Multiple sequence alignment - TraesCS5B01G282400

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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 TraesCS5B01G282400 chr5B 100.000 4124 0 0 1 4124 467168175 467164052 0.000000e+00 7616.0
1 TraesCS5B01G282400 chr5B 90.530 2207 106 34 1171 3297 469972364 469974547 0.000000e+00 2822.0
2 TraesCS5B01G282400 chr5B 93.160 424 15 5 753 1171 469967852 469968266 9.800000e-171 610.0
3 TraesCS5B01G282400 chr5B 81.961 255 15 8 3731 3958 469974742 469974992 1.960000e-43 187.0
4 TraesCS5B01G282400 chr5B 97.727 44 1 0 3321 3364 469974550 469974593 4.420000e-10 76.8
5 TraesCS5B01G282400 chr5B 97.368 38 1 0 286 323 465867407 465867444 9.570000e-07 65.8
6 TraesCS5B01G282400 chr5D 90.268 2312 134 38 1169 3403 389696079 389698376 0.000000e+00 2939.0
7 TraesCS5B01G282400 chr5D 92.122 2069 79 24 1172 3165 388814484 388812425 0.000000e+00 2841.0
8 TraesCS5B01G282400 chr5D 92.889 450 16 3 678 1126 388814918 388814484 1.250000e-179 640.0
9 TraesCS5B01G282400 chr5D 88.015 534 23 15 13 546 388815550 388815058 9.870000e-166 593.0
10 TraesCS5B01G282400 chr5D 93.016 315 16 1 753 1067 389679443 389679751 4.860000e-124 455.0
11 TraesCS5B01G282400 chr5D 90.551 254 18 4 3187 3437 388812431 388812181 8.540000e-87 331.0
12 TraesCS5B01G282400 chr5D 93.464 153 10 0 3806 3958 388810414 388810262 1.150000e-55 228.0
13 TraesCS5B01G282400 chr5D 82.353 255 14 7 3731 3958 389698457 389698707 4.210000e-45 193.0
14 TraesCS5B01G282400 chr5D 93.421 76 5 0 1065 1140 389696006 389696081 3.370000e-21 113.0
15 TraesCS5B01G282400 chr5A 93.338 1591 80 10 1459 3031 491709987 491711569 0.000000e+00 2327.0
16 TraesCS5B01G282400 chr5A 90.198 1663 105 20 1775 3388 493018141 493019794 0.000000e+00 2115.0
17 TraesCS5B01G282400 chr5A 90.486 946 49 22 3029 3958 491711595 491712515 0.000000e+00 1210.0
18 TraesCS5B01G282400 chr5A 88.927 885 42 22 238 1114 491709153 491709989 0.000000e+00 1040.0
19 TraesCS5B01G282400 chr5A 95.434 438 19 1 688 1124 493016338 493016775 0.000000e+00 697.0
20 TraesCS5B01G282400 chr5A 85.054 649 38 28 1167 1788 493016774 493017390 1.270000e-169 606.0
21 TraesCS5B01G282400 chr5A 82.000 250 14 7 3731 3953 493019861 493020106 2.530000e-42 183.0
22 TraesCS5B01G282400 chr5A 80.088 226 8 11 13 236 491707054 491707244 2.590000e-27 134.0
23 TraesCS5B01G282400 chr5A 82.022 89 8 3 266 354 490049860 490049940 7.400000e-08 69.4
24 TraesCS5B01G282400 chrUn 86.164 159 11 3 3954 4101 75399580 75399738 1.190000e-35 161.0
25 TraesCS5B01G282400 chr7B 85.714 161 11 7 3953 4101 728284952 728284792 4.270000e-35 159.0
26 TraesCS5B01G282400 chr6B 86.364 154 10 6 3959 4101 21123261 21123108 1.530000e-34 158.0
27 TraesCS5B01G282400 chr6B 96.875 32 0 1 4093 4124 517432521 517432491 7.000000e-03 52.8
28 TraesCS5B01G282400 chr3A 86.364 154 10 6 3959 4101 691600562 691600409 1.530000e-34 158.0
29 TraesCS5B01G282400 chr2B 86.364 154 9 7 3959 4101 784306385 784306233 1.530000e-34 158.0
30 TraesCS5B01G282400 chr2B 85.714 154 10 7 3959 4101 784303991 784304143 7.140000e-33 152.0
31 TraesCS5B01G282400 chr4B 82.659 173 16 4 3940 4101 415768354 415768523 1.550000e-29 141.0
32 TraesCS5B01G282400 chr3B 83.448 145 11 8 3970 4101 555154061 555153917 5.600000e-24 122.0
33 TraesCS5B01G282400 chr3B 100.000 29 0 0 4096 4124 48985465 48985493 2.000000e-03 54.7
34 TraesCS5B01G282400 chr3D 81.481 135 20 4 2761 2893 513621304 513621173 5.640000e-19 106.0
35 TraesCS5B01G282400 chr1B 100.000 29 0 0 4096 4124 679570653 679570681 2.000000e-03 54.7
36 TraesCS5B01G282400 chr2A 100.000 28 0 0 4094 4121 30146488 30146515 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G282400 chr5B 467164052 467168175 4123 True 7616.000000 7616 100.000000 1 4124 1 chr5B.!!$R1 4123
1 TraesCS5B01G282400 chr5B 469972364 469974992 2628 False 1028.600000 2822 90.072667 1171 3958 3 chr5B.!!$F3 2787
2 TraesCS5B01G282400 chr5D 389696006 389698707 2701 False 1081.666667 2939 88.680667 1065 3958 3 chr5D.!!$F2 2893
3 TraesCS5B01G282400 chr5D 388810262 388815550 5288 True 926.600000 2841 91.408200 13 3958 5 chr5D.!!$R1 3945
4 TraesCS5B01G282400 chr5A 491707054 491712515 5461 False 1177.750000 2327 88.209750 13 3958 4 chr5A.!!$F2 3945
5 TraesCS5B01G282400 chr5A 493016338 493020106 3768 False 900.250000 2115 88.171500 688 3953 4 chr5A.!!$F3 3265

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
565 2475 0.037447 AGCCTTTCCCTCTTGCAGAC 59.963 55.0 0.0 0.0 0.00 3.51 F
638 2565 0.106708 TCAGCGAGTTCAGGTTTGCT 59.893 50.0 0.0 0.0 34.38 3.91 F
676 2603 0.388907 CGGCCTCGTCCTCGTAAAAA 60.389 55.0 0.0 0.0 38.33 1.94 F
1857 4615 0.531532 CTGATTGACCTAGCCTGCCG 60.532 60.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 5252 4.189231 GTGAAGGTATCATGTTAAGCCGT 58.811 43.478 0.0 0.0 40.97 5.68 R
2510 5289 6.040247 TGACATTTACACATGATCCTACGAC 58.960 40.000 0.0 0.0 0.00 4.34 R
2670 5449 3.127895 GCAGAAACAAATACATACCGCCA 59.872 43.478 0.0 0.0 0.00 5.69 R
3690 7969 0.307760 GACTGTTGGGTGAAGCAACG 59.692 55.000 0.0 0.0 0.00 4.10 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
19 20 1.935799 AGCCCACCAATTGCATTACA 58.064 45.000 0.00 0.00 0.00 2.41
24 25 4.458642 GCCCACCAATTGCATTACAAAAAT 59.541 37.500 0.00 0.00 42.86 1.82
56 57 9.952188 ATGTTTCACTTTTAGCTAAGAAGAAAC 57.048 29.630 27.10 27.10 43.60 2.78
63 64 7.447545 ACTTTTAGCTAAGAAGAAACGGGATTT 59.552 33.333 23.50 5.75 0.00 2.17
64 65 8.851541 TTTTAGCTAAGAAGAAACGGGATTTA 57.148 30.769 6.24 0.00 0.00 1.40
65 66 8.851541 TTTAGCTAAGAAGAAACGGGATTTAA 57.148 30.769 6.24 0.00 0.00 1.52
76 77 3.822940 ACGGGATTTAATTAATCGGCCA 58.177 40.909 2.24 0.00 43.01 5.36
127 128 5.172687 TGGCAATCCAATCTTGTACTGTA 57.827 39.130 0.00 0.00 39.99 2.74
128 129 4.941263 TGGCAATCCAATCTTGTACTGTAC 59.059 41.667 10.98 10.98 39.99 2.90
129 130 4.941263 GGCAATCCAATCTTGTACTGTACA 59.059 41.667 16.26 16.26 36.79 2.90
130 131 5.414454 GGCAATCCAATCTTGTACTGTACAA 59.586 40.000 26.55 26.55 45.66 2.41
131 132 6.095440 GGCAATCCAATCTTGTACTGTACAAT 59.905 38.462 27.93 15.36 46.51 2.71
132 133 7.189512 GCAATCCAATCTTGTACTGTACAATC 58.810 38.462 27.93 0.42 46.51 2.67
133 134 7.679638 GCAATCCAATCTTGTACTGTACAATCC 60.680 40.741 27.93 3.40 46.51 3.01
150 151 6.748333 ACAATCCAATAGAACATGACAGTG 57.252 37.500 0.00 0.00 0.00 3.66
152 153 4.220693 TCCAATAGAACATGACAGTGGG 57.779 45.455 0.00 0.00 0.00 4.61
174 176 3.276857 GCACATGATTCAGTGAGATGGT 58.723 45.455 15.82 0.00 37.97 3.55
178 180 5.236695 CACATGATTCAGTGAGATGGTCATC 59.763 44.000 0.00 2.92 37.56 2.92
189 191 4.778534 AGATGGTCATCTTTGCAAACTG 57.221 40.909 8.05 9.06 45.31 3.16
190 192 2.798976 TGGTCATCTTTGCAAACTGC 57.201 45.000 8.05 5.56 45.29 4.40
522 2432 0.452184 GAAGGAGATCGCGTCTGACA 59.548 55.000 14.47 0.00 37.29 3.58
546 2456 0.679505 CGGGAGATCTATTTCCGCCA 59.320 55.000 11.53 0.00 34.17 5.69
548 2458 1.609320 GGGAGATCTATTTCCGCCAGC 60.609 57.143 0.00 0.00 34.17 4.85
549 2459 1.609320 GGAGATCTATTTCCGCCAGCC 60.609 57.143 0.00 0.00 0.00 4.85
556 2466 2.155197 ATTTCCGCCAGCCTTTCCCT 62.155 55.000 0.00 0.00 0.00 4.20
565 2475 0.037447 AGCCTTTCCCTCTTGCAGAC 59.963 55.000 0.00 0.00 0.00 3.51
567 2477 1.818642 CCTTTCCCTCTTGCAGACTG 58.181 55.000 0.00 0.00 0.00 3.51
568 2478 1.163554 CTTTCCCTCTTGCAGACTGC 58.836 55.000 20.86 20.86 45.29 4.40
587 2497 8.851145 CAGACTGCAGAATAGTAGGAGTAATTA 58.149 37.037 23.35 0.00 33.96 1.40
633 2560 1.513158 CGGATCAGCGAGTTCAGGT 59.487 57.895 0.00 0.00 0.00 4.00
636 2563 1.734465 GGATCAGCGAGTTCAGGTTTG 59.266 52.381 0.00 0.00 0.00 2.93
638 2565 0.106708 TCAGCGAGTTCAGGTTTGCT 59.893 50.000 0.00 0.00 34.38 3.91
641 2568 0.944386 GCGAGTTCAGGTTTGCTTCA 59.056 50.000 0.00 0.00 0.00 3.02
642 2569 1.069636 GCGAGTTCAGGTTTGCTTCAG 60.070 52.381 0.00 0.00 0.00 3.02
643 2570 2.213499 CGAGTTCAGGTTTGCTTCAGT 58.787 47.619 0.00 0.00 0.00 3.41
645 2572 2.213499 AGTTCAGGTTTGCTTCAGTCG 58.787 47.619 0.00 0.00 0.00 4.18
646 2573 2.158957 AGTTCAGGTTTGCTTCAGTCGA 60.159 45.455 0.00 0.00 0.00 4.20
647 2574 2.154854 TCAGGTTTGCTTCAGTCGAG 57.845 50.000 0.00 0.00 0.00 4.04
650 2577 3.070018 CAGGTTTGCTTCAGTCGAGATT 58.930 45.455 0.00 0.00 0.00 2.40
651 2578 3.499918 CAGGTTTGCTTCAGTCGAGATTT 59.500 43.478 0.00 0.00 0.00 2.17
652 2579 4.690748 CAGGTTTGCTTCAGTCGAGATTTA 59.309 41.667 0.00 0.00 0.00 1.40
654 2581 4.451096 GGTTTGCTTCAGTCGAGATTTACA 59.549 41.667 0.00 0.00 0.00 2.41
655 2582 5.049680 GGTTTGCTTCAGTCGAGATTTACAA 60.050 40.000 0.00 0.00 0.00 2.41
656 2583 5.591643 TTGCTTCAGTCGAGATTTACAAC 57.408 39.130 0.00 0.00 0.00 3.32
657 2584 3.994392 TGCTTCAGTCGAGATTTACAACC 59.006 43.478 0.00 0.00 0.00 3.77
658 2585 3.060895 GCTTCAGTCGAGATTTACAACCG 59.939 47.826 0.00 0.00 0.00 4.44
660 2587 1.659098 CAGTCGAGATTTACAACCGGC 59.341 52.381 0.00 0.00 0.00 6.13
662 2589 0.899720 TCGAGATTTACAACCGGCCT 59.100 50.000 0.00 0.00 0.00 5.19
663 2590 1.134907 TCGAGATTTACAACCGGCCTC 60.135 52.381 0.00 0.00 0.00 4.70
664 2591 1.287425 GAGATTTACAACCGGCCTCG 58.713 55.000 0.00 0.00 0.00 4.63
665 2592 0.611714 AGATTTACAACCGGCCTCGT 59.388 50.000 0.00 0.00 33.95 4.18
666 2593 1.004595 GATTTACAACCGGCCTCGTC 58.995 55.000 0.00 0.00 33.95 4.20
668 2595 1.474332 TTTACAACCGGCCTCGTCCT 61.474 55.000 0.00 0.00 33.95 3.85
669 2596 1.880819 TTACAACCGGCCTCGTCCTC 61.881 60.000 0.00 0.00 33.95 3.71
670 2597 4.796231 CAACCGGCCTCGTCCTCG 62.796 72.222 0.00 0.00 38.55 4.63
673 2600 3.136123 CCGGCCTCGTCCTCGTAA 61.136 66.667 0.00 0.00 38.33 3.18
674 2601 2.703798 CCGGCCTCGTCCTCGTAAA 61.704 63.158 0.00 0.00 38.33 2.01
675 2602 1.213537 CGGCCTCGTCCTCGTAAAA 59.786 57.895 0.00 0.00 38.33 1.52
676 2603 0.388907 CGGCCTCGTCCTCGTAAAAA 60.389 55.000 0.00 0.00 38.33 1.94
728 2666 3.522731 CCGCCTCGACCTCCTCAG 61.523 72.222 0.00 0.00 0.00 3.35
742 2680 0.815734 CCTCAGCCAATTCTGCAAGG 59.184 55.000 0.00 2.50 34.19 3.61
778 2716 2.298661 GCGGAGGGGGAGGAAAAGA 61.299 63.158 0.00 0.00 0.00 2.52
898 2836 1.606350 GCACGACTTCGAGAACCACG 61.606 60.000 5.47 0.00 43.02 4.94
912 2850 1.153628 CCACGTCATCCCTTCCGAC 60.154 63.158 0.00 0.00 0.00 4.79
936 2877 4.536687 GGCGGCGGCGAAATCAAG 62.537 66.667 36.87 3.31 41.24 3.02
955 2896 1.075970 TACTGCCTCATCCGCCTCT 60.076 57.895 0.00 0.00 0.00 3.69
961 2902 1.826054 CTCATCCGCCTCTCCGTCT 60.826 63.158 0.00 0.00 0.00 4.18
995 2936 5.654650 CACTCTCCAAGGTGATAGACTACTT 59.345 44.000 0.00 0.00 35.69 2.24
1028 2970 1.141881 CCGGATCCCACGACTTGAG 59.858 63.158 6.06 0.00 0.00 3.02
1061 3003 1.734465 GGAGTTCATCGCTGGTTTCAG 59.266 52.381 0.00 0.00 43.64 3.02
1393 3357 9.878599 CAAATTTATTAACTTAGGTATGCCTCG 57.121 33.333 5.27 1.23 45.64 4.63
1487 3471 8.242053 ACATTGAGCTTATTTGTGAGAATTCTG 58.758 33.333 14.00 0.00 0.00 3.02
1535 3523 6.652481 AGAGGAACTTATGTCATCACAAACAG 59.348 38.462 0.00 0.00 41.55 3.16
1565 3553 9.613428 CTATAAGTGTTGGATTTCAATCTGGTA 57.387 33.333 0.00 0.00 37.73 3.25
1857 4615 0.531532 CTGATTGACCTAGCCTGCCG 60.532 60.000 0.00 0.00 0.00 5.69
1858 4616 1.264749 TGATTGACCTAGCCTGCCGT 61.265 55.000 0.00 0.00 0.00 5.68
1934 4692 6.942532 TTAACATCAAGAGTGTCTTTGCTT 57.057 33.333 0.00 0.00 33.78 3.91
1948 4706 5.582269 TGTCTTTGCTTCGGAATTAGATGAG 59.418 40.000 0.00 0.00 0.00 2.90
2062 4820 8.893727 GCAATTGTACCACTATAGAGTCATTTT 58.106 33.333 6.78 0.00 31.73 1.82
2399 5178 8.095792 TCATTCGTTAATCTTGTTTAGGTACCA 58.904 33.333 15.94 0.00 0.00 3.25
2464 5243 4.201990 CCTCTATCCACAGCTGATTTTTGC 60.202 45.833 23.35 0.00 0.00 3.68
2473 5252 0.958091 CTGATTTTTGCCGTGGTCCA 59.042 50.000 0.00 0.00 0.00 4.02
2510 5289 2.259618 CTTCACCAATACGTGACTCGG 58.740 52.381 0.00 0.00 42.37 4.63
2670 5449 2.278245 TGATCCCCAACTCATCACCTT 58.722 47.619 0.00 0.00 0.00 3.50
2689 5468 4.157105 ACCTTGGCGGTATGTATTTGTTTC 59.843 41.667 0.00 0.00 46.73 2.78
2722 5501 8.469200 CAATCTTTTCCTATGCTTTTGTATGGA 58.531 33.333 0.00 0.00 0.00 3.41
2906 5689 4.974368 AAGGTGTGATCGTTTTCAACAA 57.026 36.364 0.00 0.00 0.00 2.83
2995 5778 6.183360 GGAAGTGAGATGTGCTTATGTTGTAC 60.183 42.308 0.00 0.00 0.00 2.90
3024 5807 5.689383 TTGAAGCTACCATTGAAGTCAAC 57.311 39.130 0.00 0.00 38.86 3.18
3149 5966 1.797025 GTGTTGTAGCTGTCCCACTC 58.203 55.000 0.00 0.00 0.00 3.51
3157 5974 0.173708 GCTGTCCCACTCGGTAGAAG 59.826 60.000 0.00 0.00 0.00 2.85
3200 6017 2.477375 TCGTAGCGTTGGTGATGTTTTC 59.523 45.455 0.00 0.00 0.00 2.29
3297 6114 3.494398 GGTGAAACTTGTCTGGACAGCTA 60.494 47.826 3.62 0.00 42.94 3.32
3301 6118 4.899352 AACTTGTCTGGACAGCTATTCT 57.101 40.909 3.62 0.00 42.94 2.40
3371 6205 1.523258 GATGTGATGCGGCTGAGCT 60.523 57.895 3.72 0.00 38.13 4.09
3390 6226 6.189859 TGAGCTTCTGTTATGGATGGAAATT 58.810 36.000 0.00 0.00 0.00 1.82
3532 7807 4.768448 TCGGTTATGTCCTGTCAAAGAGTA 59.232 41.667 0.00 0.00 0.00 2.59
3641 7920 2.875087 AAACCCAACGTTGCTTAACC 57.125 45.000 22.93 0.00 33.93 2.85
3661 7940 3.061322 CCGAGACAAAAATACGGTGACA 58.939 45.455 0.00 0.00 38.97 3.58
3662 7941 3.122948 CCGAGACAAAAATACGGTGACAG 59.877 47.826 0.00 0.00 38.97 3.51
3663 7942 3.423123 CGAGACAAAAATACGGTGACAGC 60.423 47.826 0.00 0.00 0.00 4.40
3664 7943 2.478894 AGACAAAAATACGGTGACAGCG 59.521 45.455 24.39 24.39 45.69 5.18
3665 7944 2.477375 GACAAAAATACGGTGACAGCGA 59.523 45.455 31.66 16.29 42.41 4.93
3666 7945 2.478894 ACAAAAATACGGTGACAGCGAG 59.521 45.455 31.66 14.17 42.41 5.03
3667 7946 2.450609 AAAATACGGTGACAGCGAGT 57.549 45.000 31.66 16.89 42.41 4.18
3668 7947 3.581024 AAAATACGGTGACAGCGAGTA 57.419 42.857 31.66 15.87 42.41 2.59
3669 7948 3.795623 AAATACGGTGACAGCGAGTAT 57.204 42.857 31.66 17.35 42.41 2.12
3670 7949 3.795623 AATACGGTGACAGCGAGTATT 57.204 42.857 31.66 21.54 42.41 1.89
3671 7950 3.795623 ATACGGTGACAGCGAGTATTT 57.204 42.857 31.66 11.99 42.41 1.40
3672 7951 1.710013 ACGGTGACAGCGAGTATTTG 58.290 50.000 31.66 2.28 42.41 2.32
3673 7952 1.000506 ACGGTGACAGCGAGTATTTGT 59.999 47.619 31.66 5.38 42.41 2.83
3674 7953 1.654105 CGGTGACAGCGAGTATTTGTC 59.346 52.381 21.96 0.00 42.41 3.18
3675 7954 2.683968 GGTGACAGCGAGTATTTGTCA 58.316 47.619 2.68 2.68 46.34 3.58
3678 7957 3.064207 TGACAGCGAGTATTTGTCAACC 58.936 45.455 4.24 0.00 45.76 3.77
3679 7958 3.064207 GACAGCGAGTATTTGTCAACCA 58.936 45.455 0.00 0.00 40.62 3.67
3680 7959 3.472652 ACAGCGAGTATTTGTCAACCAA 58.527 40.909 0.00 0.00 0.00 3.67
3681 7960 3.498397 ACAGCGAGTATTTGTCAACCAAG 59.502 43.478 0.00 0.00 33.75 3.61
3682 7961 2.484264 AGCGAGTATTTGTCAACCAAGC 59.516 45.455 0.00 0.00 33.75 4.01
3683 7962 2.484264 GCGAGTATTTGTCAACCAAGCT 59.516 45.455 0.00 0.00 33.75 3.74
3684 7963 3.667960 GCGAGTATTTGTCAACCAAGCTG 60.668 47.826 0.00 0.00 33.75 4.24
3685 7964 3.745975 CGAGTATTTGTCAACCAAGCTGA 59.254 43.478 0.00 0.00 33.75 4.26
3686 7965 4.213270 CGAGTATTTGTCAACCAAGCTGAA 59.787 41.667 0.00 0.00 33.75 3.02
3687 7966 5.277779 CGAGTATTTGTCAACCAAGCTGAAA 60.278 40.000 0.00 0.00 33.75 2.69
3688 7967 6.568462 CGAGTATTTGTCAACCAAGCTGAAAT 60.568 38.462 0.00 0.00 33.75 2.17
3689 7968 7.360861 CGAGTATTTGTCAACCAAGCTGAAATA 60.361 37.037 0.00 0.00 33.75 1.40
3690 7969 7.593825 AGTATTTGTCAACCAAGCTGAAATAC 58.406 34.615 0.00 0.00 33.75 1.89
3691 7970 4.481930 TTGTCAACCAAGCTGAAATACG 57.518 40.909 0.00 0.00 0.00 3.06
3692 7971 3.472652 TGTCAACCAAGCTGAAATACGT 58.527 40.909 0.00 0.00 0.00 3.57
3693 7972 3.880490 TGTCAACCAAGCTGAAATACGTT 59.120 39.130 0.00 0.00 0.00 3.99
3694 7973 4.219033 GTCAACCAAGCTGAAATACGTTG 58.781 43.478 0.00 0.00 0.00 4.10
3695 7974 2.979813 CAACCAAGCTGAAATACGTTGC 59.020 45.455 0.00 0.00 0.00 4.17
3696 7975 2.504367 ACCAAGCTGAAATACGTTGCT 58.496 42.857 0.00 0.00 35.30 3.91
3697 7976 2.884639 ACCAAGCTGAAATACGTTGCTT 59.115 40.909 0.00 0.00 43.61 3.91
3698 7977 3.058224 ACCAAGCTGAAATACGTTGCTTC 60.058 43.478 0.00 0.00 41.31 3.86
3699 7978 3.058293 CCAAGCTGAAATACGTTGCTTCA 60.058 43.478 0.00 0.00 41.31 3.02
3700 7979 3.813529 AGCTGAAATACGTTGCTTCAC 57.186 42.857 0.00 0.00 0.00 3.18
3701 7980 2.484264 AGCTGAAATACGTTGCTTCACC 59.516 45.455 0.00 0.00 0.00 4.02
3729 8008 6.534793 ACAGTCAACATTGTGTTTTTCAATCC 59.465 34.615 0.00 0.00 38.77 3.01
3830 8154 6.101997 AGCTGAACCAAAATATTTAAGCTGC 58.898 36.000 0.01 5.87 37.12 5.25
3834 8158 7.212976 TGAACCAAAATATTTAAGCTGCAACA 58.787 30.769 1.02 0.00 0.00 3.33
3842 8166 8.511604 AATATTTAAGCTGCAACACTGTATCT 57.488 30.769 1.02 0.00 0.00 1.98
3855 8194 8.338259 GCAACACTGTATCTAAATTGTATCAGG 58.662 37.037 0.00 0.00 0.00 3.86
3998 8337 5.674933 GCTATTTAAAATAGCGTGGCTCT 57.325 39.130 0.00 0.00 40.44 4.09
3999 8338 6.061231 GCTATTTAAAATAGCGTGGCTCTT 57.939 37.500 0.00 0.00 40.44 2.85
4000 8339 6.136743 GCTATTTAAAATAGCGTGGCTCTTC 58.863 40.000 0.00 0.00 40.44 2.87
4001 8340 6.017852 GCTATTTAAAATAGCGTGGCTCTTCT 60.018 38.462 0.00 0.00 40.44 2.85
4002 8341 5.796350 TTTAAAATAGCGTGGCTCTTCTC 57.204 39.130 0.00 0.00 40.44 2.87
4003 8342 2.317530 AAATAGCGTGGCTCTTCTCC 57.682 50.000 0.00 0.00 40.44 3.71
4004 8343 0.103208 AATAGCGTGGCTCTTCTCCG 59.897 55.000 0.00 0.00 40.44 4.63
4005 8344 0.752009 ATAGCGTGGCTCTTCTCCGA 60.752 55.000 0.00 0.00 40.44 4.55
4006 8345 0.963856 TAGCGTGGCTCTTCTCCGAA 60.964 55.000 0.00 0.00 40.44 4.30
4007 8346 1.153549 GCGTGGCTCTTCTCCGAAT 60.154 57.895 0.00 0.00 0.00 3.34
4008 8347 1.424493 GCGTGGCTCTTCTCCGAATG 61.424 60.000 0.00 0.00 0.00 2.67
4009 8348 1.424493 CGTGGCTCTTCTCCGAATGC 61.424 60.000 0.00 0.00 0.00 3.56
4010 8349 0.107945 GTGGCTCTTCTCCGAATGCT 60.108 55.000 0.00 0.00 0.00 3.79
4011 8350 1.137086 GTGGCTCTTCTCCGAATGCTA 59.863 52.381 0.00 0.00 0.00 3.49
4012 8351 2.042464 TGGCTCTTCTCCGAATGCTAT 58.958 47.619 0.00 0.00 0.00 2.97
4013 8352 2.224137 TGGCTCTTCTCCGAATGCTATG 60.224 50.000 0.00 0.00 0.00 2.23
4014 8353 1.797635 GCTCTTCTCCGAATGCTATGC 59.202 52.381 0.00 0.00 0.00 3.14
4015 8354 2.804572 GCTCTTCTCCGAATGCTATGCA 60.805 50.000 0.00 0.00 44.86 3.96
4016 8355 3.461061 CTCTTCTCCGAATGCTATGCAA 58.539 45.455 0.00 0.00 43.62 4.08
4017 8356 3.461061 TCTTCTCCGAATGCTATGCAAG 58.539 45.455 0.00 0.00 43.62 4.01
4018 8357 2.988010 TCTCCGAATGCTATGCAAGT 57.012 45.000 0.00 0.00 43.62 3.16
4019 8358 3.266510 TCTCCGAATGCTATGCAAGTT 57.733 42.857 0.00 0.00 43.62 2.66
4020 8359 4.400529 TCTCCGAATGCTATGCAAGTTA 57.599 40.909 0.00 0.00 43.62 2.24
4021 8360 4.960938 TCTCCGAATGCTATGCAAGTTAT 58.039 39.130 0.00 0.00 43.62 1.89
4022 8361 6.096673 TCTCCGAATGCTATGCAAGTTATA 57.903 37.500 0.00 0.00 43.62 0.98
4023 8362 6.159293 TCTCCGAATGCTATGCAAGTTATAG 58.841 40.000 0.00 0.00 43.62 1.31
4028 8367 3.174799 GCTATGCAAGTTATAGCGTGC 57.825 47.619 18.04 18.04 42.31 5.34
4029 8368 2.802816 GCTATGCAAGTTATAGCGTGCT 59.197 45.455 23.28 13.80 42.31 4.40
4030 8369 3.987868 GCTATGCAAGTTATAGCGTGCTA 59.012 43.478 23.28 13.10 42.31 3.49
4031 8370 4.627467 GCTATGCAAGTTATAGCGTGCTAT 59.373 41.667 23.28 17.65 42.31 2.97
4032 8371 5.805486 GCTATGCAAGTTATAGCGTGCTATA 59.195 40.000 23.28 15.72 42.31 1.31
4033 8372 6.477033 GCTATGCAAGTTATAGCGTGCTATAT 59.523 38.462 23.28 13.78 42.31 0.86
4034 8373 7.010552 GCTATGCAAGTTATAGCGTGCTATATT 59.989 37.037 23.28 10.88 42.31 1.28
4035 8374 6.706055 TGCAAGTTATAGCGTGCTATATTC 57.294 37.500 23.28 15.40 42.72 1.75
4036 8375 5.344933 TGCAAGTTATAGCGTGCTATATTCG 59.655 40.000 23.28 11.13 42.72 3.34
4037 8376 5.571741 GCAAGTTATAGCGTGCTATATTCGA 59.428 40.000 19.27 5.00 40.09 3.71
4038 8377 6.452611 GCAAGTTATAGCGTGCTATATTCGAC 60.453 42.308 19.27 14.78 40.09 4.20
4039 8378 6.250344 AGTTATAGCGTGCTATATTCGACA 57.750 37.500 19.27 4.06 40.09 4.35
4040 8379 6.853720 AGTTATAGCGTGCTATATTCGACAT 58.146 36.000 19.27 5.50 40.09 3.06
4041 8380 7.982224 AGTTATAGCGTGCTATATTCGACATA 58.018 34.615 19.27 2.81 40.09 2.29
4042 8381 8.123575 AGTTATAGCGTGCTATATTCGACATAG 58.876 37.037 19.27 8.32 40.09 2.23
4050 8389 6.448053 GCTATATTCGACATAGCGTTTTGA 57.552 37.500 17.81 0.00 40.94 2.69
4051 8390 6.873656 GCTATATTCGACATAGCGTTTTGAA 58.126 36.000 17.81 0.00 40.94 2.69
4052 8391 7.342194 GCTATATTCGACATAGCGTTTTGAAA 58.658 34.615 17.81 0.00 40.94 2.69
4053 8392 8.009974 GCTATATTCGACATAGCGTTTTGAAAT 58.990 33.333 17.81 0.00 40.94 2.17
4057 8396 8.958175 ATTCGACATAGCGTTTTGAAATAAAA 57.042 26.923 0.00 0.00 0.00 1.52
4058 8397 8.429739 TTCGACATAGCGTTTTGAAATAAAAG 57.570 30.769 0.00 0.00 0.00 2.27
4059 8398 7.577979 TCGACATAGCGTTTTGAAATAAAAGT 58.422 30.769 0.00 0.00 0.00 2.66
4060 8399 7.742963 TCGACATAGCGTTTTGAAATAAAAGTC 59.257 33.333 0.00 0.00 0.00 3.01
4061 8400 7.532546 CGACATAGCGTTTTGAAATAAAAGTCA 59.467 33.333 0.00 0.00 0.00 3.41
4062 8401 9.176181 GACATAGCGTTTTGAAATAAAAGTCAA 57.824 29.630 0.00 0.00 31.99 3.18
4063 8402 9.522804 ACATAGCGTTTTGAAATAAAAGTCAAA 57.477 25.926 0.00 0.00 40.93 2.69
4105 8444 9.860898 AAGGATTTCAACATCTAAATTTGCTAC 57.139 29.630 0.00 0.00 0.00 3.58
4106 8445 9.247861 AGGATTTCAACATCTAAATTTGCTACT 57.752 29.630 0.00 0.00 0.00 2.57
4107 8446 9.508567 GGATTTCAACATCTAAATTTGCTACTC 57.491 33.333 0.00 0.00 0.00 2.59
4108 8447 9.508567 GATTTCAACATCTAAATTTGCTACTCC 57.491 33.333 0.00 0.00 0.00 3.85
4109 8448 7.391148 TTCAACATCTAAATTTGCTACTCCC 57.609 36.000 0.00 0.00 0.00 4.30
4110 8449 6.721318 TCAACATCTAAATTTGCTACTCCCT 58.279 36.000 0.00 0.00 0.00 4.20
4111 8450 6.823689 TCAACATCTAAATTTGCTACTCCCTC 59.176 38.462 0.00 0.00 0.00 4.30
4112 8451 5.685728 ACATCTAAATTTGCTACTCCCTCC 58.314 41.667 0.00 0.00 0.00 4.30
4113 8452 4.402056 TCTAAATTTGCTACTCCCTCCG 57.598 45.455 0.00 0.00 0.00 4.63
4114 8453 3.773119 TCTAAATTTGCTACTCCCTCCGT 59.227 43.478 0.00 0.00 0.00 4.69
4115 8454 3.434940 AAATTTGCTACTCCCTCCGTT 57.565 42.857 0.00 0.00 0.00 4.44
4116 8455 2.693267 ATTTGCTACTCCCTCCGTTC 57.307 50.000 0.00 0.00 0.00 3.95
4117 8456 0.611714 TTTGCTACTCCCTCCGTTCC 59.388 55.000 0.00 0.00 0.00 3.62
4118 8457 0.543410 TTGCTACTCCCTCCGTTCCA 60.543 55.000 0.00 0.00 0.00 3.53
4119 8458 0.543410 TGCTACTCCCTCCGTTCCAA 60.543 55.000 0.00 0.00 0.00 3.53
4120 8459 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
4121 8460 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
4122 8461 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
4123 8462 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.935799 TGTAATGCAATTGGTGGGCT 58.064 45.000 7.72 0.00 36.99 5.19
1 2 2.758736 TTGTAATGCAATTGGTGGGC 57.241 45.000 7.72 0.00 36.99 5.36
2 3 6.572167 AATTTTTGTAATGCAATTGGTGGG 57.428 33.333 7.72 0.00 36.99 4.61
3 4 9.392021 GTTTAATTTTTGTAATGCAATTGGTGG 57.608 29.630 7.72 0.00 36.99 4.61
4 5 9.941664 TGTTTAATTTTTGTAATGCAATTGGTG 57.058 25.926 7.72 0.00 36.99 4.17
38 39 6.986904 ATCCCGTTTCTTCTTAGCTAAAAG 57.013 37.500 7.74 13.13 0.00 2.27
56 57 5.448632 GCTATGGCCGATTAATTAAATCCCG 60.449 44.000 1.21 4.26 40.91 5.14
124 125 7.334171 CACTGTCATGTTCTATTGGATTGTACA 59.666 37.037 0.00 0.00 0.00 2.90
125 126 7.201644 CCACTGTCATGTTCTATTGGATTGTAC 60.202 40.741 0.00 0.00 0.00 2.90
127 128 5.649395 CCACTGTCATGTTCTATTGGATTGT 59.351 40.000 0.00 0.00 0.00 2.71
128 129 5.066893 CCCACTGTCATGTTCTATTGGATTG 59.933 44.000 0.00 0.00 0.00 2.67
129 130 5.195940 CCCACTGTCATGTTCTATTGGATT 58.804 41.667 0.00 0.00 0.00 3.01
130 131 4.385643 CCCCACTGTCATGTTCTATTGGAT 60.386 45.833 0.00 0.00 0.00 3.41
131 132 3.054434 CCCCACTGTCATGTTCTATTGGA 60.054 47.826 0.00 0.00 0.00 3.53
132 133 3.282021 CCCCACTGTCATGTTCTATTGG 58.718 50.000 0.00 0.00 0.00 3.16
133 134 2.684881 GCCCCACTGTCATGTTCTATTG 59.315 50.000 0.00 0.00 0.00 1.90
150 151 1.065199 TCTCACTGAATCATGTGCCCC 60.065 52.381 7.60 0.00 34.49 5.80
152 153 2.617308 CCATCTCACTGAATCATGTGCC 59.383 50.000 7.60 0.00 34.49 5.01
189 191 3.688159 CAGGGGCTGTGCAAAGGC 61.688 66.667 22.01 22.01 41.86 4.35
190 192 3.688159 GCAGGGGCTGTGCAAAGG 61.688 66.667 5.91 0.00 40.86 3.11
199 201 5.974156 AAATAAATAAATTGGCAGGGGCT 57.026 34.783 0.00 0.00 40.87 5.19
232 234 9.771534 GTTCCTCTCTGCTTTAGTTTCATATAT 57.228 33.333 0.00 0.00 0.00 0.86
233 235 8.758829 TGTTCCTCTCTGCTTTAGTTTCATATA 58.241 33.333 0.00 0.00 0.00 0.86
234 236 7.550906 GTGTTCCTCTCTGCTTTAGTTTCATAT 59.449 37.037 0.00 0.00 0.00 1.78
235 237 6.874134 GTGTTCCTCTCTGCTTTAGTTTCATA 59.126 38.462 0.00 0.00 0.00 2.15
236 238 5.703130 GTGTTCCTCTCTGCTTTAGTTTCAT 59.297 40.000 0.00 0.00 0.00 2.57
256 2166 1.006102 CCTCTCTGTTCGCCGTGTT 60.006 57.895 0.00 0.00 0.00 3.32
318 2228 1.460273 GGAGCAGGATCCTCGTCCTC 61.460 65.000 23.94 19.44 45.51 3.71
320 2230 1.743321 CTGGAGCAGGATCCTCGTCC 61.743 65.000 24.27 24.27 40.29 4.79
321 2231 1.739049 CTGGAGCAGGATCCTCGTC 59.261 63.158 12.69 11.29 40.29 4.20
322 2232 3.947173 CTGGAGCAGGATCCTCGT 58.053 61.111 12.69 0.74 40.29 4.18
405 2315 1.311651 GGAGGCAGAGCAGAAAAGGC 61.312 60.000 0.00 0.00 0.00 4.35
406 2316 1.023513 CGGAGGCAGAGCAGAAAAGG 61.024 60.000 0.00 0.00 0.00 3.11
522 2432 0.680061 GAAATAGATCTCCCGGCGGT 59.320 55.000 26.32 5.67 0.00 5.68
546 2456 2.468015 TCTGCAAGAGGGAAAGGCT 58.532 52.632 0.00 0.00 38.67 4.58
594 2515 3.259902 GGGTCGTTTGAGAGGTTGTATC 58.740 50.000 0.00 0.00 0.00 2.24
605 2526 1.079405 GCTGATCCGGGTCGTTTGA 60.079 57.895 10.84 0.00 0.00 2.69
606 2527 2.452813 CGCTGATCCGGGTCGTTTG 61.453 63.158 10.84 1.31 0.00 2.93
633 2560 5.049680 GGTTGTAAATCTCGACTGAAGCAAA 60.050 40.000 0.00 0.00 0.00 3.68
636 2563 3.060895 CGGTTGTAAATCTCGACTGAAGC 59.939 47.826 0.00 0.00 0.00 3.86
638 2565 3.581755 CCGGTTGTAAATCTCGACTGAA 58.418 45.455 0.00 0.00 0.00 3.02
641 2568 1.405121 GGCCGGTTGTAAATCTCGACT 60.405 52.381 1.90 0.00 0.00 4.18
642 2569 1.004595 GGCCGGTTGTAAATCTCGAC 58.995 55.000 1.90 0.00 0.00 4.20
643 2570 0.899720 AGGCCGGTTGTAAATCTCGA 59.100 50.000 1.90 0.00 0.00 4.04
645 2572 1.287425 CGAGGCCGGTTGTAAATCTC 58.713 55.000 1.90 0.00 0.00 2.75
646 2573 0.611714 ACGAGGCCGGTTGTAAATCT 59.388 50.000 1.90 0.00 40.78 2.40
647 2574 1.004595 GACGAGGCCGGTTGTAAATC 58.995 55.000 1.90 0.00 40.78 2.17
650 2577 1.880819 GAGGACGAGGCCGGTTGTAA 61.881 60.000 1.90 0.00 40.78 2.41
651 2578 2.283388 AGGACGAGGCCGGTTGTA 60.283 61.111 1.90 0.00 40.78 2.41
652 2579 3.692406 GAGGACGAGGCCGGTTGT 61.692 66.667 1.90 0.00 40.78 3.32
654 2581 3.925630 TACGAGGACGAGGCCGGTT 62.926 63.158 1.90 0.00 42.66 4.44
655 2582 3.925630 TTACGAGGACGAGGCCGGT 62.926 63.158 1.90 0.00 42.66 5.28
656 2583 2.216750 TTTTACGAGGACGAGGCCGG 62.217 60.000 0.00 0.00 42.66 6.13
657 2584 0.388907 TTTTTACGAGGACGAGGCCG 60.389 55.000 0.00 0.00 42.66 6.13
658 2585 3.520187 TTTTTACGAGGACGAGGCC 57.480 52.632 0.00 0.00 42.66 5.19
728 2666 1.467920 AGCTACCTTGCAGAATTGGC 58.532 50.000 0.00 0.00 34.99 4.52
742 2680 0.464554 GCCACCATGGGAGAAGCTAC 60.465 60.000 18.09 0.00 38.19 3.58
778 2716 2.086869 CCGCAACATCACCATCTTCTT 58.913 47.619 0.00 0.00 0.00 2.52
898 2836 1.226603 CGTCGTCGGAAGGGATGAC 60.227 63.158 5.13 5.13 45.32 3.06
936 2877 1.068250 GAGGCGGATGAGGCAGTAC 59.932 63.158 0.00 0.00 39.37 2.73
955 2896 2.596338 TGTGTCGCCTCAGACGGA 60.596 61.111 0.00 0.00 43.70 4.69
961 2902 1.112916 TTGGAGAGTGTGTCGCCTCA 61.113 55.000 0.00 0.00 45.26 3.86
995 2936 2.125552 CGGAGGCGTGCATCTTGA 60.126 61.111 6.46 0.00 0.00 3.02
1028 2970 3.628646 AACTCCGCATCCCAGTGGC 62.629 63.158 2.61 0.00 39.04 5.01
1203 3145 5.329399 ACAAATTATACCCAAGCCAGTTCA 58.671 37.500 0.00 0.00 0.00 3.18
1445 3429 7.112122 AGCTCAATGTGAATTAGGTGTGAATA 58.888 34.615 0.00 0.00 0.00 1.75
1449 3433 5.633830 AAGCTCAATGTGAATTAGGTGTG 57.366 39.130 0.00 0.00 0.00 3.82
1663 3652 5.041287 CGTGACTCGTATCATAAACACCAT 58.959 41.667 0.00 0.00 34.52 3.55
1773 3767 9.498176 AATGCAAAGCTTAAAGAAATGAAAGAT 57.502 25.926 0.00 0.00 0.00 2.40
1857 4615 9.086758 TCCCCTTTATCTTACTAGCAATAGTAC 57.913 37.037 0.00 0.00 32.76 2.73
1858 4616 9.664777 TTCCCCTTTATCTTACTAGCAATAGTA 57.335 33.333 0.00 0.00 0.00 1.82
1934 4692 6.706270 GCTATTGTTTCCTCATCTAATTCCGA 59.294 38.462 0.00 0.00 0.00 4.55
2082 4840 8.906867 ACCATAGGATTTTGTTATTGATGTCAG 58.093 33.333 0.00 0.00 0.00 3.51
2373 5151 8.095792 TGGTACCTAAACAAGATTAACGAATGA 58.904 33.333 14.36 0.00 0.00 2.57
2399 5178 6.040209 ACCAACATGTATGCACATCAAATT 57.960 33.333 0.00 0.00 43.73 1.82
2473 5252 4.189231 GTGAAGGTATCATGTTAAGCCGT 58.811 43.478 0.00 0.00 40.97 5.68
2510 5289 6.040247 TGACATTTACACATGATCCTACGAC 58.960 40.000 0.00 0.00 0.00 4.34
2670 5449 3.127895 GCAGAAACAAATACATACCGCCA 59.872 43.478 0.00 0.00 0.00 5.69
2689 5468 3.317430 GCATAGGAAAAGATTGGAGGCAG 59.683 47.826 0.00 0.00 0.00 4.85
2764 5547 0.517316 GTTAACTTGCCGTCCTGCAG 59.483 55.000 6.78 6.78 43.21 4.41
2946 5729 6.153680 CCACCCTACTCAGATAGCTATTTAGG 59.846 46.154 7.87 11.93 0.00 2.69
2995 5778 4.209538 TCAATGGTAGCTTCAATGGGATG 58.790 43.478 0.00 0.00 0.00 3.51
3024 5807 0.451783 GTAGTCCAGGCGGCAAAATG 59.548 55.000 13.08 0.00 0.00 2.32
3149 5966 0.391263 GGAGCACCAACCTTCTACCG 60.391 60.000 0.00 0.00 35.97 4.02
3157 5974 2.331265 GTGACAAGGAGCACCAACC 58.669 57.895 2.07 0.00 38.94 3.77
3200 6017 6.949578 AAAGGTGCGATGATGTTTTTATTG 57.050 33.333 0.00 0.00 0.00 1.90
3297 6114 1.315981 TGCCTCTCGCGTCTGAGAAT 61.316 55.000 21.13 0.00 44.03 2.40
3301 6118 1.315981 ATCTTGCCTCTCGCGTCTGA 61.316 55.000 5.77 2.38 42.08 3.27
3371 6205 6.152661 GGTGTCAATTTCCATCCATAACAGAA 59.847 38.462 0.00 0.00 0.00 3.02
3390 6226 4.102524 ACACAGAATACTTTCCAGGTGTCA 59.897 41.667 0.00 0.00 37.47 3.58
3508 7783 4.039973 ACTCTTTGACAGGACATAACCGAA 59.960 41.667 0.00 0.00 34.73 4.30
3511 7786 6.879400 AGATACTCTTTGACAGGACATAACC 58.121 40.000 0.00 0.00 0.00 2.85
3582 7857 7.704899 GCGCACCTATCCAAATTTAAGTTATTT 59.295 33.333 0.30 0.00 0.00 1.40
3596 7871 0.539518 TAGCTTTGCGCACCTATCCA 59.460 50.000 11.12 0.00 42.61 3.41
3625 7904 0.515564 CTCGGTTAAGCAACGTTGGG 59.484 55.000 28.33 5.81 35.34 4.12
3641 7920 3.423123 GCTGTCACCGTATTTTTGTCTCG 60.423 47.826 0.00 0.00 0.00 4.04
3661 7940 2.484264 GCTTGGTTGACAAATACTCGCT 59.516 45.455 0.00 0.00 38.91 4.93
3662 7941 2.484264 AGCTTGGTTGACAAATACTCGC 59.516 45.455 0.00 0.00 38.91 5.03
3663 7942 3.745975 TCAGCTTGGTTGACAAATACTCG 59.254 43.478 0.00 0.00 38.91 4.18
3664 7943 5.689383 TTCAGCTTGGTTGACAAATACTC 57.311 39.130 0.00 0.00 38.91 2.59
3665 7944 6.655078 ATTTCAGCTTGGTTGACAAATACT 57.345 33.333 0.00 0.00 38.91 2.12
3666 7945 6.523201 CGTATTTCAGCTTGGTTGACAAATAC 59.477 38.462 0.00 0.00 38.91 1.89
3667 7946 6.205853 ACGTATTTCAGCTTGGTTGACAAATA 59.794 34.615 0.00 0.00 38.91 1.40
3668 7947 5.009610 ACGTATTTCAGCTTGGTTGACAAAT 59.990 36.000 0.00 0.00 38.91 2.32
3669 7948 4.336993 ACGTATTTCAGCTTGGTTGACAAA 59.663 37.500 0.00 0.00 38.91 2.83
3670 7949 3.880490 ACGTATTTCAGCTTGGTTGACAA 59.120 39.130 0.00 0.00 37.55 3.18
3671 7950 3.472652 ACGTATTTCAGCTTGGTTGACA 58.527 40.909 0.00 0.00 0.00 3.58
3672 7951 4.219033 CAACGTATTTCAGCTTGGTTGAC 58.781 43.478 0.00 0.00 36.34 3.18
3673 7952 3.304391 GCAACGTATTTCAGCTTGGTTGA 60.304 43.478 5.30 0.00 36.34 3.18
3674 7953 2.979813 GCAACGTATTTCAGCTTGGTTG 59.020 45.455 0.00 0.00 37.07 3.77
3675 7954 2.884639 AGCAACGTATTTCAGCTTGGTT 59.115 40.909 0.00 0.00 29.98 3.67
3676 7955 2.504367 AGCAACGTATTTCAGCTTGGT 58.496 42.857 0.00 0.00 29.98 3.67
3677 7956 3.058293 TGAAGCAACGTATTTCAGCTTGG 60.058 43.478 11.24 0.00 44.73 3.61
3678 7957 3.908382 GTGAAGCAACGTATTTCAGCTTG 59.092 43.478 11.24 0.00 44.73 4.01
3680 7959 2.484264 GGTGAAGCAACGTATTTCAGCT 59.516 45.455 21.51 9.46 42.77 4.24
3681 7960 2.414161 GGGTGAAGCAACGTATTTCAGC 60.414 50.000 21.04 21.04 44.37 4.26
3682 7961 2.811431 TGGGTGAAGCAACGTATTTCAG 59.189 45.455 8.89 0.00 32.00 3.02
3683 7962 2.852449 TGGGTGAAGCAACGTATTTCA 58.148 42.857 0.00 0.00 0.00 2.69
3684 7963 3.003897 TGTTGGGTGAAGCAACGTATTTC 59.996 43.478 0.00 0.00 0.00 2.17
3685 7964 2.952978 TGTTGGGTGAAGCAACGTATTT 59.047 40.909 0.00 0.00 0.00 1.40
3686 7965 2.552315 CTGTTGGGTGAAGCAACGTATT 59.448 45.455 0.00 0.00 0.00 1.89
3687 7966 2.151202 CTGTTGGGTGAAGCAACGTAT 58.849 47.619 0.00 0.00 0.00 3.06
3688 7967 1.134340 ACTGTTGGGTGAAGCAACGTA 60.134 47.619 0.00 0.00 0.00 3.57
3689 7968 0.393808 ACTGTTGGGTGAAGCAACGT 60.394 50.000 0.00 0.00 0.00 3.99
3690 7969 0.307760 GACTGTTGGGTGAAGCAACG 59.692 55.000 0.00 0.00 0.00 4.10
3691 7970 1.388547 TGACTGTTGGGTGAAGCAAC 58.611 50.000 0.00 0.00 0.00 4.17
3692 7971 1.748493 GTTGACTGTTGGGTGAAGCAA 59.252 47.619 0.00 0.00 0.00 3.91
3693 7972 1.340502 TGTTGACTGTTGGGTGAAGCA 60.341 47.619 0.00 0.00 0.00 3.91
3694 7973 1.388547 TGTTGACTGTTGGGTGAAGC 58.611 50.000 0.00 0.00 0.00 3.86
3695 7974 3.381272 ACAATGTTGACTGTTGGGTGAAG 59.619 43.478 0.00 0.00 0.00 3.02
3696 7975 3.130164 CACAATGTTGACTGTTGGGTGAA 59.870 43.478 0.00 0.00 0.00 3.18
3697 7976 2.687425 CACAATGTTGACTGTTGGGTGA 59.313 45.455 0.00 0.00 0.00 4.02
3698 7977 2.426738 ACACAATGTTGACTGTTGGGTG 59.573 45.455 0.00 0.00 38.02 4.61
3699 7978 2.733956 ACACAATGTTGACTGTTGGGT 58.266 42.857 0.00 3.15 34.82 4.51
3700 7979 3.799281 AACACAATGTTGACTGTTGGG 57.201 42.857 0.00 0.00 39.45 4.12
3701 7980 5.636965 TGAAAAACACAATGTTGACTGTTGG 59.363 36.000 0.00 0.00 40.14 3.77
3729 8008 6.597262 TGTACATTTTGCCTGTATACATCG 57.403 37.500 5.91 0.89 32.13 3.84
3830 8154 8.830580 CCCTGATACAATTTAGATACAGTGTTG 58.169 37.037 0.00 0.00 0.00 3.33
3842 8166 8.707449 ACTACCGATTTACCCTGATACAATTTA 58.293 33.333 0.00 0.00 0.00 1.40
3855 8194 3.998341 TCTGTTTGCACTACCGATTTACC 59.002 43.478 0.00 0.00 0.00 2.85
3969 8308 7.519970 GCCACGCTATTTTAAATAGCACACTAT 60.520 37.037 34.36 17.84 45.32 2.12
3970 8309 6.238266 GCCACGCTATTTTAAATAGCACACTA 60.238 38.462 34.36 2.27 45.32 2.74
3971 8310 5.448632 GCCACGCTATTTTAAATAGCACACT 60.449 40.000 34.36 18.92 45.32 3.55
3972 8311 4.733405 GCCACGCTATTTTAAATAGCACAC 59.267 41.667 34.36 22.54 45.32 3.82
3973 8312 4.638421 AGCCACGCTATTTTAAATAGCACA 59.362 37.500 34.36 4.17 45.32 4.57
3974 8313 5.007724 AGAGCCACGCTATTTTAAATAGCAC 59.992 40.000 34.36 24.48 45.32 4.40
3975 8314 5.123227 AGAGCCACGCTATTTTAAATAGCA 58.877 37.500 34.36 4.81 45.32 3.49
3976 8315 5.674933 AGAGCCACGCTATTTTAAATAGC 57.325 39.130 29.51 29.51 39.88 2.97
3977 8316 7.307455 GGAGAAGAGCCACGCTATTTTAAATAG 60.307 40.741 17.63 17.63 40.30 1.73
3978 8317 6.482308 GGAGAAGAGCCACGCTATTTTAAATA 59.518 38.462 0.00 0.00 40.30 1.40
3979 8318 5.297029 GGAGAAGAGCCACGCTATTTTAAAT 59.703 40.000 0.00 0.00 40.30 1.40
3980 8319 4.634443 GGAGAAGAGCCACGCTATTTTAAA 59.366 41.667 0.00 0.00 40.30 1.52
3981 8320 4.189231 GGAGAAGAGCCACGCTATTTTAA 58.811 43.478 0.00 0.00 40.30 1.52
3982 8321 3.737047 CGGAGAAGAGCCACGCTATTTTA 60.737 47.826 0.00 0.00 40.30 1.52
3983 8322 2.633488 GGAGAAGAGCCACGCTATTTT 58.367 47.619 0.00 0.00 40.30 1.82
3984 8323 1.471676 CGGAGAAGAGCCACGCTATTT 60.472 52.381 0.00 0.00 40.30 1.40
3985 8324 0.103208 CGGAGAAGAGCCACGCTATT 59.897 55.000 0.00 0.00 43.01 1.73
3986 8325 0.752009 TCGGAGAAGAGCCACGCTAT 60.752 55.000 0.00 0.00 39.88 2.97
3987 8326 0.963856 TTCGGAGAAGAGCCACGCTA 60.964 55.000 0.00 0.00 45.90 4.26
3988 8327 1.608717 ATTCGGAGAAGAGCCACGCT 61.609 55.000 0.00 0.00 45.90 5.07
3989 8328 1.153549 ATTCGGAGAAGAGCCACGC 60.154 57.895 0.00 0.00 45.90 5.34
3990 8329 1.424493 GCATTCGGAGAAGAGCCACG 61.424 60.000 0.00 0.00 45.90 4.94
3991 8330 0.107945 AGCATTCGGAGAAGAGCCAC 60.108 55.000 6.44 0.00 45.90 5.01
3992 8331 1.485124 TAGCATTCGGAGAAGAGCCA 58.515 50.000 6.44 0.00 45.90 4.75
3993 8332 2.411904 CATAGCATTCGGAGAAGAGCC 58.588 52.381 6.44 0.00 45.90 4.70
3994 8333 1.797635 GCATAGCATTCGGAGAAGAGC 59.202 52.381 0.00 2.97 45.90 4.09
3995 8334 3.103447 TGCATAGCATTCGGAGAAGAG 57.897 47.619 0.00 0.00 35.69 2.85
3996 8335 3.118629 ACTTGCATAGCATTCGGAGAAGA 60.119 43.478 0.00 0.00 38.76 2.87
3997 8336 3.201290 ACTTGCATAGCATTCGGAGAAG 58.799 45.455 0.00 0.00 38.76 2.85
3998 8337 3.266510 ACTTGCATAGCATTCGGAGAA 57.733 42.857 0.00 0.00 38.76 2.87
3999 8338 2.988010 ACTTGCATAGCATTCGGAGA 57.012 45.000 0.00 0.00 38.76 3.71
4000 8339 5.163913 GCTATAACTTGCATAGCATTCGGAG 60.164 44.000 10.66 0.00 46.65 4.63
4001 8340 4.690748 GCTATAACTTGCATAGCATTCGGA 59.309 41.667 10.66 0.00 46.65 4.55
4002 8341 4.962693 GCTATAACTTGCATAGCATTCGG 58.037 43.478 10.66 0.00 46.65 4.30
4008 8347 2.802816 AGCACGCTATAACTTGCATAGC 59.197 45.455 7.28 6.25 44.86 2.97
4009 8348 7.993821 ATATAGCACGCTATAACTTGCATAG 57.006 36.000 19.70 0.00 42.57 2.23
4010 8349 7.220108 CGAATATAGCACGCTATAACTTGCATA 59.780 37.037 19.70 4.19 42.57 3.14
4011 8350 6.035005 CGAATATAGCACGCTATAACTTGCAT 59.965 38.462 19.70 3.28 42.57 3.96
4012 8351 5.344933 CGAATATAGCACGCTATAACTTGCA 59.655 40.000 19.70 1.13 42.57 4.08
4013 8352 5.571741 TCGAATATAGCACGCTATAACTTGC 59.428 40.000 19.70 4.89 42.57 4.01
4014 8353 6.581166 TGTCGAATATAGCACGCTATAACTTG 59.419 38.462 19.70 14.19 42.57 3.16
4015 8354 6.675026 TGTCGAATATAGCACGCTATAACTT 58.325 36.000 19.70 12.13 42.57 2.66
4016 8355 6.250344 TGTCGAATATAGCACGCTATAACT 57.750 37.500 19.70 11.71 42.57 2.24
4017 8356 8.259240 CTATGTCGAATATAGCACGCTATAAC 57.741 38.462 19.70 14.34 42.57 1.89
4027 8366 6.448053 TCAAAACGCTATGTCGAATATAGC 57.552 37.500 23.25 23.25 45.96 2.97
4032 8371 8.958175 TTTTATTTCAAAACGCTATGTCGAAT 57.042 26.923 0.00 0.00 0.00 3.34
4033 8372 8.071368 ACTTTTATTTCAAAACGCTATGTCGAA 58.929 29.630 0.00 0.00 0.00 3.71
4034 8373 7.577979 ACTTTTATTTCAAAACGCTATGTCGA 58.422 30.769 0.00 0.00 0.00 4.20
4035 8374 7.532546 TGACTTTTATTTCAAAACGCTATGTCG 59.467 33.333 0.00 0.00 0.00 4.35
4036 8375 8.722342 TGACTTTTATTTCAAAACGCTATGTC 57.278 30.769 0.00 0.00 0.00 3.06
4037 8376 9.522804 TTTGACTTTTATTTCAAAACGCTATGT 57.477 25.926 0.00 0.00 38.48 2.29
4079 8418 9.860898 GTAGCAAATTTAGATGTTGAAATCCTT 57.139 29.630 0.00 0.00 0.00 3.36
4080 8419 9.247861 AGTAGCAAATTTAGATGTTGAAATCCT 57.752 29.630 0.00 0.00 0.00 3.24
4081 8420 9.508567 GAGTAGCAAATTTAGATGTTGAAATCC 57.491 33.333 0.00 0.00 0.00 3.01
4082 8421 9.508567 GGAGTAGCAAATTTAGATGTTGAAATC 57.491 33.333 0.00 0.00 0.00 2.17
4083 8422 8.470002 GGGAGTAGCAAATTTAGATGTTGAAAT 58.530 33.333 0.00 0.00 0.00 2.17
4084 8423 7.669722 AGGGAGTAGCAAATTTAGATGTTGAAA 59.330 33.333 0.00 0.00 0.00 2.69
4085 8424 7.175104 AGGGAGTAGCAAATTTAGATGTTGAA 58.825 34.615 0.00 0.00 0.00 2.69
4086 8425 6.721318 AGGGAGTAGCAAATTTAGATGTTGA 58.279 36.000 0.00 0.00 0.00 3.18
4087 8426 6.038714 GGAGGGAGTAGCAAATTTAGATGTTG 59.961 42.308 0.00 0.00 0.00 3.33
4088 8427 6.122964 GGAGGGAGTAGCAAATTTAGATGTT 58.877 40.000 0.00 0.00 0.00 2.71
4089 8428 5.685075 CGGAGGGAGTAGCAAATTTAGATGT 60.685 44.000 0.00 0.00 0.00 3.06
4090 8429 4.752101 CGGAGGGAGTAGCAAATTTAGATG 59.248 45.833 0.00 0.00 0.00 2.90
4091 8430 4.409247 ACGGAGGGAGTAGCAAATTTAGAT 59.591 41.667 0.00 0.00 0.00 1.98
4092 8431 3.773119 ACGGAGGGAGTAGCAAATTTAGA 59.227 43.478 0.00 0.00 0.00 2.10
4093 8432 4.138487 ACGGAGGGAGTAGCAAATTTAG 57.862 45.455 0.00 0.00 0.00 1.85
4094 8433 4.510571 GAACGGAGGGAGTAGCAAATTTA 58.489 43.478 0.00 0.00 0.00 1.40
4095 8434 3.344515 GAACGGAGGGAGTAGCAAATTT 58.655 45.455 0.00 0.00 0.00 1.82
4096 8435 2.355818 GGAACGGAGGGAGTAGCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
4097 8436 1.209747 GGAACGGAGGGAGTAGCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
4098 8437 0.611714 GGAACGGAGGGAGTAGCAAA 59.388 55.000 0.00 0.00 0.00 3.68
4099 8438 0.543410 TGGAACGGAGGGAGTAGCAA 60.543 55.000 0.00 0.00 0.00 3.91
4100 8439 0.543410 TTGGAACGGAGGGAGTAGCA 60.543 55.000 0.00 0.00 0.00 3.49
4101 8440 0.611714 TTTGGAACGGAGGGAGTAGC 59.388 55.000 0.00 0.00 0.00 3.58
4102 8441 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.