Multiple sequence alignment - TraesCS6D01G344400

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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 TraesCS6D01G344400 chr6D 100.000 3403 0 0 1 3403 444131207 444134609 0.000000e+00 6285.0
1 TraesCS6D01G344400 chr6B 88.373 2348 164 53 1 2286 668771491 668773791 0.000000e+00 2723.0
2 TraesCS6D01G344400 chr6B 84.649 456 41 20 2318 2759 668773791 668774231 8.730000e-116 427.0
3 TraesCS6D01G344400 chr6B 78.967 542 49 25 2858 3364 668774345 668774856 3.300000e-80 309.0
4 TraesCS6D01G344400 chr6B 85.484 62 6 3 1476 1535 668773140 668773200 1.020000e-05 62.1
5 TraesCS6D01G344400 chr6B 90.698 43 4 0 1643 1685 31682793 31682835 1.320000e-04 58.4
6 TraesCS6D01G344400 chr6A 88.529 2005 118 57 816 2780 591727965 591729897 0.000000e+00 2326.0
7 TraesCS6D01G344400 chr6A 83.678 484 38 18 320 778 591727504 591727971 5.250000e-113 418.0
8 TraesCS6D01G344400 chr6A 86.207 145 11 5 3018 3162 591729987 591730122 7.610000e-32 148.0
9 TraesCS6D01G344400 chr6A 87.500 112 7 4 196 300 591727334 591727445 4.610000e-24 122.0
10 TraesCS6D01G344400 chr3A 83.965 686 59 26 2146 2812 193127009 193126356 8.070000e-171 610.0
11 TraesCS6D01G344400 chr3A 79.902 204 22 10 2912 3103 193126300 193126104 7.660000e-27 132.0
12 TraesCS6D01G344400 chr5A 83.480 684 57 25 2148 2812 278172708 278173354 1.360000e-163 586.0
13 TraesCS6D01G344400 chr5A 81.592 201 18 10 2912 3100 278173410 278173603 7.610000e-32 148.0
14 TraesCS6D01G344400 chr1D 92.073 164 12 1 1473 1635 163675171 163675008 2.640000e-56 230.0
15 TraesCS6D01G344400 chr3D 95.745 94 3 1 1543 1635 16901522 16901615 2.120000e-32 150.0
16 TraesCS6D01G344400 chr7B 90.698 43 4 0 1643 1685 572053216 572053174 1.320000e-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 TraesCS6D01G344400 chr6D 444131207 444134609 3402 False 6285.000 6285 100.00000 1 3403 1 chr6D.!!$F1 3402
1 TraesCS6D01G344400 chr6B 668771491 668774856 3365 False 880.275 2723 84.36825 1 3364 4 chr6B.!!$F2 3363
2 TraesCS6D01G344400 chr6A 591727334 591730122 2788 False 753.500 2326 86.47850 196 3162 4 chr6A.!!$F1 2966
3 TraesCS6D01G344400 chr3A 193126104 193127009 905 True 371.000 610 81.93350 2146 3103 2 chr3A.!!$R1 957
4 TraesCS6D01G344400 chr5A 278172708 278173603 895 False 367.000 586 82.53600 2148 3100 2 chr5A.!!$F1 952

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
98 108 0.109551 GAAAGAAAAGGCGCCTCAGC 60.110 55.0 32.93 21.15 0.00 4.26 F
542 623 0.460987 GCTGCGTCTGTGCCTATCTT 60.461 55.0 0.00 0.00 0.00 2.40 F
1008 1106 0.766674 CACCCGGATATCTCCCCCAA 60.767 60.0 0.73 0.00 38.45 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1214 2.202797 TGGATTCGCTCGCTGCTC 60.203 61.111 0.0 0.0 40.11 4.26 R
2102 2231 0.602372 GGATCTGATCCGGCAAGCTC 60.602 60.000 20.2 0.0 40.13 4.09 R
2762 2959 0.312729 TCAGACTGTTGCGCGAGTTA 59.687 50.000 12.1 0.0 0.00 2.24 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
31 32 3.771160 GGACCCGCACTCCACGAT 61.771 66.667 0.00 0.00 0.00 3.73
32 33 2.509336 GACCCGCACTCCACGATG 60.509 66.667 0.00 0.00 0.00 3.84
33 34 4.760047 ACCCGCACTCCACGATGC 62.760 66.667 0.00 0.00 38.52 3.91
37 38 3.084579 GCACTCCACGATGCGAAG 58.915 61.111 0.00 0.00 30.97 3.79
77 82 1.334149 GGCGAGCCGAAAATATGCTTC 60.334 52.381 0.00 0.00 34.99 3.86
78 83 1.657538 GCGAGCCGAAAATATGCTTCG 60.658 52.381 11.46 11.46 44.11 3.79
92 102 0.729478 GCTTCGGAAAGAAAAGGCGC 60.729 55.000 0.00 0.00 38.57 6.53
93 103 0.109735 CTTCGGAAAGAAAAGGCGCC 60.110 55.000 21.89 21.89 38.57 6.53
94 104 0.536460 TTCGGAAAGAAAAGGCGCCT 60.536 50.000 27.08 27.08 35.61 5.52
95 105 0.953960 TCGGAAAGAAAAGGCGCCTC 60.954 55.000 32.93 18.58 0.00 4.70
96 106 1.234615 CGGAAAGAAAAGGCGCCTCA 61.235 55.000 32.93 0.00 0.00 3.86
97 107 0.523519 GGAAAGAAAAGGCGCCTCAG 59.476 55.000 32.93 0.00 0.00 3.35
98 108 0.109551 GAAAGAAAAGGCGCCTCAGC 60.110 55.000 32.93 21.15 0.00 4.26
99 109 0.538287 AAAGAAAAGGCGCCTCAGCT 60.538 50.000 32.93 23.12 36.60 4.24
100 110 1.239968 AAGAAAAGGCGCCTCAGCTG 61.240 55.000 32.93 7.63 36.60 4.24
101 111 1.672356 GAAAAGGCGCCTCAGCTGA 60.672 57.895 32.93 17.19 36.60 4.26
102 112 1.228245 AAAAGGCGCCTCAGCTGAA 60.228 52.632 32.93 1.63 36.60 3.02
103 113 0.823356 AAAAGGCGCCTCAGCTGAAA 60.823 50.000 32.93 0.00 36.60 2.69
104 114 0.823356 AAAGGCGCCTCAGCTGAAAA 60.823 50.000 32.93 0.00 36.60 2.29
105 115 0.823356 AAGGCGCCTCAGCTGAAAAA 60.823 50.000 32.93 0.00 36.60 1.94
106 116 0.610232 AGGCGCCTCAGCTGAAAAAT 60.610 50.000 27.08 0.00 36.60 1.82
107 117 1.094785 GGCGCCTCAGCTGAAAAATA 58.905 50.000 22.15 0.00 36.60 1.40
108 118 1.064654 GGCGCCTCAGCTGAAAAATAG 59.935 52.381 22.15 4.57 36.60 1.73
109 119 1.064654 GCGCCTCAGCTGAAAAATAGG 59.935 52.381 18.85 14.99 36.60 2.57
136 146 4.664677 ACCACGACGTGCTCTGCC 62.665 66.667 22.46 0.00 31.34 4.85
287 303 3.874543 ACACAGCATAATCCGCGAATAAA 59.125 39.130 8.23 0.00 0.00 1.40
288 304 4.515191 ACACAGCATAATCCGCGAATAAAT 59.485 37.500 8.23 0.00 0.00 1.40
290 306 5.565259 CACAGCATAATCCGCGAATAAATTC 59.435 40.000 8.23 0.00 0.00 2.17
291 311 5.088739 CAGCATAATCCGCGAATAAATTCC 58.911 41.667 8.23 0.00 33.28 3.01
296 316 7.169140 GCATAATCCGCGAATAAATTCCTTTTT 59.831 33.333 8.23 0.00 33.28 1.94
373 438 6.925718 ACTCATCAATTATATCAGTCACGGTG 59.074 38.462 0.56 0.56 0.00 4.94
535 616 2.537560 AACTGTGCTGCGTCTGTGC 61.538 57.895 0.00 0.00 0.00 4.57
538 619 2.048222 GTGCTGCGTCTGTGCCTA 60.048 61.111 0.00 0.00 0.00 3.93
539 620 1.448540 GTGCTGCGTCTGTGCCTAT 60.449 57.895 0.00 0.00 0.00 2.57
540 621 1.153568 TGCTGCGTCTGTGCCTATC 60.154 57.895 0.00 0.00 0.00 2.08
541 622 1.142748 GCTGCGTCTGTGCCTATCT 59.857 57.895 0.00 0.00 0.00 1.98
542 623 0.460987 GCTGCGTCTGTGCCTATCTT 60.461 55.000 0.00 0.00 0.00 2.40
543 624 2.009042 GCTGCGTCTGTGCCTATCTTT 61.009 52.381 0.00 0.00 0.00 2.52
545 626 2.744202 CTGCGTCTGTGCCTATCTTTTT 59.256 45.455 0.00 0.00 0.00 1.94
673 764 1.652124 CCGAAACGTCCACTATTCACG 59.348 52.381 0.00 0.00 39.48 4.35
674 765 2.587956 CGAAACGTCCACTATTCACGA 58.412 47.619 0.00 0.00 37.00 4.35
742 835 4.785453 CGCAAGTCCAGGGGCTCC 62.785 72.222 0.00 0.00 0.00 4.70
841 934 6.035435 CACGTCAGACCAATAAAGATCTCTTG 59.965 42.308 0.00 0.73 36.12 3.02
842 935 5.006165 CGTCAGACCAATAAAGATCTCTTGC 59.994 44.000 0.00 0.00 36.12 4.01
853 946 1.423161 GATCTCTTGCCCCCTAAGCAT 59.577 52.381 0.00 0.00 40.59 3.79
856 949 2.172717 TCTCTTGCCCCCTAAGCATAAC 59.827 50.000 0.00 0.00 40.59 1.89
857 950 1.134220 TCTTGCCCCCTAAGCATAACG 60.134 52.381 0.00 0.00 40.59 3.18
966 1064 1.727335 CGCTCGGTTTCTTCTTCTTCC 59.273 52.381 0.00 0.00 0.00 3.46
967 1065 2.610727 CGCTCGGTTTCTTCTTCTTCCT 60.611 50.000 0.00 0.00 0.00 3.36
968 1066 2.997303 GCTCGGTTTCTTCTTCTTCCTC 59.003 50.000 0.00 0.00 0.00 3.71
973 1071 7.470841 GCTCGGTTTCTTCTTCTTCCTCTATAT 60.471 40.741 0.00 0.00 0.00 0.86
1008 1106 0.766674 CACCCGGATATCTCCCCCAA 60.767 60.000 0.73 0.00 38.45 4.12
1281 1400 4.760047 CCTCCCAAGGTGGTCGCG 62.760 72.222 0.00 0.00 37.94 5.87
1750 1872 3.190878 CCAAGAAGATGGTGCCGC 58.809 61.111 0.00 0.00 35.65 6.53
1824 1946 2.623431 AGCTCTCTCCCCCTCCCT 60.623 66.667 0.00 0.00 0.00 4.20
1839 1961 1.377333 CCCTGGGTTCTTCTTCCGC 60.377 63.158 3.97 0.00 0.00 5.54
1996 2118 1.278337 CTCGTCTCGCCTCATCTCG 59.722 63.158 0.00 0.00 0.00 4.04
2018 2141 3.185391 GTCGGAAGCAACAAGAAGAAGAG 59.815 47.826 0.00 0.00 0.00 2.85
2020 2143 3.481453 GGAAGCAACAAGAAGAAGAGGT 58.519 45.455 0.00 0.00 0.00 3.85
2175 2308 0.251033 TTCAGAGGAAGGGTCGTCGA 60.251 55.000 0.00 0.00 42.35 4.20
2267 2414 2.028130 TGTTTGGTTCGCCTTGATGTT 58.972 42.857 0.00 0.00 38.36 2.71
2302 2449 4.748102 TGTTAATTGTCGGTCAGTCAGAAC 59.252 41.667 0.00 0.00 0.00 3.01
2381 2535 4.346709 TCTCAGGTTTGGTTACAGTGATGA 59.653 41.667 0.00 0.00 0.00 2.92
2412 2566 1.002900 AGTTTATGTGTGCGTGTGTGC 60.003 47.619 0.00 0.00 0.00 4.57
2413 2567 0.041751 TTTATGTGTGCGTGTGTGCG 60.042 50.000 0.00 0.00 37.81 5.34
2429 2601 0.177141 TGCGGGTCGAAGATTAAGGG 59.823 55.000 0.00 0.00 40.67 3.95
2434 2606 3.492137 CGGGTCGAAGATTAAGGGTAAGG 60.492 52.174 0.00 0.00 40.67 2.69
2435 2607 3.453717 GGGTCGAAGATTAAGGGTAAGGT 59.546 47.826 0.00 0.00 40.67 3.50
2436 2608 4.651045 GGGTCGAAGATTAAGGGTAAGGTA 59.349 45.833 0.00 0.00 40.67 3.08
2437 2609 5.306419 GGGTCGAAGATTAAGGGTAAGGTAT 59.694 44.000 0.00 0.00 40.67 2.73
2438 2610 6.221659 GGTCGAAGATTAAGGGTAAGGTATG 58.778 44.000 0.00 0.00 40.67 2.39
2439 2611 6.041296 GGTCGAAGATTAAGGGTAAGGTATGA 59.959 42.308 0.00 0.00 40.67 2.15
2440 2612 7.146648 GTCGAAGATTAAGGGTAAGGTATGAG 58.853 42.308 0.00 0.00 40.67 2.90
2441 2613 6.837568 TCGAAGATTAAGGGTAAGGTATGAGT 59.162 38.462 0.00 0.00 0.00 3.41
2452 2624 8.871125 AGGGTAAGGTATGAGTTATTATGAGTG 58.129 37.037 0.00 0.00 0.00 3.51
2457 2629 8.668510 AGGTATGAGTTATTATGAGTGCAAAG 57.331 34.615 0.00 0.00 0.00 2.77
2474 2646 7.730084 AGTGCAAAGTTATATATGCTGAGAGA 58.270 34.615 7.39 0.00 39.49 3.10
2476 2648 8.441608 GTGCAAAGTTATATATGCTGAGAGATG 58.558 37.037 7.39 0.00 39.49 2.90
2547 2730 3.929610 GAGAAGTGTGTCTAGTTGCATCC 59.070 47.826 0.00 0.00 0.00 3.51
2567 2750 2.545952 CCGCTAGGCTATGTGTAGTTGG 60.546 54.545 0.00 0.00 0.00 3.77
2586 2769 6.970484 AGTTGGTTTAGCAACTGAGTTAATG 58.030 36.000 22.32 0.00 39.82 1.90
2587 2770 6.546034 AGTTGGTTTAGCAACTGAGTTAATGT 59.454 34.615 22.32 0.00 39.82 2.71
2591 2774 7.717875 TGGTTTAGCAACTGAGTTAATGTTAGT 59.282 33.333 0.00 0.00 32.90 2.24
2593 2776 9.595357 GTTTAGCAACTGAGTTAATGTTAGTTC 57.405 33.333 0.00 0.00 29.78 3.01
2645 2831 8.543774 AGATATCCAAAAGTCTGTGTCTGTATT 58.456 33.333 0.00 0.00 0.00 1.89
2738 2935 4.318332 TGGTGTGTGATCATCTGTTCTTC 58.682 43.478 0.00 0.00 0.00 2.87
2752 2949 9.159364 TCATCTGTTCTTCATTCTTGTTCATAG 57.841 33.333 0.00 0.00 0.00 2.23
2770 2967 6.089920 TCATAGTGATTTGTTTAACTCGCG 57.910 37.500 0.00 0.00 32.95 5.87
2785 3014 0.733909 TCGCGCAACAGTCTGATCAG 60.734 55.000 17.07 17.07 0.00 2.90
2792 3021 3.063180 GCAACAGTCTGATCAGGAATTCG 59.937 47.826 22.42 8.92 0.00 3.34
2814 3045 3.814283 GCTGAGCTCTCCCTTTATGAATG 59.186 47.826 16.19 0.00 0.00 2.67
2815 3046 4.387598 CTGAGCTCTCCCTTTATGAATGG 58.612 47.826 16.19 0.00 0.00 3.16
2818 3049 5.133322 TGAGCTCTCCCTTTATGAATGGATT 59.867 40.000 16.19 0.00 30.49 3.01
2819 3050 5.383476 AGCTCTCCCTTTATGAATGGATTG 58.617 41.667 0.00 0.00 30.49 2.67
2822 3053 6.150809 GCTCTCCCTTTATGAATGGATTGATC 59.849 42.308 0.00 0.00 30.49 2.92
2823 3054 7.398289 TCTCCCTTTATGAATGGATTGATCT 57.602 36.000 0.00 0.00 30.49 2.75
2824 3055 7.456725 TCTCCCTTTATGAATGGATTGATCTC 58.543 38.462 0.00 0.00 30.49 2.75
2826 3057 7.819500 TCCCTTTATGAATGGATTGATCTCTT 58.180 34.615 0.00 0.00 0.00 2.85
2827 3058 7.722728 TCCCTTTATGAATGGATTGATCTCTTG 59.277 37.037 0.00 0.00 0.00 3.02
2831 3078 4.445453 TGAATGGATTGATCTCTTGACCG 58.555 43.478 0.00 0.00 0.00 4.79
2842 3089 3.599343 TCTCTTGACCGGTGATGAAATG 58.401 45.455 14.63 0.00 0.00 2.32
2844 3091 3.073678 TCTTGACCGGTGATGAAATGTG 58.926 45.455 14.63 0.00 0.00 3.21
2846 3093 2.857483 TGACCGGTGATGAAATGTGTT 58.143 42.857 14.63 0.00 0.00 3.32
2847 3094 2.551887 TGACCGGTGATGAAATGTGTTG 59.448 45.455 14.63 0.00 0.00 3.33
2851 3098 2.551887 CGGTGATGAAATGTGTTGGTGA 59.448 45.455 0.00 0.00 0.00 4.02
2852 3099 3.191162 CGGTGATGAAATGTGTTGGTGAT 59.809 43.478 0.00 0.00 0.00 3.06
2853 3100 4.487948 GGTGATGAAATGTGTTGGTGATG 58.512 43.478 0.00 0.00 0.00 3.07
2854 3101 4.022068 GGTGATGAAATGTGTTGGTGATGT 60.022 41.667 0.00 0.00 0.00 3.06
2855 3102 5.509501 GGTGATGAAATGTGTTGGTGATGTT 60.510 40.000 0.00 0.00 0.00 2.71
2856 3103 5.984926 GTGATGAAATGTGTTGGTGATGTTT 59.015 36.000 0.00 0.00 0.00 2.83
2884 3131 3.828451 CCAGATTGTTTTCCTCATGGTGT 59.172 43.478 0.00 0.00 34.23 4.16
2889 3136 1.000274 GTTTTCCTCATGGTGTGTGGC 60.000 52.381 0.00 0.00 40.52 5.01
2921 3168 8.225107 CAGGATTTTGTTGACAATAATTTGCAG 58.775 33.333 0.00 0.00 36.22 4.41
2928 3175 3.171277 GACAATAATTTGCAGACCACGC 58.829 45.455 0.00 0.00 36.22 5.34
2962 3209 2.556257 GCAATTCGTTTGGTTTTGGGT 58.444 42.857 3.68 0.00 35.75 4.51
2978 3241 2.715005 GTTGCTGTTGCGTGCTCA 59.285 55.556 0.00 0.00 43.34 4.26
2979 3242 1.283793 GTTGCTGTTGCGTGCTCAT 59.716 52.632 0.00 0.00 43.34 2.90
2997 3260 5.355071 TGCTCATTAGATAGCCTTGTGTTTG 59.645 40.000 0.00 0.00 37.97 2.93
3005 3268 2.132996 CCTTGTGTTTGGCAGCCCA 61.133 57.895 9.64 0.00 40.06 5.36
3045 3311 3.347216 GTGGTGATTGAATGCCACTACT 58.653 45.455 16.52 0.00 45.64 2.57
3100 3366 4.767255 CTCCACCAGCCAGCCGTC 62.767 72.222 0.00 0.00 0.00 4.79
3102 3368 4.335647 CCACCAGCCAGCCGTCTT 62.336 66.667 0.00 0.00 0.00 3.01
3103 3369 3.052082 CACCAGCCAGCCGTCTTG 61.052 66.667 0.00 0.00 0.00 3.02
3104 3370 3.560251 ACCAGCCAGCCGTCTTGT 61.560 61.111 0.00 0.00 0.00 3.16
3105 3371 3.052082 CCAGCCAGCCGTCTTGTG 61.052 66.667 0.00 0.00 0.00 3.33
3106 3372 3.052082 CAGCCAGCCGTCTTGTGG 61.052 66.667 0.00 0.00 0.00 4.17
3131 3397 5.876357 AGCTGATTTTCCACACCTAACTTA 58.124 37.500 0.00 0.00 0.00 2.24
3132 3398 6.485171 AGCTGATTTTCCACACCTAACTTAT 58.515 36.000 0.00 0.00 0.00 1.73
3145 3411 5.882557 CACCTAACTTATCTGGCTGTTGATT 59.117 40.000 0.00 0.00 0.00 2.57
3146 3412 7.047891 CACCTAACTTATCTGGCTGTTGATTA 58.952 38.462 0.00 0.00 0.00 1.75
3151 3417 8.757982 AACTTATCTGGCTGTTGATTAATCAT 57.242 30.769 18.61 3.58 36.56 2.45
3152 3418 8.757982 ACTTATCTGGCTGTTGATTAATCATT 57.242 30.769 18.61 0.00 36.56 2.57
3163 3429 7.905265 TGTTGATTAATCATTCCAACAACCAT 58.095 30.769 18.61 0.00 42.50 3.55
3164 3430 7.818446 TGTTGATTAATCATTCCAACAACCATG 59.182 33.333 18.61 0.00 42.50 3.66
3166 3432 5.999205 TTAATCATTCCAACAACCATGCT 57.001 34.783 0.00 0.00 0.00 3.79
3169 3435 2.821378 TCATTCCAACAACCATGCTGAG 59.179 45.455 0.43 0.00 0.00 3.35
3172 3438 1.252904 CCAACAACCATGCTGAGGGG 61.253 60.000 0.43 0.00 0.00 4.79
3173 3439 0.251297 CAACAACCATGCTGAGGGGA 60.251 55.000 0.43 0.00 0.00 4.81
3174 3440 0.038744 AACAACCATGCTGAGGGGAG 59.961 55.000 0.43 0.00 0.00 4.30
3178 3444 1.383664 CCATGCTGAGGGGAGGAGA 60.384 63.158 0.00 0.00 0.00 3.71
3187 3453 4.331108 CTGAGGGGAGGAGAAAAGAAAAG 58.669 47.826 0.00 0.00 0.00 2.27
3190 3456 5.013183 TGAGGGGAGGAGAAAAGAAAAGTAG 59.987 44.000 0.00 0.00 0.00 2.57
3191 3457 4.914581 AGGGGAGGAGAAAAGAAAAGTAGT 59.085 41.667 0.00 0.00 0.00 2.73
3192 3458 6.089502 AGGGGAGGAGAAAAGAAAAGTAGTA 58.910 40.000 0.00 0.00 0.00 1.82
3193 3459 6.736179 AGGGGAGGAGAAAAGAAAAGTAGTAT 59.264 38.462 0.00 0.00 0.00 2.12
3194 3460 6.824196 GGGGAGGAGAAAAGAAAAGTAGTATG 59.176 42.308 0.00 0.00 0.00 2.39
3195 3461 7.311109 GGGGAGGAGAAAAGAAAAGTAGTATGA 60.311 40.741 0.00 0.00 0.00 2.15
3196 3462 7.766738 GGGAGGAGAAAAGAAAAGTAGTATGAG 59.233 40.741 0.00 0.00 0.00 2.90
3197 3463 7.279090 GGAGGAGAAAAGAAAAGTAGTATGAGC 59.721 40.741 0.00 0.00 0.00 4.26
3198 3464 7.912719 AGGAGAAAAGAAAAGTAGTATGAGCT 58.087 34.615 0.00 0.00 0.00 4.09
3199 3465 7.821846 AGGAGAAAAGAAAAGTAGTATGAGCTG 59.178 37.037 0.00 0.00 0.00 4.24
3200 3466 7.065204 GGAGAAAAGAAAAGTAGTATGAGCTGG 59.935 40.741 0.00 0.00 0.00 4.85
3201 3467 6.881602 AGAAAAGAAAAGTAGTATGAGCTGGG 59.118 38.462 0.00 0.00 0.00 4.45
3202 3468 5.763876 AAGAAAAGTAGTATGAGCTGGGT 57.236 39.130 0.00 0.00 0.00 4.51
3203 3469 5.091261 AGAAAAGTAGTATGAGCTGGGTG 57.909 43.478 0.00 0.00 0.00 4.61
3204 3470 4.532521 AGAAAAGTAGTATGAGCTGGGTGT 59.467 41.667 0.00 0.00 0.00 4.16
3205 3471 3.895232 AAGTAGTATGAGCTGGGTGTG 57.105 47.619 0.00 0.00 0.00 3.82
3206 3472 2.111384 AGTAGTATGAGCTGGGTGTGG 58.889 52.381 0.00 0.00 0.00 4.17
3207 3473 1.139058 GTAGTATGAGCTGGGTGTGGG 59.861 57.143 0.00 0.00 0.00 4.61
3208 3474 1.224592 GTATGAGCTGGGTGTGGGG 59.775 63.158 0.00 0.00 0.00 4.96
3209 3475 2.000701 TATGAGCTGGGTGTGGGGG 61.001 63.158 0.00 0.00 0.00 5.40
3210 3476 2.484868 TATGAGCTGGGTGTGGGGGA 62.485 60.000 0.00 0.00 0.00 4.81
3211 3477 3.721706 GAGCTGGGTGTGGGGGAG 61.722 72.222 0.00 0.00 0.00 4.30
3212 3478 4.270153 AGCTGGGTGTGGGGGAGA 62.270 66.667 0.00 0.00 0.00 3.71
3213 3479 3.256960 GCTGGGTGTGGGGGAGAA 61.257 66.667 0.00 0.00 0.00 2.87
3214 3480 3.081554 CTGGGTGTGGGGGAGAAG 58.918 66.667 0.00 0.00 0.00 2.85
3215 3481 1.538876 CTGGGTGTGGGGGAGAAGA 60.539 63.158 0.00 0.00 0.00 2.87
3216 3482 1.073319 TGGGTGTGGGGGAGAAGAA 60.073 57.895 0.00 0.00 0.00 2.52
3217 3483 0.477597 TGGGTGTGGGGGAGAAGAAT 60.478 55.000 0.00 0.00 0.00 2.40
3218 3484 1.203505 TGGGTGTGGGGGAGAAGAATA 60.204 52.381 0.00 0.00 0.00 1.75
3220 3486 1.212195 GGTGTGGGGGAGAAGAATACC 59.788 57.143 0.00 0.00 0.00 2.73
3223 3489 1.913419 GTGGGGGAGAAGAATACCACA 59.087 52.381 6.76 0.00 45.72 4.17
3237 3503 8.472007 AAGAATACCACAATTCAGTTTGGTTA 57.528 30.769 0.00 0.00 42.50 2.85
3243 3509 4.582656 CACAATTCAGTTTGGTTAGACCCA 59.417 41.667 0.00 0.00 37.50 4.51
3257 3523 5.461526 GTTAGACCCAGAAATTTGCTGAAC 58.538 41.667 5.92 0.00 35.39 3.18
3276 3543 3.601685 TGGTGACGCGTCTGCTGA 61.602 61.111 36.27 16.27 39.65 4.26
3279 3546 3.977244 TGACGCGTCTGCTGAGCA 61.977 61.111 36.27 14.61 39.65 4.26
3280 3547 2.734723 GACGCGTCTGCTGAGCAA 60.735 61.111 31.12 0.00 38.41 3.91
3283 3550 1.439365 CGCGTCTGCTGAGCAAAAC 60.439 57.895 9.07 9.03 38.41 2.43
3284 3551 1.835483 CGCGTCTGCTGAGCAAAACT 61.835 55.000 9.07 0.00 38.41 2.66
3317 3585 1.673033 CGCCACTTGAACCTTCGAGAT 60.673 52.381 8.98 0.00 40.46 2.75
3339 3619 3.531283 GCTCCGATCAGCCTCAGA 58.469 61.111 0.00 0.00 32.76 3.27
3340 3620 1.067250 GCTCCGATCAGCCTCAGAC 59.933 63.158 0.00 0.00 32.76 3.51
3364 3644 1.374758 GTGGTTGCCGTCTCTCAGG 60.375 63.158 0.00 0.00 0.00 3.86
3365 3645 1.533033 TGGTTGCCGTCTCTCAGGA 60.533 57.895 0.00 0.00 0.00 3.86
3366 3646 0.904865 TGGTTGCCGTCTCTCAGGAT 60.905 55.000 0.00 0.00 0.00 3.24
3367 3647 0.250513 GGTTGCCGTCTCTCAGGATT 59.749 55.000 0.00 0.00 0.00 3.01
3368 3648 1.363744 GTTGCCGTCTCTCAGGATTG 58.636 55.000 0.00 0.00 0.00 2.67
3369 3649 1.066858 GTTGCCGTCTCTCAGGATTGA 60.067 52.381 0.00 0.00 0.00 2.57
3370 3650 1.489481 TGCCGTCTCTCAGGATTGAT 58.511 50.000 0.00 0.00 31.68 2.57
3371 3651 2.666317 TGCCGTCTCTCAGGATTGATA 58.334 47.619 0.00 0.00 31.68 2.15
3372 3652 2.625314 TGCCGTCTCTCAGGATTGATAG 59.375 50.000 0.00 0.00 31.68 2.08
3373 3653 2.609244 GCCGTCTCTCAGGATTGATAGC 60.609 54.545 0.00 0.00 31.68 2.97
3374 3654 2.351253 CCGTCTCTCAGGATTGATAGCG 60.351 54.545 0.00 0.00 32.44 4.26
3375 3655 2.351253 CGTCTCTCAGGATTGATAGCGG 60.351 54.545 0.00 0.00 30.83 5.52
3376 3656 1.615883 TCTCTCAGGATTGATAGCGGC 59.384 52.381 0.00 0.00 31.68 6.53
3377 3657 0.315251 TCTCAGGATTGATAGCGGCG 59.685 55.000 0.51 0.51 31.68 6.46
3378 3658 0.032678 CTCAGGATTGATAGCGGCGT 59.967 55.000 9.37 0.00 31.68 5.68
3379 3659 0.032130 TCAGGATTGATAGCGGCGTC 59.968 55.000 9.37 0.13 0.00 5.19
3380 3660 0.032678 CAGGATTGATAGCGGCGTCT 59.967 55.000 9.37 8.98 0.00 4.18
3381 3661 1.269723 CAGGATTGATAGCGGCGTCTA 59.730 52.381 9.37 11.08 0.00 2.59
3382 3662 1.269998 AGGATTGATAGCGGCGTCTAC 59.730 52.381 9.37 6.42 0.00 2.59
3383 3663 1.328439 GATTGATAGCGGCGTCTACG 58.672 55.000 9.37 0.00 43.27 3.51
3384 3664 0.666913 ATTGATAGCGGCGTCTACGT 59.333 50.000 9.37 0.00 42.22 3.57
3385 3665 0.028505 TTGATAGCGGCGTCTACGTC 59.971 55.000 9.37 6.85 42.22 4.34
3386 3666 0.812811 TGATAGCGGCGTCTACGTCT 60.813 55.000 9.37 0.00 42.59 4.18
3387 3667 0.110733 GATAGCGGCGTCTACGTCTC 60.111 60.000 9.37 0.00 42.59 3.36
3388 3668 1.505477 ATAGCGGCGTCTACGTCTCC 61.505 60.000 9.37 0.00 42.59 3.71
3389 3669 2.584261 TAGCGGCGTCTACGTCTCCT 62.584 60.000 9.37 4.29 42.59 3.69
3390 3670 3.048941 GCGGCGTCTACGTCTCCTT 62.049 63.158 9.37 0.00 42.59 3.36
3391 3671 1.226323 CGGCGTCTACGTCTCCTTG 60.226 63.158 5.50 0.00 42.59 3.61
3392 3672 1.881602 GGCGTCTACGTCTCCTTGT 59.118 57.895 4.24 0.00 41.36 3.16
3393 3673 0.179169 GGCGTCTACGTCTCCTTGTC 60.179 60.000 4.24 0.00 41.36 3.18
3394 3674 0.520404 GCGTCTACGTCTCCTTGTCA 59.480 55.000 4.24 0.00 42.22 3.58
3395 3675 1.466024 GCGTCTACGTCTCCTTGTCAG 60.466 57.143 4.24 0.00 42.22 3.51
3396 3676 1.805345 CGTCTACGTCTCCTTGTCAGT 59.195 52.381 0.00 0.00 34.11 3.41
3397 3677 2.159680 CGTCTACGTCTCCTTGTCAGTC 60.160 54.545 0.00 0.00 34.11 3.51
3398 3678 2.812591 GTCTACGTCTCCTTGTCAGTCA 59.187 50.000 0.00 0.00 0.00 3.41
3399 3679 3.252701 GTCTACGTCTCCTTGTCAGTCAA 59.747 47.826 0.00 0.00 34.61 3.18
3400 3680 7.802305 CGTCTACGTCTCCTTGTCAGTCAAG 62.802 52.000 0.00 0.70 42.32 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.509336 CATCGTGGAGTGCGGGTC 60.509 66.667 0.00 0.00 0.00 4.46
37 38 1.911293 TTTCGCGTCCAGCTTGATGC 61.911 55.000 19.51 19.51 45.59 3.91
40 41 1.667830 CCTTTCGCGTCCAGCTTGA 60.668 57.895 5.77 0.00 45.59 3.02
41 42 2.863153 CCTTTCGCGTCCAGCTTG 59.137 61.111 5.77 0.00 45.59 4.01
42 43 3.050275 GCCTTTCGCGTCCAGCTT 61.050 61.111 5.77 0.00 45.59 3.74
77 82 1.234615 TGAGGCGCCTTTTCTTTCCG 61.235 55.000 33.34 0.00 0.00 4.30
78 83 0.523519 CTGAGGCGCCTTTTCTTTCC 59.476 55.000 33.34 15.82 0.00 3.13
79 84 0.109551 GCTGAGGCGCCTTTTCTTTC 60.110 55.000 33.34 16.88 0.00 2.62
92 102 6.824305 TCTTTTCCTATTTTTCAGCTGAGG 57.176 37.500 17.43 13.51 0.00 3.86
93 103 8.517878 TCAATCTTTTCCTATTTTTCAGCTGAG 58.482 33.333 17.43 3.86 0.00 3.35
94 104 8.299570 GTCAATCTTTTCCTATTTTTCAGCTGA 58.700 33.333 13.74 13.74 0.00 4.26
95 105 7.543520 GGTCAATCTTTTCCTATTTTTCAGCTG 59.456 37.037 7.63 7.63 0.00 4.24
96 106 7.233348 TGGTCAATCTTTTCCTATTTTTCAGCT 59.767 33.333 0.00 0.00 0.00 4.24
97 107 7.329471 GTGGTCAATCTTTTCCTATTTTTCAGC 59.671 37.037 0.00 0.00 0.00 4.26
98 108 7.538678 CGTGGTCAATCTTTTCCTATTTTTCAG 59.461 37.037 0.00 0.00 0.00 3.02
99 109 7.229707 TCGTGGTCAATCTTTTCCTATTTTTCA 59.770 33.333 0.00 0.00 0.00 2.69
100 110 7.537649 GTCGTGGTCAATCTTTTCCTATTTTTC 59.462 37.037 0.00 0.00 0.00 2.29
101 111 7.368059 GTCGTGGTCAATCTTTTCCTATTTTT 58.632 34.615 0.00 0.00 0.00 1.94
102 112 6.348213 CGTCGTGGTCAATCTTTTCCTATTTT 60.348 38.462 0.00 0.00 0.00 1.82
103 113 5.121768 CGTCGTGGTCAATCTTTTCCTATTT 59.878 40.000 0.00 0.00 0.00 1.40
104 114 4.630069 CGTCGTGGTCAATCTTTTCCTATT 59.370 41.667 0.00 0.00 0.00 1.73
105 115 4.181578 CGTCGTGGTCAATCTTTTCCTAT 58.818 43.478 0.00 0.00 0.00 2.57
106 116 3.006110 ACGTCGTGGTCAATCTTTTCCTA 59.994 43.478 0.00 0.00 0.00 2.94
107 117 2.224209 ACGTCGTGGTCAATCTTTTCCT 60.224 45.455 0.00 0.00 0.00 3.36
108 118 2.096417 CACGTCGTGGTCAATCTTTTCC 60.096 50.000 17.75 0.00 0.00 3.13
109 119 2.661979 GCACGTCGTGGTCAATCTTTTC 60.662 50.000 25.70 1.73 33.64 2.29
218 228 2.005266 ACAGAGGGGCAGCCATGAT 61.005 57.895 15.19 0.00 0.00 2.45
219 229 2.611800 ACAGAGGGGCAGCCATGA 60.612 61.111 15.19 0.00 0.00 3.07
220 230 2.439701 CACAGAGGGGCAGCCATG 60.440 66.667 15.19 8.65 0.00 3.66
221 231 2.611800 TCACAGAGGGGCAGCCAT 60.612 61.111 15.19 0.00 0.00 4.40
222 232 3.640407 GTCACAGAGGGGCAGCCA 61.640 66.667 15.19 0.00 0.00 4.75
334 393 3.601981 GAGTGGTAATCGCTCGCG 58.398 61.111 0.00 0.00 42.30 5.87
346 405 6.367149 CCGTGACTGATATAATTGATGAGTGG 59.633 42.308 0.16 0.00 0.00 4.00
373 438 0.531974 TTCTCATTATCGCCGCACCC 60.532 55.000 0.00 0.00 0.00 4.61
509 587 2.633657 CAGCACAGTTGACGTGGC 59.366 61.111 0.00 0.00 34.85 5.01
545 626 6.130723 CACAGACGCGTACTCAAAAATAAAA 58.869 36.000 13.97 0.00 0.00 1.52
546 627 5.672051 CACAGACGCGTACTCAAAAATAAA 58.328 37.500 13.97 0.00 0.00 1.40
547 628 4.376615 GCACAGACGCGTACTCAAAAATAA 60.377 41.667 13.97 0.00 0.00 1.40
548 629 3.122278 GCACAGACGCGTACTCAAAAATA 59.878 43.478 13.97 0.00 0.00 1.40
550 631 1.259507 GCACAGACGCGTACTCAAAAA 59.740 47.619 13.97 0.00 0.00 1.94
551 632 0.856641 GCACAGACGCGTACTCAAAA 59.143 50.000 13.97 0.00 0.00 2.44
552 633 0.942410 GGCACAGACGCGTACTCAAA 60.942 55.000 13.97 0.00 0.00 2.69
553 634 1.372499 GGCACAGACGCGTACTCAA 60.372 57.895 13.97 0.00 0.00 3.02
554 635 0.956902 TAGGCACAGACGCGTACTCA 60.957 55.000 13.97 0.00 0.00 3.41
555 636 0.381089 ATAGGCACAGACGCGTACTC 59.619 55.000 13.97 0.00 35.29 2.59
556 637 0.381089 GATAGGCACAGACGCGTACT 59.619 55.000 13.97 8.73 35.29 2.73
559 640 2.494918 GGATAGGCACAGACGCGT 59.505 61.111 13.85 13.85 0.00 6.01
561 642 1.972660 AAGGGGATAGGCACAGACGC 61.973 60.000 0.00 0.00 0.00 5.19
562 643 0.105039 GAAGGGGATAGGCACAGACG 59.895 60.000 0.00 0.00 0.00 4.18
563 644 0.470341 GGAAGGGGATAGGCACAGAC 59.530 60.000 0.00 0.00 0.00 3.51
564 645 0.694444 GGGAAGGGGATAGGCACAGA 60.694 60.000 0.00 0.00 0.00 3.41
654 745 2.340577 GTCGTGAATAGTGGACGTTTCG 59.659 50.000 0.00 0.00 34.69 3.46
709 802 0.732196 TGCGTGAAATTTCATGGCGC 60.732 50.000 31.63 31.63 44.96 6.53
715 808 2.293122 CCTGGACTTGCGTGAAATTTCA 59.707 45.455 16.91 16.91 34.20 2.69
742 835 0.322997 TTATTGGCGAGGGTTGGGTG 60.323 55.000 0.00 0.00 0.00 4.61
747 840 1.675552 CCGAATTATTGGCGAGGGTT 58.324 50.000 0.00 0.00 0.00 4.11
812 905 2.465860 TTATTGGTCTGACGTGGTGG 57.534 50.000 0.00 0.00 0.00 4.61
841 934 2.047002 TTTCGTTATGCTTAGGGGGC 57.953 50.000 0.00 0.00 0.00 5.80
880 974 4.142447 CCTCTCCGACTCGAAGTGATAAAA 60.142 45.833 0.00 0.00 0.00 1.52
884 978 1.384525 CCTCTCCGACTCGAAGTGAT 58.615 55.000 0.00 0.00 0.00 3.06
887 981 0.617413 TACCCTCTCCGACTCGAAGT 59.383 55.000 0.00 0.00 0.00 3.01
888 982 1.671845 CTTACCCTCTCCGACTCGAAG 59.328 57.143 0.00 0.00 0.00 3.79
949 1047 7.899648 ATATAGAGGAAGAAGAAGAAACCGA 57.100 36.000 0.00 0.00 0.00 4.69
966 1064 1.806623 GCCGGGCCGCATTATATAGAG 60.807 57.143 23.20 2.86 0.00 2.43
967 1065 0.177141 GCCGGGCCGCATTATATAGA 59.823 55.000 23.20 0.00 0.00 1.98
968 1066 1.151777 CGCCGGGCCGCATTATATAG 61.152 60.000 23.20 4.30 0.00 1.31
993 1091 2.639839 AGAACATTGGGGGAGATATCCG 59.360 50.000 0.00 0.00 0.00 4.18
1008 1106 3.037549 GGATCTGTGGGAGAGAGAACAT 58.962 50.000 0.00 0.00 32.80 2.71
1095 1214 2.202797 TGGATTCGCTCGCTGCTC 60.203 61.111 0.00 0.00 40.11 4.26
1107 1226 2.231529 CGGGACTAGATCGAGTGGATT 58.768 52.381 13.66 0.00 34.82 3.01
1183 1302 2.960957 AAGGCGTCGAGATGCATCCG 62.961 60.000 23.06 23.27 44.82 4.18
1280 1399 2.281761 AAGAGCCAGCAACCACCG 60.282 61.111 0.00 0.00 0.00 4.94
1281 1400 2.328099 CGAAGAGCCAGCAACCACC 61.328 63.158 0.00 0.00 0.00 4.61
1824 1946 2.345991 CGGCGGAAGAAGAACCCA 59.654 61.111 0.00 0.00 0.00 4.51
1845 1967 4.148825 CGGGTGGCCTCTTCCTCG 62.149 72.222 3.32 4.20 0.00 4.63
1996 2118 3.131396 TCTTCTTCTTGTTGCTTCCGAC 58.869 45.455 0.00 0.00 0.00 4.79
2018 2141 3.370209 GGAGAGTTATTACCACCACCACC 60.370 52.174 0.00 0.00 0.00 4.61
2020 2143 2.841881 GGGAGAGTTATTACCACCACCA 59.158 50.000 0.00 0.00 0.00 4.17
2102 2231 0.602372 GGATCTGATCCGGCAAGCTC 60.602 60.000 20.20 0.00 40.13 4.09
2171 2304 3.519930 GACCTCCGCTCCCTCGAC 61.520 72.222 0.00 0.00 0.00 4.20
2267 2414 5.933463 CCGACAATTAACAACCTACCTAACA 59.067 40.000 0.00 0.00 0.00 2.41
2302 2449 3.418047 ACCAAGAACCAACCCTTAATCG 58.582 45.455 0.00 0.00 0.00 3.34
2381 2535 9.502145 CACGCACACATAAACTTCAATTATTAT 57.498 29.630 0.00 0.00 0.00 1.28
2412 2566 3.492137 CCTTACCCTTAATCTTCGACCCG 60.492 52.174 0.00 0.00 0.00 5.28
2413 2567 3.453717 ACCTTACCCTTAATCTTCGACCC 59.546 47.826 0.00 0.00 0.00 4.46
2429 2601 9.542462 TTGCACTCATAATAACTCATACCTTAC 57.458 33.333 0.00 0.00 0.00 2.34
2452 2624 8.768957 TCATCTCTCAGCATATATAACTTTGC 57.231 34.615 0.00 0.00 35.34 3.68
2457 2629 9.964303 CCATACTCATCTCTCAGCATATATAAC 57.036 37.037 0.00 0.00 0.00 1.89
2466 2638 5.527951 CAACTACCATACTCATCTCTCAGC 58.472 45.833 0.00 0.00 0.00 4.26
2474 2646 4.102210 AGCTGATGCAACTACCATACTCAT 59.898 41.667 0.00 0.00 42.74 2.90
2476 2648 3.806521 CAGCTGATGCAACTACCATACTC 59.193 47.826 8.42 0.00 42.74 2.59
2547 2730 2.100916 ACCAACTACACATAGCCTAGCG 59.899 50.000 0.00 0.00 30.75 4.26
2567 2750 9.595357 GAACTAACATTAACTCAGTTGCTAAAC 57.405 33.333 0.00 0.00 36.47 2.01
2645 2831 7.593644 CACGAATTATAACACTATGATCGACCA 59.406 37.037 0.00 0.00 0.00 4.02
2683 2869 8.530311 CAAGAGCTCATATAATCTACCACTGAT 58.470 37.037 17.77 0.00 0.00 2.90
2752 2949 2.911120 TGCGCGAGTTAAACAAATCAC 58.089 42.857 12.10 0.00 0.00 3.06
2762 2959 0.312729 TCAGACTGTTGCGCGAGTTA 59.687 50.000 12.10 0.00 0.00 2.24
2767 2964 1.690283 CCTGATCAGACTGTTGCGCG 61.690 60.000 24.62 0.00 0.00 6.86
2770 2967 3.063180 CGAATTCCTGATCAGACTGTTGC 59.937 47.826 24.62 6.16 0.00 4.17
2785 3014 0.531753 GGGAGAGCTCAGCGAATTCC 60.532 60.000 17.77 11.79 0.00 3.01
2792 3021 3.550437 TTCATAAAGGGAGAGCTCAGC 57.450 47.619 17.77 7.30 0.00 4.26
2814 3045 2.168521 TCACCGGTCAAGAGATCAATCC 59.831 50.000 2.59 0.00 0.00 3.01
2815 3046 3.526931 TCACCGGTCAAGAGATCAATC 57.473 47.619 2.59 0.00 0.00 2.67
2818 3049 2.456577 TCATCACCGGTCAAGAGATCA 58.543 47.619 2.59 0.00 0.00 2.92
2819 3050 3.526931 TTCATCACCGGTCAAGAGATC 57.473 47.619 2.59 0.00 0.00 2.75
2822 3053 3.125829 CACATTTCATCACCGGTCAAGAG 59.874 47.826 2.59 0.00 0.00 2.85
2823 3054 3.073678 CACATTTCATCACCGGTCAAGA 58.926 45.455 2.59 0.00 0.00 3.02
2824 3055 2.813754 ACACATTTCATCACCGGTCAAG 59.186 45.455 2.59 0.00 0.00 3.02
2826 3057 2.551887 CAACACATTTCATCACCGGTCA 59.448 45.455 2.59 0.00 0.00 4.02
2827 3058 2.095263 CCAACACATTTCATCACCGGTC 60.095 50.000 2.59 0.00 0.00 4.79
2831 3078 4.022068 ACATCACCAACACATTTCATCACC 60.022 41.667 0.00 0.00 0.00 4.02
2856 3103 6.464180 CCATGAGGAAAACAATCTGGGAAAAA 60.464 38.462 0.00 0.00 36.89 1.94
2860 3107 3.075882 ACCATGAGGAAAACAATCTGGGA 59.924 43.478 0.00 0.00 38.69 4.37
2862 3109 3.828451 ACACCATGAGGAAAACAATCTGG 59.172 43.478 0.00 0.00 38.69 3.86
2870 3117 1.327303 GCCACACACCATGAGGAAAA 58.673 50.000 0.00 0.00 41.39 2.29
2872 3119 0.405198 ATGCCACACACCATGAGGAA 59.595 50.000 0.00 0.00 41.39 3.36
2884 3131 3.433343 ACAAAATCCTGATGATGCCACA 58.567 40.909 0.00 0.00 32.68 4.17
2889 3136 9.811995 ATTATTGTCAACAAAATCCTGATGATG 57.188 29.630 0.00 0.00 39.55 3.07
2928 3175 1.128692 GAATTGCCAAAGACGACGGAG 59.871 52.381 0.00 0.00 0.00 4.63
2962 3209 1.197492 CTAATGAGCACGCAACAGCAA 59.803 47.619 0.00 0.00 0.00 3.91
3003 3266 1.550072 CACCCCCAAAGTAAGCAATGG 59.450 52.381 0.00 0.00 0.00 3.16
3005 3268 1.149077 ACCACCCCCAAAGTAAGCAAT 59.851 47.619 0.00 0.00 0.00 3.56
3019 3285 0.532115 GCATTCAATCACCACCACCC 59.468 55.000 0.00 0.00 0.00 4.61
3045 3311 1.930251 AGCCAGAGAGACAAGTGCTA 58.070 50.000 0.00 0.00 0.00 3.49
3100 3366 4.425577 GTGGAAAATCAGCTACCACAAG 57.574 45.455 0.00 0.00 46.75 3.16
3104 3370 2.375174 AGGTGTGGAAAATCAGCTACCA 59.625 45.455 0.00 0.00 39.98 3.25
3105 3371 3.073274 AGGTGTGGAAAATCAGCTACC 57.927 47.619 0.00 0.00 39.98 3.18
3106 3372 5.246307 AGTTAGGTGTGGAAAATCAGCTAC 58.754 41.667 4.05 0.00 41.94 3.58
3131 3397 6.131264 TGGAATGATTAATCAACAGCCAGAT 58.869 36.000 21.50 0.00 40.69 2.90
3132 3398 5.508567 TGGAATGATTAATCAACAGCCAGA 58.491 37.500 21.50 4.32 40.69 3.86
3145 3411 5.015515 TCAGCATGGTTGTTGGAATGATTA 58.984 37.500 0.00 0.00 35.03 1.75
3146 3412 3.833650 TCAGCATGGTTGTTGGAATGATT 59.166 39.130 0.00 0.00 35.03 2.57
3151 3417 1.619654 CCTCAGCATGGTTGTTGGAA 58.380 50.000 0.00 0.00 35.03 3.53
3152 3418 0.251297 CCCTCAGCATGGTTGTTGGA 60.251 55.000 0.00 0.00 35.03 3.53
3163 3429 0.987294 CTTTTCTCCTCCCCTCAGCA 59.013 55.000 0.00 0.00 0.00 4.41
3164 3430 1.280457 TCTTTTCTCCTCCCCTCAGC 58.720 55.000 0.00 0.00 0.00 4.26
3166 3432 3.722101 ACTTTTCTTTTCTCCTCCCCTCA 59.278 43.478 0.00 0.00 0.00 3.86
3169 3435 5.244189 ACTACTTTTCTTTTCTCCTCCCC 57.756 43.478 0.00 0.00 0.00 4.81
3172 3438 8.038351 AGCTCATACTACTTTTCTTTTCTCCTC 58.962 37.037 0.00 0.00 0.00 3.71
3173 3439 7.821846 CAGCTCATACTACTTTTCTTTTCTCCT 59.178 37.037 0.00 0.00 0.00 3.69
3174 3440 7.065204 CCAGCTCATACTACTTTTCTTTTCTCC 59.935 40.741 0.00 0.00 0.00 3.71
3178 3444 6.431234 CACCCAGCTCATACTACTTTTCTTTT 59.569 38.462 0.00 0.00 0.00 2.27
3187 3453 1.139058 CCCACACCCAGCTCATACTAC 59.861 57.143 0.00 0.00 0.00 2.73
3190 3456 1.224592 CCCCACACCCAGCTCATAC 59.775 63.158 0.00 0.00 0.00 2.39
3191 3457 2.000701 CCCCCACACCCAGCTCATA 61.001 63.158 0.00 0.00 0.00 2.15
3192 3458 3.341629 CCCCCACACCCAGCTCAT 61.342 66.667 0.00 0.00 0.00 2.90
3193 3459 4.590553 TCCCCCACACCCAGCTCA 62.591 66.667 0.00 0.00 0.00 4.26
3194 3460 3.721706 CTCCCCCACACCCAGCTC 61.722 72.222 0.00 0.00 0.00 4.09
3195 3461 3.810687 TTCTCCCCCACACCCAGCT 62.811 63.158 0.00 0.00 0.00 4.24
3196 3462 3.256960 TTCTCCCCCACACCCAGC 61.257 66.667 0.00 0.00 0.00 4.85
3197 3463 1.133809 TTCTTCTCCCCCACACCCAG 61.134 60.000 0.00 0.00 0.00 4.45
3198 3464 0.477597 ATTCTTCTCCCCCACACCCA 60.478 55.000 0.00 0.00 0.00 4.51
3199 3465 1.212195 GTATTCTTCTCCCCCACACCC 59.788 57.143 0.00 0.00 0.00 4.61
3200 3466 1.212195 GGTATTCTTCTCCCCCACACC 59.788 57.143 0.00 0.00 0.00 4.16
3201 3467 1.913419 TGGTATTCTTCTCCCCCACAC 59.087 52.381 0.00 0.00 0.00 3.82
3202 3468 1.913419 GTGGTATTCTTCTCCCCCACA 59.087 52.381 0.00 0.00 41.51 4.17
3203 3469 1.913419 TGTGGTATTCTTCTCCCCCAC 59.087 52.381 0.00 0.00 42.08 4.61
3204 3470 2.352561 TGTGGTATTCTTCTCCCCCA 57.647 50.000 0.00 0.00 0.00 4.96
3205 3471 3.953542 ATTGTGGTATTCTTCTCCCCC 57.046 47.619 0.00 0.00 0.00 5.40
3206 3472 4.855340 TGAATTGTGGTATTCTTCTCCCC 58.145 43.478 0.00 0.00 35.89 4.81
3207 3473 5.501156 ACTGAATTGTGGTATTCTTCTCCC 58.499 41.667 0.00 0.00 35.89 4.30
3208 3474 7.308435 CAAACTGAATTGTGGTATTCTTCTCC 58.692 38.462 0.00 0.00 35.89 3.71
3209 3475 7.040409 ACCAAACTGAATTGTGGTATTCTTCTC 60.040 37.037 0.00 0.00 42.60 2.87
3210 3476 6.777580 ACCAAACTGAATTGTGGTATTCTTCT 59.222 34.615 0.00 0.00 42.60 2.85
3211 3477 6.981722 ACCAAACTGAATTGTGGTATTCTTC 58.018 36.000 0.00 0.00 42.60 2.87
3212 3478 6.976934 ACCAAACTGAATTGTGGTATTCTT 57.023 33.333 0.00 0.00 42.60 2.52
3213 3479 6.976934 AACCAAACTGAATTGTGGTATTCT 57.023 33.333 0.00 0.00 43.62 2.40
3214 3480 8.021396 GTCTAACCAAACTGAATTGTGGTATTC 58.979 37.037 0.00 0.00 43.62 1.75
3215 3481 7.039993 GGTCTAACCAAACTGAATTGTGGTATT 60.040 37.037 0.00 0.00 43.62 1.89
3216 3482 6.433093 GGTCTAACCAAACTGAATTGTGGTAT 59.567 38.462 0.00 0.00 43.62 2.73
3217 3483 5.766174 GGTCTAACCAAACTGAATTGTGGTA 59.234 40.000 0.00 0.00 43.62 3.25
3218 3484 4.583073 GGTCTAACCAAACTGAATTGTGGT 59.417 41.667 0.00 0.00 46.38 4.16
3220 3486 4.582656 TGGGTCTAACCAAACTGAATTGTG 59.417 41.667 0.00 0.00 41.02 3.33
3223 3489 5.319043 TCTGGGTCTAACCAAACTGAATT 57.681 39.130 0.00 0.00 41.02 2.17
3237 3503 2.554032 CGTTCAGCAAATTTCTGGGTCT 59.446 45.455 13.94 0.00 32.63 3.85
3243 3509 2.948979 TCACCACGTTCAGCAAATTTCT 59.051 40.909 0.00 0.00 0.00 2.52
3271 3538 1.785041 GCACGGAGTTTTGCTCAGCA 61.785 55.000 0.00 0.00 45.88 4.41
3274 3541 2.892334 GCGCACGGAGTTTTGCTCA 61.892 57.895 0.30 0.00 45.88 4.26
3276 3543 2.591715 AGCGCACGGAGTTTTGCT 60.592 55.556 11.47 0.00 41.61 3.91
3279 3546 2.110213 TCCAGCGCACGGAGTTTT 59.890 55.556 11.47 0.00 41.61 2.43
3280 3547 2.665185 GTCCAGCGCACGGAGTTT 60.665 61.111 17.95 0.00 41.61 2.66
3337 3617 2.594592 GGCAACCACGCAAGGTCT 60.595 61.111 0.00 0.00 42.25 3.85
3339 3619 4.868116 ACGGCAACCACGCAAGGT 62.868 61.111 0.00 0.00 45.91 3.50
3340 3620 4.025401 GACGGCAACCACGCAAGG 62.025 66.667 0.00 0.00 46.39 3.61
3364 3644 1.328439 CGTAGACGCCGCTATCAATC 58.672 55.000 0.00 0.00 0.00 2.67
3365 3645 0.666913 ACGTAGACGCCGCTATCAAT 59.333 50.000 1.14 0.00 44.43 2.57
3366 3646 0.028505 GACGTAGACGCCGCTATCAA 59.971 55.000 1.14 0.00 44.43 2.57
3367 3647 0.812811 AGACGTAGACGCCGCTATCA 60.813 55.000 1.14 0.00 44.43 2.15
3368 3648 0.110733 GAGACGTAGACGCCGCTATC 60.111 60.000 1.14 0.00 44.43 2.08
3369 3649 1.505477 GGAGACGTAGACGCCGCTAT 61.505 60.000 1.14 0.00 44.43 2.97
3370 3650 2.176273 GGAGACGTAGACGCCGCTA 61.176 63.158 1.14 0.00 44.43 4.26
3371 3651 3.507009 GGAGACGTAGACGCCGCT 61.507 66.667 1.14 0.00 44.43 5.52
3372 3652 3.048941 AAGGAGACGTAGACGCCGC 62.049 63.158 1.14 0.00 46.94 6.53
3373 3653 1.226323 CAAGGAGACGTAGACGCCG 60.226 63.158 1.14 0.00 46.94 6.46
3374 3654 0.179169 GACAAGGAGACGTAGACGCC 60.179 60.000 1.14 0.00 42.66 5.68
3375 3655 0.520404 TGACAAGGAGACGTAGACGC 59.480 55.000 1.14 0.00 44.43 5.19
3376 3656 1.805345 ACTGACAAGGAGACGTAGACG 59.195 52.381 0.00 0.00 46.33 4.18
3377 3657 2.812591 TGACTGACAAGGAGACGTAGAC 59.187 50.000 0.00 0.00 0.00 2.59
3378 3658 3.136009 TGACTGACAAGGAGACGTAGA 57.864 47.619 0.00 0.00 0.00 2.59
3379 3659 3.917329 TTGACTGACAAGGAGACGTAG 57.083 47.619 0.00 0.00 34.20 3.51


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

AutoCloner maintained by Alex Coulton.