACAGTG 59.138 40.000 0.00 0.00 43.30 3.66
316 328 0.040204 GGGATGGGCCTGATTATGGG 59.960 60.000 4.53 0.00 36.66 4.00
317 329 0.779358 TGGGATGGGCCTGATTATGG 59.221 55.000 4.53 0.00 36.66 2.74
318 330 1.548582 GGTGGGATGGGCCTGATTATG 60.549 57.143 4.53 0.00 36.66 1.90
337 349 1.242076 GCGGGAGATTTGGATCATGG 58.758 55.000 0.00 0.00 34.60 3.66
338 350 1.242076 GGCGGGAGATTTGGATCATG 58.758 55.000 0.00 0.00 34.60 3.07
437 454 2.167861 CGGCAAAGCTAGCGTCCTC 61.168 63.158 9.55 0.00 0.00 3.71
538 557 1.369091 ACGTACCGTAGCCGTAGGTG 61.369 60.000 0.00 0.00 45.79 4.00
600 619 1.812571 ACTAAAATTCAGCGGGCACTG 59.187 47.619 0.61 0.61 39.12 3.66
648 687 1.665916 CGCATGCAGGCTAGCGTAT 60.666 57.895 22.31 0.00 44.67 3.06
673 712 2.010670 CGTGGTTGCTGAAACGACA 58.989 52.632 13.19 0.00 45.07 4.35
716 764 3.789224 CCCGACGAACTGAAAAACAAAAG 59.211 43.478 0.00 0.00 0.00 2.27
721 769 2.598205 CGAACCCGACGAACTGAAAAAC 60.598 50.000 0.00 0.00 38.22 2.43
733 787 5.684626 CAGTAGTAATTATCACGAACCCGAC 59.315 44.000 0.00 0.00 39.50 4.79
736 790 5.462398 CAGCAGTAGTAATTATCACGAACCC 59.538 44.000 0.00 0.00 0.00 4.11
763 817 2.301870 TCTGGTAAACCGACTGATTGCT 59.698 45.455 0.00 0.00 39.43 3.91
836 898 5.160607 TCCAAGTAACTGGATTCAATCGT 57.839 39.130 0.00 0.00 40.71 3.73
861 924 3.609175 GCAGAGAGAGAGACACGCATATC 60.609 52.174 0.00 0.00 0.00 1.63
940 1003 1.654954 GCCAGGAAGATGCAGCACTG 61.655 60.000 4.07 9.47 0.00 3.66
977 1042 1.814248 GCTTAATAAGAGCCGGGTGGG 60.814 57.143 12.94 0.00 39.58 4.61
978 1043 1.594331 GCTTAATAAGAGCCGGGTGG 58.406 55.000 12.94 0.00 34.06 4.61
991 1056 3.946395 AGGAACTAGAGCTCGGGCTTAAT 60.946 47.826 13.22 3.09 44.27 1.40
1051 1116 0.603707 ACAATCAGTGTGACTGCCCG 60.604 55.000 0.00 0.00 45.54 6.13
1067 1132 1.270785 TGCCTTGATTCTCGAGCACAA 60.271 47.619 7.81 12.15 0.00 3.33
1128 1193 3.258228 CTTCTTCCTCTTCTTCGGCTTC 58.742 50.000 0.00 0.00 0.00 3.86
1262 1330 3.047877 CTGGTTCCGCCGTTGGTC 61.048 66.667 0.00 0.00 41.21 4.02
1476 1556 2.277072 CTCTCCTCCTCCAGCCGA 59.723 66.667 0.00 0.00 0.00 5.54
1665 1745 2.363147 AGCTCCTCCCAGACGTCC 60.363 66.667 13.01 0.00 0.00 4.79
1702 1782 1.155042 CGCTTCTGCTTCAGCTTCTT 58.845 50.000 0.00 0.00 42.66 2.52
1709 1798 4.681421 CAGGACGCTTCTGCTTCA 57.319 55.556 0.00 0.00 38.95 3.02
1787 1876 0.859232 AGTTAACTTGTCAGTGCGCG 59.141 50.000 0.00 0.00 31.60 6.86
1876 1973 2.876879 CTGAAAACCACGCACGCGA 61.877 57.895 19.66 0.00 42.83 5.87
1884 1981 0.951558 ATCACGGCACTGAAAACCAC 59.048 50.000 0.00 0.00 0.00 4.16
1923 2020 4.648626 TCAGGTGCCAGCCACAGC 62.649 66.667 0.00 0.00 46.50 4.40
1924 2021 2.359602 CTCAGGTGCCAGCCACAG 60.360 66.667 0.00 0.00 46.50 3.66
1964 2061 9.706691 GATGATATCTTTACAGGATTAACGGAA 57.293 33.333 3.98 0.00 0.00 4.30
1995 2096 4.272504 ACGCAATATTCACGGGAAATGTAG 59.727 41.667 3.14 5.86 36.43 2.74
2066 2276 1.594293 CGTTTGGTCGACTGCCACT 60.594 57.895 16.46 0.00 35.46 4.00
2071 2281 2.935955 GCCACGTTTGGTCGACTG 59.064 61.111 16.46 4.31 45.98 3.51
2072 2282 2.660552 CGCCACGTTTGGTCGACT 60.661 61.111 16.46 0.00 45.98 4.18
2073 2283 4.364409 GCGCCACGTTTGGTCGAC 62.364 66.667 7.13 7.13 45.98 4.20
2132 2360 1.070445 CTCGGCCTCATGATGGTCC 59.930 63.158 0.00 5.45 0.00 4.46
2156 2384 0.842030 TCCTCTCCCACCAAGCATGT 60.842 55.000 0.00 0.00 0.00 3.21
2175 2403 4.335647 CCACGCCCTGTCTGCCTT 62.336 66.667 0.00 0.00 0.00 4.35
2182 2410 4.008933 GAGCAGACCACGCCCTGT 62.009 66.667 0.00 0.00 33.19 4.00
2300 2536 3.650070 TCACATCAGTCAGTCAGTCAC 57.350 47.619 0.00 0.00 0.00 3.67
2308 2552 1.788258 ACGCAGTTCACATCAGTCAG 58.212 50.000 0.00 0.00 37.78 3.51
2388 2632 1.598701 GATGCCTGACCAAGCAACCC 61.599 60.000 0.00 0.00 43.36 4.11
2452 2696 2.556459 CGTGAGAGGGGCGATCGAT 61.556 63.158 21.57 0.00 0.00 3.59
2515 2786 1.133598 CAAGCACCTATACGGACACGA 59.866 52.381 0.00 0.00 44.60 4.35
2522 2793 7.653713 AGAATTTCTATGTCAAGCACCTATACG 59.346 37.037 0.00 0.00 0.00 3.06
2526 2797 8.893219 CATAGAATTTCTATGTCAAGCACCTA 57.107 34.615 27.48 0.00 46.92 3.08
2527 2798 7.798596 CATAGAATTTCTATGTCAAGCACCT 57.201 36.000 27.48 1.39 46.92 4.00
2716 3005 3.493350 CGAGACTCTAACAATGGGATGGG 60.493 52.174 0.03 0.00 0.00 4.00
2717 3006 3.384789 TCGAGACTCTAACAATGGGATGG 59.615 47.826 0.03 0.00 0.00 3.51
2718 3007 4.655762 TCGAGACTCTAACAATGGGATG 57.344 45.455 0.03 0.00 0.00 3.51
2719 3008 4.466370 TGTTCGAGACTCTAACAATGGGAT 59.534 41.667 17.57 0.00 30.54 3.85
2720 3009 3.830178 TGTTCGAGACTCTAACAATGGGA 59.170 43.478 17.57 0.00 30.54 4.37
2721 3010 4.188247 TGTTCGAGACTCTAACAATGGG 57.812 45.455 17.57 0.00 30.54 4.00
2722 3011 6.539649 TTTTGTTCGAGACTCTAACAATGG 57.460 37.500 26.69 0.69 40.26 3.16
2723 3012 7.796838 TCATTTTGTTCGAGACTCTAACAATG 58.203 34.615 26.69 23.09 40.26 2.82
2724 3013 7.962964 TCATTTTGTTCGAGACTCTAACAAT 57.037 32.000 26.69 15.65 40.26 2.71
2725 3014 7.518370 GCTTCATTTTGTTCGAGACTCTAACAA 60.518 37.037 23.99 23.99 39.33 2.83
2726 3015 6.073765 GCTTCATTTTGTTCGAGACTCTAACA 60.074 38.462 16.32 16.32 31.43 2.41
2727 3016 6.300356 GCTTCATTTTGTTCGAGACTCTAAC 58.700 40.000 11.87 11.87 0.00 2.34
2728 3017 5.408604 GGCTTCATTTTGTTCGAGACTCTAA 59.591 40.000 0.03 0.00 0.00 2.10
2729 3018 4.929808 GGCTTCATTTTGTTCGAGACTCTA 59.070 41.667 0.03 0.00 0.00 2.43
2730 3019 3.748568 GGCTTCATTTTGTTCGAGACTCT 59.251 43.478 0.03 0.00 0.00 3.24
2731 3020 3.748568 AGGCTTCATTTTGTTCGAGACTC 59.251 43.478 0.00 0.00 0.00 3.36
2732 3021 3.744660 AGGCTTCATTTTGTTCGAGACT 58.255 40.909 0.00 0.00 0.00 3.24
2733 3022 3.120165 GGAGGCTTCATTTTGTTCGAGAC 60.120 47.826 0.00 0.00 0.00 3.36
2734 3023 3.074412 GGAGGCTTCATTTTGTTCGAGA 58.926 45.455 0.00 0.00 0.00 4.04
2735 3024 2.162408 GGGAGGCTTCATTTTGTTCGAG 59.838 50.000 0.00 0.00 0.00 4.04
2736 3025 2.159382 GGGAGGCTTCATTTTGTTCGA 58.841 47.619 0.00 0.00 0.00 3.71
2737 3026 1.202348 GGGGAGGCTTCATTTTGTTCG 59.798 52.381 0.00 0.00 0.00 3.95
2738 3027 1.202348 CGGGGAGGCTTCATTTTGTTC 59.798 52.381 0.00 0.00 0.00 3.18
2739 3028 1.256812 CGGGGAGGCTTCATTTTGTT 58.743 50.000 0.00 0.00 0.00 2.83
2740 3029 0.112412 ACGGGGAGGCTTCATTTTGT 59.888 50.000 0.00 0.00 0.00 2.83
2741 3030 0.527565 CACGGGGAGGCTTCATTTTG 59.472 55.000 0.00 0.00 0.00 2.44
2742 3031 1.250840 GCACGGGGAGGCTTCATTTT 61.251 55.000 0.00 0.00 0.00 1.82
2743 3032 1.678970 GCACGGGGAGGCTTCATTT 60.679 57.895 0.00 0.00 0.00 2.32
2744 3033 2.044946 GCACGGGGAGGCTTCATT 60.045 61.111 0.00 0.00 0.00 2.57
2745 3034 4.473520 CGCACGGGGAGGCTTCAT 62.474 66.667 0.00 0.00 0.00 2.57
2747 3036 4.699522 AACGCACGGGGAGGCTTC 62.700 66.667 0.00 0.00 0.00 3.86
2748 3037 4.265056 AAACGCACGGGGAGGCTT 62.265 61.111 0.00 0.00 0.00 4.35
2751 3040 3.622060 ATCCAAACGCACGGGGAGG 62.622 63.158 6.53 0.00 31.96 4.30
2752 3041 1.241315 AAATCCAAACGCACGGGGAG 61.241 55.000 6.53 0.00 31.96 4.30
2753 3042 0.824182 AAAATCCAAACGCACGGGGA 60.824 50.000 0.00 0.00 0.00 4.81
2754 3043 0.388006 GAAAATCCAAACGCACGGGG 60.388 55.000 0.00 0.00 0.00 5.73
2755 3044 0.727793 CGAAAATCCAAACGCACGGG 60.728 55.000 0.00 0.00 0.00 5.28
2756 3045 0.236187 TCGAAAATCCAAACGCACGG 59.764 50.000 0.00 0.00 0.00 4.94
2757 3046 1.314581 GTCGAAAATCCAAACGCACG 58.685 50.000 0.00 0.00 0.00 5.34
2758 3047 1.681825 GGTCGAAAATCCAAACGCAC 58.318 50.000 0.00 0.00 0.00 5.34
2759 3048 0.236187 CGGTCGAAAATCCAAACGCA 59.764 50.000 0.00 0.00 0.00 5.24
2760 3049 0.236449 ACGGTCGAAAATCCAAACGC 59.764 50.000 0.00 0.00 0.00 4.84
2761 3050 1.136169 GGACGGTCGAAAATCCAAACG 60.136 52.381 1.43 0.00 0.00 3.60
2762 3051 1.136169 CGGACGGTCGAAAATCCAAAC 60.136 52.381 1.43 0.00 0.00 2.93
2763 3052 1.149987 CGGACGGTCGAAAATCCAAA 58.850 50.000 1.43 0.00 0.00 3.28
2764 3053 0.317799 TCGGACGGTCGAAAATCCAA 59.682 50.000 1.43 0.00 36.12 3.53
2765 3054 0.533491 ATCGGACGGTCGAAAATCCA 59.467 50.000 6.46 0.00 42.69 3.41
2766 3055 1.206523 GATCGGACGGTCGAAAATCC 58.793 55.000 6.46 0.00 42.69 3.01
2767 3056 0.844503 CGATCGGACGGTCGAAAATC 59.155 55.000 21.35 0.00 42.69 2.17
2768 3057 0.452987 TCGATCGGACGGTCGAAAAT 59.547 50.000 25.29 0.00 43.14 1.82
2769 3058 0.179181 CTCGATCGGACGGTCGAAAA 60.179 55.000 26.80 8.96 45.08 2.29
2770 3059 1.426621 CTCGATCGGACGGTCGAAA 59.573 57.895 26.80 9.62 45.08 3.46
2771 3060 3.095911 CTCGATCGGACGGTCGAA 58.904 61.111 26.80 13.48 45.08 3.71
2772 3061 3.570638 GCTCGATCGGACGGTCGA 61.571 66.667 25.62 25.62 43.79 4.20
2773 3062 3.509296 GAGCTCGATCGGACGGTCG 62.509 68.421 20.07 20.07 39.11 4.79
2774 3063 2.328639 GAGCTCGATCGGACGGTC 59.671 66.667 16.41 14.51 0.00 4.79
2775 3064 3.210528 GGAGCTCGATCGGACGGT 61.211 66.667 16.41 9.68 0.00 4.83
2776 3065 3.967335 GGGAGCTCGATCGGACGG 61.967 72.222 16.41 4.73 0.00 4.79
2777 3066 4.315122 CGGGAGCTCGATCGGACG 62.315 72.222 16.41 7.37 0.00 4.79
2778 3067 3.967335 CCGGGAGCTCGATCGGAC 61.967 72.222 26.98 7.75 44.69 4.79
2780 3069 3.967335 GTCCGGGAGCTCGATCGG 61.967 72.222 25.84 25.84 43.42 4.18
2781 3070 4.315122 CGTCCGGGAGCTCGATCG 62.315 72.222 9.36 9.36 0.00 3.69
2782 3071 4.632458 GCGTCCGGGAGCTCGATC 62.632 72.222 7.83 0.00 0.00 3.69
2799 3088 4.570663 GATCCGACGGCCAGGACG 62.571 72.222 15.24 15.24 39.66 4.79
2800 3089 4.570663 CGATCCGACGGCCAGGAC 62.571 72.222 9.66 7.35 39.66 3.85
2807 3096 3.237946 CTACCTCGCGATCCGACGG 62.238 68.421 10.36 7.84 41.89 4.79
2808 3097 2.160487 CTCTACCTCGCGATCCGACG 62.160 65.000 10.36 0.00 41.89 5.12
2809 3098 1.570475 CTCTACCTCGCGATCCGAC 59.430 63.158 10.36 0.00 41.89 4.79
2810 3099 2.252346 GCTCTACCTCGCGATCCGA 61.252 63.158 10.36 3.23 45.15 4.55
2811 3100 2.060004 TTGCTCTACCTCGCGATCCG 62.060 60.000 10.36 2.40 38.61 4.18
2812 3101 0.315568 ATTGCTCTACCTCGCGATCC 59.684 55.000 10.36 0.00 0.00 3.36
2813 3102 1.667467 GGATTGCTCTACCTCGCGATC 60.667 57.143 10.36 0.00 43.27 3.69
2814 3103 0.315568 GGATTGCTCTACCTCGCGAT 59.684 55.000 10.36 0.00 33.08 4.58
2815 3104 1.734137 GGATTGCTCTACCTCGCGA 59.266 57.895 9.26 9.26 0.00 5.87
2816 3105 1.658717 CGGATTGCTCTACCTCGCG 60.659 63.158 0.00 0.00 0.00 5.87
2817 3106 1.300233 CCGGATTGCTCTACCTCGC 60.300 63.158 0.00 0.00 0.00 5.03
2818 3107 1.364171 CCCGGATTGCTCTACCTCG 59.636 63.158 0.73 0.00 0.00 4.63
2819 3108 1.069935 GCCCGGATTGCTCTACCTC 59.930 63.158 0.73 0.00 0.00 3.85
2820 3109 2.444256 GGCCCGGATTGCTCTACCT 61.444 63.158 0.73 0.00 0.00 3.08
2821 3110 2.111251 GGCCCGGATTGCTCTACC 59.889 66.667 0.73 0.00 0.00 3.18
2822 3111 2.280186 CGGCCCGGATTGCTCTAC 60.280 66.667 0.73 0.00 0.00 2.59
2823 3112 2.762459 ACGGCCCGGATTGCTCTA 60.762 61.111 8.57 0.00 0.00 2.43
2824 3113 4.162690 GACGGCCCGGATTGCTCT 62.163 66.667 8.57 0.00 0.00 4.09
2836 3125 4.329697 ATCTCGCGATCGGACGGC 62.330 66.667 18.30 0.00 36.13 5.68
2837 3126 2.427575 CATCTCGCGATCGGACGG 60.428 66.667 18.30 7.17 36.13 4.79
2838 3127 2.427575 CCATCTCGCGATCGGACG 60.428 66.667 18.30 12.96 36.13 4.79
2839 3128 1.081774 CTCCATCTCGCGATCGGAC 60.082 63.158 18.30 0.00 36.13 4.79
2840 3129 2.909209 GCTCCATCTCGCGATCGGA 61.909 63.158 18.30 14.91 36.13 4.55
2841 3130 2.429907 GCTCCATCTCGCGATCGG 60.430 66.667 18.30 10.95 36.13 4.18
2847 3136 1.880340 CCAGAACGCTCCATCTCGC 60.880 63.158 0.00 0.00 0.00 5.03
2848 3137 1.880340 GCCAGAACGCTCCATCTCG 60.880 63.158 0.00 0.00 0.00 4.04
2849 3138 1.522580 GGCCAGAACGCTCCATCTC 60.523 63.158 0.00 0.00 0.00 2.75
2850 3139 2.586792 GGCCAGAACGCTCCATCT 59.413 61.111 0.00 0.00 0.00 2.90
2851 3140 2.892425 CGGCCAGAACGCTCCATC 60.892 66.667 2.24 0.00 0.00 3.51
2852 3141 3.665675 GACGGCCAGAACGCTCCAT 62.666 63.158 2.24 0.00 34.00 3.41
2853 3142 4.373116 GACGGCCAGAACGCTCCA 62.373 66.667 2.24 0.00 34.00 3.86
2857 3146 4.814294 ATCCGACGGCCAGAACGC 62.814 66.667 9.66 0.00 34.00 4.84
2858 3147 2.582498 GATCCGACGGCCAGAACG 60.582 66.667 9.66 1.95 37.36 3.95
2859 3148 2.582498 CGATCCGACGGCCAGAAC 60.582 66.667 9.66 0.00 0.00 3.01
2860 3149 2.752640 TCGATCCGACGGCCAGAA 60.753 61.111 9.66 0.00 0.00 3.02
2861 3150 3.209812 CTCGATCCGACGGCCAGA 61.210 66.667 9.66 6.91 0.00 3.86
2862 3151 4.933064 GCTCGATCCGACGGCCAG 62.933 72.222 9.66 2.33 0.00 4.85
2866 3155 1.972223 ATAGGGCTCGATCCGACGG 60.972 63.158 7.84 7.84 0.00 4.79
2867 3156 1.210413 CATAGGGCTCGATCCGACG 59.790 63.158 0.00 0.00 0.00 5.12
2868 3157 1.080434 GCATAGGGCTCGATCCGAC 60.080 63.158 0.00 0.00 40.25 4.79
2869 3158 3.366629 GCATAGGGCTCGATCCGA 58.633 61.111 0.00 0.00 40.25 4.55
2878 3167 0.811616 CACGAACCTGAGCATAGGGC 60.812 60.000 10.57 2.31 42.35 5.19
2879 3168 0.811616 GCACGAACCTGAGCATAGGG 60.812 60.000 10.57 0.00 42.35 3.53
2880 3169 0.811616 GGCACGAACCTGAGCATAGG 60.812 60.000 4.85 4.85 43.71 2.57
2881 3170 0.108186 TGGCACGAACCTGAGCATAG 60.108 55.000 0.00 0.00 0.00 2.23
2882 3171 0.391130 GTGGCACGAACCTGAGCATA 60.391 55.000 0.00 0.00 0.00 3.14
2883 3172 1.672356 GTGGCACGAACCTGAGCAT 60.672 57.895 0.00 0.00 0.00 3.79
2884 3173 2.280797 GTGGCACGAACCTGAGCA 60.281 61.111 0.00 0.00 0.00 4.26
2885 3174 3.050275 GGTGGCACGAACCTGAGC 61.050 66.667 12.17 0.00 34.66 4.26
2886 3175 2.738521 CGGTGGCACGAACCTGAG 60.739 66.667 12.17 0.00 35.39 3.35
2887 3176 4.980805 GCGGTGGCACGAACCTGA 62.981 66.667 12.17 0.00 39.62 3.86
2891 3180 3.869473 TACAGGCGGTGGCACGAAC 62.869 63.158 12.17 3.73 42.47 3.95
2892 3181 2.661840 TTTACAGGCGGTGGCACGAA 62.662 55.000 12.17 0.00 42.47 3.85
2893 3182 2.457743 ATTTACAGGCGGTGGCACGA 62.458 55.000 12.17 0.00 42.47 4.35
2894 3183 1.977594 GATTTACAGGCGGTGGCACG 61.978 60.000 12.17 8.28 42.47 5.34
2895 3184 0.676782 AGATTTACAGGCGGTGGCAC 60.677 55.000 9.70 9.70 42.47 5.01
2896 3185 0.392461 GAGATTTACAGGCGGTGGCA 60.392 55.000 0.00 0.00 42.47 4.92
2897 3186 1.429148 CGAGATTTACAGGCGGTGGC 61.429 60.000 0.00 0.00 38.90 5.01
2898 3187 0.108329 ACGAGATTTACAGGCGGTGG 60.108 55.000 0.00 0.00 0.00 4.61
2899 3188 0.999406 CACGAGATTTACAGGCGGTG 59.001 55.000 0.00 0.00 0.00 4.94
2900 3189 0.739813 GCACGAGATTTACAGGCGGT 60.740 55.000 0.00 0.00 0.00 5.68
2901 3190 1.429148 GGCACGAGATTTACAGGCGG 61.429 60.000 0.00 0.00 0.00 6.13
2902 3191 1.429148 GGGCACGAGATTTACAGGCG 61.429 60.000 0.00 0.00 0.00 5.52
2903 3192 1.095807 GGGGCACGAGATTTACAGGC 61.096 60.000 0.00 0.00 0.00 4.85
2904 3193 0.251916 TGGGGCACGAGATTTACAGG 59.748 55.000 0.00 0.00 0.00 4.00
2905 3194 1.942657 CATGGGGCACGAGATTTACAG 59.057 52.381 0.00 0.00 0.00 2.74
2906 3195 1.408127 CCATGGGGCACGAGATTTACA 60.408 52.381 2.85 0.00 0.00 2.41
2907 3196 1.134220 TCCATGGGGCACGAGATTTAC 60.134 52.381 13.02 0.00 0.00 2.01
2908 3197 1.140852 CTCCATGGGGCACGAGATTTA 59.859 52.381 13.02 0.00 0.00 1.40
2909 3198 0.107017 CTCCATGGGGCACGAGATTT 60.107 55.000 13.02 0.00 0.00 2.17
2910 3199 1.528824 CTCCATGGGGCACGAGATT 59.471 57.895 13.02 0.00 0.00 2.40
2911 3200 2.446848 CCTCCATGGGGCACGAGAT 61.447 63.158 13.02 0.00 0.00 2.75
2912 3201 3.083349 CCTCCATGGGGCACGAGA 61.083 66.667 13.02 0.00 0.00 4.04
2921 3210 1.064166 AGTCAAGAATGCCCTCCATGG 60.064 52.381 4.97 4.97 33.49 3.66
2922 3211 2.431954 AGTCAAGAATGCCCTCCATG 57.568 50.000 0.00 0.00 33.49 3.66
2923 3212 3.463048 AAAGTCAAGAATGCCCTCCAT 57.537 42.857 0.00 0.00 35.06 3.41
2924 3213 2.978156 AAAGTCAAGAATGCCCTCCA 57.022 45.000 0.00 0.00 0.00 3.86
2925 3214 3.057245 GTGAAAAGTCAAGAATGCCCTCC 60.057 47.826 0.00 0.00 34.87 4.30
2926 3215 3.569701 TGTGAAAAGTCAAGAATGCCCTC 59.430 43.478 0.00 0.00 34.87 4.30
2927 3216 3.319122 GTGTGAAAAGTCAAGAATGCCCT 59.681 43.478 0.00 0.00 34.87 5.19
2928 3217 3.642705 GTGTGAAAAGTCAAGAATGCCC 58.357 45.455 0.00 0.00 34.87 5.36
2929 3218 3.243068 ACGTGTGAAAAGTCAAGAATGCC 60.243 43.478 0.00 0.00 34.87 4.40
2930 3219 3.952535 ACGTGTGAAAAGTCAAGAATGC 58.047 40.909 0.00 0.00 34.87 3.56
2931 3220 4.203828 CGACGTGTGAAAAGTCAAGAATG 58.796 43.478 0.00 0.00 37.14 2.67
2932 3221 3.247648 CCGACGTGTGAAAAGTCAAGAAT 59.752 43.478 0.00 0.00 37.14 2.40
2933 3222 2.605818 CCGACGTGTGAAAAGTCAAGAA 59.394 45.455 0.00 0.00 37.14 2.52
2934 3223 2.198406 CCGACGTGTGAAAAGTCAAGA 58.802 47.619 0.00 0.00 37.14 3.02
2935 3224 1.332904 GCCGACGTGTGAAAAGTCAAG 60.333 52.381 0.00 0.00 37.14 3.02
2936 3225 0.653636 GCCGACGTGTGAAAAGTCAA 59.346 50.000 0.00 0.00 37.14 3.18
2937 3226 1.484227 CGCCGACGTGTGAAAAGTCA 61.484 55.000 0.00 0.00 37.14 3.41
2938 3227 1.200839 CGCCGACGTGTGAAAAGTC 59.799 57.895 0.00 0.00 34.30 3.01
2939 3228 3.315796 CGCCGACGTGTGAAAAGT 58.684 55.556 0.00 0.00 33.53 2.66
2950 3239 2.533129 CGAGTTCCTTTTATACGCCGAC 59.467 50.000 0.00 0.00 0.00 4.79
2951 3240 2.801063 CGAGTTCCTTTTATACGCCGA 58.199 47.619 0.00 0.00 0.00 5.54
2952 3241 1.257155 GCGAGTTCCTTTTATACGCCG 59.743 52.381 0.00 0.00 38.94 6.46
2954 3243 1.596260 GGGCGAGTTCCTTTTATACGC 59.404 52.381 0.00 0.00 43.00 4.42
2955 3244 3.121544 GAGGGCGAGTTCCTTTTATACG 58.878 50.000 0.00 0.00 34.21 3.06
2956 3245 3.464907 GGAGGGCGAGTTCCTTTTATAC 58.535 50.000 0.00 0.00 34.21 1.47
2957 3246 2.101917 CGGAGGGCGAGTTCCTTTTATA 59.898 50.000 0.00 0.00 34.21 0.98
2958 3247 1.134491 CGGAGGGCGAGTTCCTTTTAT 60.134 52.381 0.00 0.00 34.21 1.40
2959 3248 0.248289 CGGAGGGCGAGTTCCTTTTA 59.752 55.000 0.00 0.00 34.21 1.52
2960 3249 1.003718 CGGAGGGCGAGTTCCTTTT 60.004 57.895 0.00 0.00 34.21 2.27
2961 3250 1.765597 AACGGAGGGCGAGTTCCTTT 61.766 55.000 0.00 0.00 34.21 3.11
2962 3251 2.214920 AACGGAGGGCGAGTTCCTT 61.215 57.895 0.00 0.00 34.21 3.36
2963 3252 2.603776 AACGGAGGGCGAGTTCCT 60.604 61.111 0.00 0.00 37.33 3.36
2964 3253 2.434359 CAACGGAGGGCGAGTTCC 60.434 66.667 0.00 0.00 0.00 3.62
2965 3254 3.119096 GCAACGGAGGGCGAGTTC 61.119 66.667 0.00 0.00 0.00 3.01
2983 3272 4.704833 TGGAGTGAAGCAGCGGGC 62.705 66.667 0.00 0.00 45.30 6.13
2984 3273 2.435586 CTGGAGTGAAGCAGCGGG 60.436 66.667 0.00 0.00 0.00 6.13
2985 3274 3.123620 GCTGGAGTGAAGCAGCGG 61.124 66.667 0.00 0.00 40.52 5.52
2986 3275 3.123620 GGCTGGAGTGAAGCAGCG 61.124 66.667 0.00 0.00 42.69 5.18
2987 3276 3.123620 CGGCTGGAGTGAAGCAGC 61.124 66.667 0.00 0.00 42.69 5.25
2988 3277 3.123620 GCGGCTGGAGTGAAGCAG 61.124 66.667 0.00 0.00 42.69 4.24
2989 3278 4.704833 GGCGGCTGGAGTGAAGCA 62.705 66.667 0.00 0.00 42.69 3.91


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

AutoCloner maintained by Alex Coulton.