Multiple sequence alignment - TraesCS5D01G109600

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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 TraesCS5D01G109600 chr5D 100.000 5668 0 0 1 5668 123880657 123886324 0.000000e+00 10467.0
1 TraesCS5D01G109600 chr5D 82.979 188 23 6 4701 4887 151671541 151671720 1.630000e-35 161.0
2 TraesCS5D01G109600 chr5A 96.760 2963 62 12 2732 5668 137277582 137280536 0.000000e+00 4909.0
3 TraesCS5D01G109600 chr5A 93.652 2552 96 33 159 2649 137275038 137277584 0.000000e+00 3755.0
4 TraesCS5D01G109600 chr5A 89.881 168 9 1 4 163 137266769 137266936 5.750000e-50 209.0
5 TraesCS5D01G109600 chr5A 84.483 174 21 3 4707 4880 585431774 585431607 3.510000e-37 167.0
6 TraesCS5D01G109600 chr5B 95.567 1940 43 14 2797 4709 136626268 136628191 0.000000e+00 3066.0
7 TraesCS5D01G109600 chr5B 96.009 1804 54 8 853 2649 136622355 136624147 0.000000e+00 2916.0
8 TraesCS5D01G109600 chr5B 94.913 806 28 3 4876 5668 136628190 136628995 0.000000e+00 1249.0
9 TraesCS5D01G109600 chr5B 84.538 498 66 3 1 490 136568297 136568791 3.070000e-132 483.0
10 TraesCS5D01G109600 chr5B 84.685 222 26 5 566 783 136621525 136621742 1.240000e-51 215.0
11 TraesCS5D01G109600 chr5B 92.857 98 7 0 2639 2736 83791121 83791218 5.920000e-30 143.0
12 TraesCS5D01G109600 chr5B 100.000 34 0 0 2732 2765 136624145 136624178 4.740000e-06 63.9
13 TraesCS5D01G109600 chr6A 85.143 175 20 3 4706 4880 48520038 48520206 2.100000e-39 174.0
14 TraesCS5D01G109600 chr6A 84.324 185 21 5 4705 4888 594496706 594496529 2.100000e-39 174.0
15 TraesCS5D01G109600 chr6A 91.429 105 4 4 2647 2751 47446850 47446949 7.660000e-29 139.0
16 TraesCS5D01G109600 chr6A 91.429 105 4 4 2647 2751 47458579 47458678 7.660000e-29 139.0
17 TraesCS5D01G109600 chr3B 85.380 171 19 3 4707 4877 428703659 428703823 7.550000e-39 172.0
18 TraesCS5D01G109600 chr3B 94.845 97 3 1 2643 2739 481548764 481548670 3.540000e-32 150.0
19 TraesCS5D01G109600 chr3B 95.699 93 2 1 2644 2736 81169656 81169746 1.270000e-31 148.0
20 TraesCS5D01G109600 chr1D 84.571 175 19 5 4704 4877 473998772 473998939 3.510000e-37 167.0
21 TraesCS5D01G109600 chr1B 83.978 181 20 6 4705 4884 69844839 69844667 1.260000e-36 165.0
22 TraesCS5D01G109600 chr4A 94.898 98 3 2 2647 2744 615121051 615120956 9.840000e-33 152.0
23 TraesCS5D01G109600 chr1A 95.652 92 2 2 2647 2738 449853583 449853672 4.580000e-31 147.0
24 TraesCS5D01G109600 chr3D 90.826 109 6 2 2636 2742 185712750 185712856 5.920000e-30 143.0
25 TraesCS5D01G109600 chr7B 88.496 113 9 3 2639 2750 695952581 695952690 3.560000e-27 134.0
26 TraesCS5D01G109600 chr7B 100.000 31 0 0 360 390 404058279 404058249 2.210000e-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 TraesCS5D01G109600 chr5D 123880657 123886324 5667 False 10467.00 10467 100.0000 1 5668 1 chr5D.!!$F1 5667
1 TraesCS5D01G109600 chr5A 137275038 137280536 5498 False 4332.00 4909 95.2060 159 5668 2 chr5A.!!$F2 5509
2 TraesCS5D01G109600 chr5B 136621525 136628995 7470 False 1501.98 3066 94.2348 566 5668 5 chr5B.!!$F3 5102

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
110 111 0.106116 CCCCTCTAGACGCCTACCTT 60.106 60.000 0.00 0.0 0.00 3.50 F
1318 1895 0.249868 GCGTGATTCCATCCGATCCA 60.250 55.000 0.00 0.0 0.00 3.41 F
1450 2032 1.147191 AGCATGGATGGAATGGATGCT 59.853 47.619 0.00 0.0 40.96 3.79 F
1453 2035 1.405872 TGGATGGAATGGATGCTTGC 58.594 50.000 0.00 0.0 0.00 4.01 F
1539 2121 1.887242 GCAGCATGTCGGGCGATAA 60.887 57.895 0.00 0.0 39.31 1.75 F
2656 3239 2.237143 TGCCTGAAACATACTCCCTCTG 59.763 50.000 0.00 0.0 0.00 3.35 F
3521 6169 1.071471 CGGTGAACTTGGCCACTCT 59.929 57.895 3.88 0.0 33.99 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1904 0.249657 GCGCGGGAGAAGAATGATCT 60.250 55.000 8.83 0.0 37.57 2.75 R
3080 5718 3.216800 AGAGCAAAGTTTCTGCACATCA 58.783 40.909 2.54 0.0 42.48 3.07 R
3356 6004 2.552155 CCAGTACCAAAGCTTGTAGCCA 60.552 50.000 0.00 0.0 43.77 4.75 R
3392 6040 2.936032 GGCTCCCCAGTGGAAGGT 60.936 66.667 11.95 0.0 44.57 3.50 R
3521 6169 4.157246 TCCTGGTAAAGCACTTAGACTCA 58.843 43.478 0.00 0.0 0.00 3.41 R
4027 6675 1.114627 GACCAATTTGCCATCCTCCC 58.885 55.000 0.00 0.0 0.00 4.30 R
5286 7960 1.951209 TGGGCAGGTAGATCTTGTGA 58.049 50.000 0.00 0.0 0.00 3.58 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
21 22 4.668576 ATCAGCAACAAATCACGTGTAG 57.331 40.909 16.51 6.60 0.00 2.74
22 23 2.805671 TCAGCAACAAATCACGTGTAGG 59.194 45.455 16.51 6.58 0.00 3.18
23 24 2.548057 CAGCAACAAATCACGTGTAGGT 59.452 45.455 16.51 7.23 0.00 3.08
24 25 3.003275 CAGCAACAAATCACGTGTAGGTT 59.997 43.478 16.51 12.69 0.00 3.50
25 26 3.630312 AGCAACAAATCACGTGTAGGTTT 59.370 39.130 16.51 9.81 0.00 3.27
26 27 4.097286 AGCAACAAATCACGTGTAGGTTTT 59.903 37.500 16.51 6.43 0.00 2.43
27 28 4.801516 GCAACAAATCACGTGTAGGTTTTT 59.198 37.500 16.51 4.78 0.00 1.94
55 56 5.700846 GGTATATATAGCCATCGGACATCG 58.299 45.833 10.31 0.00 40.90 3.84
56 57 4.855715 ATATATAGCCATCGGACATCGG 57.144 45.455 0.00 0.00 39.77 4.18
57 58 2.209690 TATAGCCATCGGACATCGGA 57.790 50.000 0.00 0.00 39.77 4.55
58 59 0.891373 ATAGCCATCGGACATCGGAG 59.109 55.000 0.00 0.00 39.77 4.63
59 60 1.179174 TAGCCATCGGACATCGGAGG 61.179 60.000 0.00 0.00 39.77 4.30
60 61 2.797278 GCCATCGGACATCGGAGGT 61.797 63.158 0.00 0.00 39.77 3.85
61 62 1.461091 GCCATCGGACATCGGAGGTA 61.461 60.000 0.00 0.00 39.77 3.08
62 63 0.314302 CCATCGGACATCGGAGGTAC 59.686 60.000 0.00 0.00 39.77 3.34
63 64 0.314302 CATCGGACATCGGAGGTACC 59.686 60.000 2.73 2.73 39.77 3.34
64 65 0.826672 ATCGGACATCGGAGGTACCC 60.827 60.000 8.74 0.00 39.77 3.69
90 91 4.586235 CCCCATGGGCCACGGATC 62.586 72.222 26.87 0.00 35.35 3.36
91 92 4.586235 CCCATGGGCCACGGATCC 62.586 72.222 22.59 0.00 0.00 3.36
92 93 4.586235 CCATGGGCCACGGATCCC 62.586 72.222 14.92 1.67 42.93 3.85
93 94 4.586235 CATGGGCCACGGATCCCC 62.586 72.222 9.28 0.57 41.92 4.81
98 99 2.122989 GCCACGGATCCCCCTCTA 60.123 66.667 6.06 0.00 0.00 2.43
99 100 2.210711 GCCACGGATCCCCCTCTAG 61.211 68.421 6.06 0.00 0.00 2.43
100 101 1.542175 CCACGGATCCCCCTCTAGA 59.458 63.158 6.06 0.00 0.00 2.43
101 102 0.828343 CCACGGATCCCCCTCTAGAC 60.828 65.000 6.06 0.00 0.00 2.59
102 103 1.150992 ACGGATCCCCCTCTAGACG 59.849 63.158 6.06 0.00 0.00 4.18
103 104 2.269529 CGGATCCCCCTCTAGACGC 61.270 68.421 6.06 0.00 0.00 5.19
104 105 1.909287 GGATCCCCCTCTAGACGCC 60.909 68.421 0.00 0.00 0.00 5.68
105 106 1.154221 GATCCCCCTCTAGACGCCT 59.846 63.158 0.00 0.00 0.00 5.52
106 107 0.404812 GATCCCCCTCTAGACGCCTA 59.595 60.000 0.00 0.00 0.00 3.93
107 108 0.112801 ATCCCCCTCTAGACGCCTAC 59.887 60.000 0.00 0.00 0.00 3.18
108 109 1.531128 CCCCCTCTAGACGCCTACC 60.531 68.421 0.00 0.00 0.00 3.18
109 110 1.537669 CCCCTCTAGACGCCTACCT 59.462 63.158 0.00 0.00 0.00 3.08
110 111 0.106116 CCCCTCTAGACGCCTACCTT 60.106 60.000 0.00 0.00 0.00 3.50
111 112 1.033574 CCCTCTAGACGCCTACCTTG 58.966 60.000 0.00 0.00 0.00 3.61
112 113 0.386113 CCTCTAGACGCCTACCTTGC 59.614 60.000 0.00 0.00 0.00 4.01
113 114 1.103803 CTCTAGACGCCTACCTTGCA 58.896 55.000 0.00 0.00 0.00 4.08
114 115 1.476891 CTCTAGACGCCTACCTTGCAA 59.523 52.381 0.00 0.00 0.00 4.08
115 116 1.476891 TCTAGACGCCTACCTTGCAAG 59.523 52.381 19.93 19.93 0.00 4.01
128 129 3.077907 GCAAGGGTGCCTACAGGA 58.922 61.111 0.00 0.00 45.68 3.86
129 130 1.078143 GCAAGGGTGCCTACAGGAG 60.078 63.158 0.00 0.00 45.68 3.69
146 147 2.612251 GGCTCCTAGGGCCTCTCT 59.388 66.667 25.84 0.00 45.57 3.10
147 148 1.074850 GGCTCCTAGGGCCTCTCTT 60.075 63.158 25.84 0.00 45.57 2.85
148 149 1.406860 GGCTCCTAGGGCCTCTCTTG 61.407 65.000 25.84 0.00 45.57 3.02
149 150 1.406860 GCTCCTAGGGCCTCTCTTGG 61.407 65.000 10.74 6.21 0.00 3.61
215 217 9.048446 ACACTCATGAATTTTCTTGGATTTTTG 57.952 29.630 0.00 0.00 34.27 2.44
216 218 8.500773 CACTCATGAATTTTCTTGGATTTTTGG 58.499 33.333 0.00 0.00 34.27 3.28
290 292 7.613801 ACATAAACTGTAAATGGGCACTGAATA 59.386 33.333 7.08 0.00 35.91 1.75
291 293 6.909550 AAACTGTAAATGGGCACTGAATAA 57.090 33.333 0.00 0.00 0.00 1.40
328 330 9.476761 CACTCAAAAATCTTTAACAAACTTTGC 57.523 29.630 1.14 0.00 0.00 3.68
339 341 9.687717 CTTTAACAAACTTTGCAAACTTACATG 57.312 29.630 8.05 4.29 0.00 3.21
343 345 8.801715 ACAAACTTTGCAAACTTACATGATAG 57.198 30.769 8.05 0.00 0.00 2.08
347 349 7.752695 ACTTTGCAAACTTACATGATAGTAGC 58.247 34.615 8.05 10.26 0.00 3.58
354 356 8.554528 CAAACTTACATGATAGTAGCCATGAAG 58.445 37.037 17.32 16.40 41.88 3.02
379 382 8.832521 AGCATACAAAAATTATTGATGCATTGG 58.167 29.630 0.00 0.00 41.27 3.16
403 406 6.090483 AGACGTATCAAGACCTATCCATTG 57.910 41.667 0.00 0.00 0.00 2.82
431 434 6.934645 CAGAGACCAAATTGTTGAGTAGGTTA 59.065 38.462 0.00 0.00 36.83 2.85
463 466 6.070538 ACCTGCCATCCATAGAAGTATGTATC 60.071 42.308 0.00 0.00 35.15 2.24
480 483 8.201464 AGTATGTATCATTTTGTACCACATCGA 58.799 33.333 0.00 0.00 0.00 3.59
503 506 1.544314 GCAAGTGGCCTCTCAAAGAGT 60.544 52.381 7.99 0.00 40.72 3.24
537 540 4.946772 TCTCTAGAGTGATGAAGGACACAG 59.053 45.833 19.21 0.00 39.18 3.66
618 622 1.161563 TCAAAAACCACGGTCCGCTC 61.162 55.000 12.28 0.00 0.00 5.03
663 667 7.366191 GGTGAGGGGTCAATTTAGGATTAACTA 60.366 40.741 0.00 0.00 0.00 2.24
721 739 9.023962 ACATGTGTTTGGTATGTCTAATTTGAT 57.976 29.630 0.00 0.00 29.55 2.57
758 776 6.624526 CGTGCAAAATTGAAGAAAATGACAAC 59.375 34.615 0.00 0.00 0.00 3.32
813 923 6.323996 TCCATATGACGAATTAGAGTTGGTCT 59.676 38.462 3.65 0.00 37.60 3.85
1030 1602 3.560251 CCATCCCGGGCGAGGAAT 61.560 66.667 18.49 0.00 36.85 3.01
1228 1805 5.358160 CAGCTTGCTTATTAGGCTACCTTTT 59.642 40.000 0.00 0.00 34.61 2.27
1229 1806 5.590663 AGCTTGCTTATTAGGCTACCTTTTC 59.409 40.000 0.00 0.00 34.61 2.29
1231 1808 6.095580 GCTTGCTTATTAGGCTACCTTTTCTT 59.904 38.462 0.00 0.00 34.61 2.52
1232 1809 7.625828 TTGCTTATTAGGCTACCTTTTCTTC 57.374 36.000 0.00 0.00 34.61 2.87
1318 1895 0.249868 GCGTGATTCCATCCGATCCA 60.250 55.000 0.00 0.00 0.00 3.41
1327 1904 1.276138 CCATCCGATCCAATCCGATCA 59.724 52.381 0.00 0.00 38.91 2.92
1384 1961 2.801342 GCTCGATCTTAGCTTCCTGGTG 60.801 54.545 9.11 0.00 37.01 4.17
1442 2024 2.449464 CCAAGTCAAGCATGGATGGAA 58.551 47.619 0.00 0.00 38.16 3.53
1443 2025 3.028850 CCAAGTCAAGCATGGATGGAAT 58.971 45.455 0.00 0.00 38.16 3.01
1444 2026 3.181479 CCAAGTCAAGCATGGATGGAATG 60.181 47.826 0.00 0.00 38.16 2.67
1445 2027 2.662866 AGTCAAGCATGGATGGAATGG 58.337 47.619 0.00 0.00 0.00 3.16
1446 2028 2.242965 AGTCAAGCATGGATGGAATGGA 59.757 45.455 0.00 0.00 0.00 3.41
1447 2029 3.117246 AGTCAAGCATGGATGGAATGGAT 60.117 43.478 0.00 0.00 0.00 3.41
1448 2030 3.005472 GTCAAGCATGGATGGAATGGATG 59.995 47.826 0.00 0.00 0.00 3.51
1449 2031 1.629043 AGCATGGATGGAATGGATGC 58.371 50.000 0.00 0.00 37.65 3.91
1450 2032 1.147191 AGCATGGATGGAATGGATGCT 59.853 47.619 0.00 0.00 40.96 3.79
1451 2033 1.968493 GCATGGATGGAATGGATGCTT 59.032 47.619 0.00 0.00 35.61 3.91
1452 2034 2.288825 GCATGGATGGAATGGATGCTTG 60.289 50.000 0.00 0.00 35.61 4.01
1453 2035 1.405872 TGGATGGAATGGATGCTTGC 58.594 50.000 0.00 0.00 0.00 4.01
1517 2099 8.463607 TCCTCTTTTAGCGGTTTAATTAATTGG 58.536 33.333 11.05 0.00 0.00 3.16
1539 2121 1.887242 GCAGCATGTCGGGCGATAA 60.887 57.895 0.00 0.00 39.31 1.75
1600 2183 5.278463 GCATATTCAAGTGTTCAACCAGTGT 60.278 40.000 0.00 0.00 0.00 3.55
1617 2200 5.163405 ACCAGTGTAACCATGCTAGTATCTG 60.163 44.000 0.00 0.00 37.80 2.90
1692 2275 5.414454 TGTTGTTTCCTGTCCATACTAATGC 59.586 40.000 0.00 0.00 0.00 3.56
1769 2352 3.433274 GTGATGTGAGCGAACATGAAGAA 59.567 43.478 11.43 0.00 40.87 2.52
2064 2647 3.509967 TCCTATTCAACTTCGTGAGAGCA 59.490 43.478 0.00 0.00 43.69 4.26
2550 3133 5.228220 CGTCTCATTTTTACTAGCTGACTCG 59.772 44.000 0.00 0.00 0.00 4.18
2561 3144 2.760374 AGCTGACTCGGAACTTTTCTG 58.240 47.619 0.00 0.00 37.39 3.02
2622 3205 2.623878 TTCCAAACGTCAGCTAACCA 57.376 45.000 0.00 0.00 0.00 3.67
2623 3206 2.851263 TCCAAACGTCAGCTAACCAT 57.149 45.000 0.00 0.00 0.00 3.55
2646 3229 8.351461 CCATTTTGTTAATTTTGCCTGAAACAT 58.649 29.630 0.00 0.00 0.00 2.71
2649 3232 9.606631 TTTTGTTAATTTTGCCTGAAACATACT 57.393 25.926 0.00 0.00 0.00 2.12
2650 3233 8.810652 TTGTTAATTTTGCCTGAAACATACTC 57.189 30.769 0.00 0.00 0.00 2.59
2651 3234 7.375053 TGTTAATTTTGCCTGAAACATACTCC 58.625 34.615 0.00 0.00 0.00 3.85
2652 3235 5.405935 AATTTTGCCTGAAACATACTCCC 57.594 39.130 0.00 0.00 0.00 4.30
2653 3236 3.806949 TTTGCCTGAAACATACTCCCT 57.193 42.857 0.00 0.00 0.00 4.20
2654 3237 3.350219 TTGCCTGAAACATACTCCCTC 57.650 47.619 0.00 0.00 0.00 4.30
2655 3238 2.551270 TGCCTGAAACATACTCCCTCT 58.449 47.619 0.00 0.00 0.00 3.69
2656 3239 2.237143 TGCCTGAAACATACTCCCTCTG 59.763 50.000 0.00 0.00 0.00 3.35
2657 3240 2.237392 GCCTGAAACATACTCCCTCTGT 59.763 50.000 0.00 0.00 0.00 3.41
2658 3241 3.451178 GCCTGAAACATACTCCCTCTGTA 59.549 47.826 0.00 0.00 0.00 2.74
2659 3242 4.081087 GCCTGAAACATACTCCCTCTGTAA 60.081 45.833 0.00 0.00 0.00 2.41
2660 3243 5.570844 GCCTGAAACATACTCCCTCTGTAAA 60.571 44.000 0.00 0.00 0.00 2.01
2661 3244 5.875359 CCTGAAACATACTCCCTCTGTAAAC 59.125 44.000 0.00 0.00 0.00 2.01
2662 3245 6.295916 CCTGAAACATACTCCCTCTGTAAACT 60.296 42.308 0.00 0.00 0.00 2.66
2663 3246 7.093465 CCTGAAACATACTCCCTCTGTAAACTA 60.093 40.741 0.00 0.00 0.00 2.24
2664 3247 8.197592 TGAAACATACTCCCTCTGTAAACTAA 57.802 34.615 0.00 0.00 0.00 2.24
2665 3248 8.822805 TGAAACATACTCCCTCTGTAAACTAAT 58.177 33.333 0.00 0.00 0.00 1.73
2673 3256 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2674 3257 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2675 3258 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2676 3259 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2677 3260 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2685 3268 9.694137 AACTAATATAAGAGCGTTTAGATCACC 57.306 33.333 0.00 0.00 37.82 4.02
2686 3269 8.857098 ACTAATATAAGAGCGTTTAGATCACCA 58.143 33.333 0.00 0.00 37.82 4.17
2687 3270 7.948278 AATATAAGAGCGTTTAGATCACCAC 57.052 36.000 0.00 0.00 37.82 4.16
2688 3271 3.963428 AAGAGCGTTTAGATCACCACT 57.037 42.857 0.00 0.00 37.82 4.00
2689 3272 3.963428 AGAGCGTTTAGATCACCACTT 57.037 42.857 0.00 0.00 37.82 3.16
2690 3273 4.273148 AGAGCGTTTAGATCACCACTTT 57.727 40.909 0.00 0.00 37.82 2.66
2691 3274 5.401531 AGAGCGTTTAGATCACCACTTTA 57.598 39.130 0.00 0.00 37.82 1.85
2692 3275 5.411781 AGAGCGTTTAGATCACCACTTTAG 58.588 41.667 0.00 0.00 37.82 1.85
2693 3276 5.047235 AGAGCGTTTAGATCACCACTTTAGT 60.047 40.000 0.00 0.00 37.82 2.24
2694 3277 4.929808 AGCGTTTAGATCACCACTTTAGTG 59.070 41.667 2.86 2.86 45.23 2.74
2695 3278 4.689345 GCGTTTAGATCACCACTTTAGTGT 59.311 41.667 8.91 0.00 44.21 3.55
2696 3279 5.178809 GCGTTTAGATCACCACTTTAGTGTT 59.821 40.000 8.91 0.00 44.21 3.32
2697 3280 6.617953 GCGTTTAGATCACCACTTTAGTGTTC 60.618 42.308 8.91 0.00 44.21 3.18
2698 3281 6.645415 CGTTTAGATCACCACTTTAGTGTTCT 59.355 38.462 8.91 8.91 44.21 3.01
2699 3282 7.811236 CGTTTAGATCACCACTTTAGTGTTCTA 59.189 37.037 8.91 7.33 44.21 2.10
2700 3283 9.654663 GTTTAGATCACCACTTTAGTGTTCTAT 57.345 33.333 8.91 0.00 42.12 1.98
2706 3289 8.263940 TCACCACTTTAGTGTTCTATAAATGC 57.736 34.615 8.91 0.00 44.21 3.56
2707 3290 8.100791 TCACCACTTTAGTGTTCTATAAATGCT 58.899 33.333 8.91 0.00 44.21 3.79
2708 3291 8.391106 CACCACTTTAGTGTTCTATAAATGCTC 58.609 37.037 8.91 0.00 44.21 4.26
2709 3292 8.322091 ACCACTTTAGTGTTCTATAAATGCTCT 58.678 33.333 8.91 0.00 44.21 4.09
2710 3293 9.167311 CCACTTTAGTGTTCTATAAATGCTCTT 57.833 33.333 8.91 0.00 44.21 2.85
2727 3310 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
2728 3311 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
2729 3312 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
2730 3313 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
2822 5460 9.747898 AACCCTTTTCTTGTTTATTTCCTTTTT 57.252 25.926 0.00 0.00 0.00 1.94
3080 5718 2.670934 CGGCTTCCTGTTGCTGCT 60.671 61.111 0.00 0.00 0.00 4.24
3221 5869 4.901250 AGTGGGTTCATGTGGATTCTTTTT 59.099 37.500 0.00 0.00 0.00 1.94
3356 6004 4.221482 TCCTCGCAGTATCATGCTATCAAT 59.779 41.667 0.00 0.00 44.24 2.57
3521 6169 1.071471 CGGTGAACTTGGCCACTCT 59.929 57.895 3.88 0.00 33.99 3.24
3575 6223 7.395617 AGATCATGCACAAGAATATAGAGCAT 58.604 34.615 0.00 0.00 39.55 3.79
3638 6286 1.154225 GCAAAATGGCAGGTCGTCG 60.154 57.895 0.00 0.00 0.00 5.12
3680 6328 2.702478 GGGTAAAGTATTACGGAGGGCT 59.298 50.000 0.00 0.00 41.95 5.19
4040 6688 1.383799 CTGTGGGGAGGATGGCAAA 59.616 57.895 0.00 0.00 0.00 3.68
4072 6720 0.471780 TCACAGAGGCACTTCTCCCA 60.472 55.000 0.00 0.00 41.55 4.37
4130 6778 7.327975 ACTGTGTGAAGATTATTCGATGGTTA 58.672 34.615 0.00 0.00 0.00 2.85
4492 7158 4.410099 TCTTACGAGGGGAAAGTAACTGA 58.590 43.478 0.00 0.00 0.00 3.41
4750 7416 4.828072 AAGTCCTTGTAGAGATTCCACC 57.172 45.455 0.00 0.00 0.00 4.61
4765 7431 4.530710 TTCCACCATAGACTACACACAC 57.469 45.455 0.00 0.00 0.00 3.82
4774 7440 7.077605 CCATAGACTACACACACAACAAAATG 58.922 38.462 0.00 0.00 0.00 2.32
4776 7442 6.751514 AGACTACACACACAACAAAATGAA 57.248 33.333 0.00 0.00 0.00 2.57
4777 7443 7.151999 AGACTACACACACAACAAAATGAAA 57.848 32.000 0.00 0.00 0.00 2.69
4778 7444 7.771183 AGACTACACACACAACAAAATGAAAT 58.229 30.769 0.00 0.00 0.00 2.17
4779 7445 7.701924 AGACTACACACACAACAAAATGAAATG 59.298 33.333 0.00 0.00 0.00 2.32
4781 7447 6.890663 ACACACACAACAAAATGAAATGAG 57.109 33.333 0.00 0.00 0.00 2.90
4782 7448 6.397272 ACACACACAACAAAATGAAATGAGT 58.603 32.000 0.00 0.00 0.00 3.41
4783 7449 6.310956 ACACACACAACAAAATGAAATGAGTG 59.689 34.615 0.00 0.00 38.17 3.51
4784 7450 6.530887 CACACACAACAAAATGAAATGAGTGA 59.469 34.615 8.27 0.00 36.51 3.41
4785 7451 7.063191 CACACACAACAAAATGAAATGAGTGAA 59.937 33.333 8.27 0.00 36.51 3.18
4786 7452 7.063308 ACACACAACAAAATGAAATGAGTGAAC 59.937 33.333 8.27 0.00 36.51 3.18
4798 7464 8.603898 TGAAATGAGTGAACCCTATACTCTAA 57.396 34.615 0.00 0.00 41.01 2.10
4804 7470 5.048507 GTGAACCCTATACTCTAAAAGGCG 58.951 45.833 0.00 0.00 0.00 5.52
4805 7471 4.713321 TGAACCCTATACTCTAAAAGGCGT 59.287 41.667 0.00 0.00 0.00 5.68
4806 7472 5.188359 TGAACCCTATACTCTAAAAGGCGTT 59.812 40.000 0.00 0.00 0.00 4.84
4813 7480 9.924650 CCTATACTCTAAAAGGCGTTTGTATAT 57.075 33.333 8.71 4.45 0.00 0.86
4828 7495 7.253223 GCGTTTGTATATATCCGAATGTAGTCG 60.253 40.741 0.00 0.00 40.77 4.18
4829 7496 7.253223 CGTTTGTATATATCCGAATGTAGTCGC 60.253 40.741 0.00 0.00 39.74 5.19
4846 7513 6.649973 TGTAGTCGCTATAGTGGAATCTCTAC 59.350 42.308 13.24 14.15 0.00 2.59
4859 7526 9.084533 AGTGGAATCTCTACAAGGACTTATATC 57.915 37.037 0.00 0.00 29.47 1.63
4956 7623 5.598005 TGGGATGAAGTTGAACATGAAAGTT 59.402 36.000 0.00 0.00 0.00 2.66
4964 7637 7.865706 AGTTGAACATGAAAGTTACTGAAGT 57.134 32.000 0.00 0.00 0.00 3.01
4973 7646 6.223852 TGAAAGTTACTGAAGTCATCTCACC 58.776 40.000 0.00 0.00 0.00 4.02
5286 7960 6.784031 ACTCAATCCACCAGAGAGTAAAAAT 58.216 36.000 0.00 0.00 37.75 1.82
5321 7995 1.876156 GCCCAAGAACACAAGACTCTG 59.124 52.381 0.00 0.00 0.00 3.35
5532 8215 3.849951 CGGTGAGGGGATGGTCGG 61.850 72.222 0.00 0.00 0.00 4.79
5645 8328 3.607741 CTCACAGCTTCTGTCCATCATT 58.392 45.455 0.00 0.00 43.43 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.436704 CCTACACGTGATTTGTTGCTGAT 59.563 43.478 25.01 0.00 0.00 2.90
1 2 2.805671 CCTACACGTGATTTGTTGCTGA 59.194 45.455 25.01 0.00 0.00 4.26
2 3 2.548057 ACCTACACGTGATTTGTTGCTG 59.452 45.455 25.01 0.92 0.00 4.41
3 4 2.846193 ACCTACACGTGATTTGTTGCT 58.154 42.857 25.01 0.00 0.00 3.91
4 5 3.619233 AACCTACACGTGATTTGTTGC 57.381 42.857 25.01 0.00 0.00 4.17
24 25 6.419791 CGATGGCTATATATACCCCCAAAAA 58.580 40.000 2.24 0.00 0.00 1.94
25 26 5.104277 CCGATGGCTATATATACCCCCAAAA 60.104 44.000 2.24 0.00 0.00 2.44
26 27 4.410883 CCGATGGCTATATATACCCCCAAA 59.589 45.833 2.24 0.00 0.00 3.28
27 28 3.971305 CCGATGGCTATATATACCCCCAA 59.029 47.826 2.24 0.00 0.00 4.12
28 29 3.208005 TCCGATGGCTATATATACCCCCA 59.792 47.826 2.24 3.83 0.00 4.96
29 30 3.577415 GTCCGATGGCTATATATACCCCC 59.423 52.174 2.24 0.00 0.00 5.40
30 31 4.220724 TGTCCGATGGCTATATATACCCC 58.779 47.826 2.24 0.94 0.00 4.95
31 32 5.335740 CGATGTCCGATGGCTATATATACCC 60.336 48.000 0.00 0.00 41.76 3.69
32 33 5.335740 CCGATGTCCGATGGCTATATATACC 60.336 48.000 0.00 0.00 41.76 2.73
33 34 5.472478 TCCGATGTCCGATGGCTATATATAC 59.528 44.000 0.00 0.00 41.76 1.47
34 35 5.627135 TCCGATGTCCGATGGCTATATATA 58.373 41.667 0.00 0.00 41.76 0.86
35 36 4.470602 TCCGATGTCCGATGGCTATATAT 58.529 43.478 0.00 0.00 41.76 0.86
36 37 3.883489 CTCCGATGTCCGATGGCTATATA 59.117 47.826 0.00 0.00 41.76 0.86
37 38 2.690497 CTCCGATGTCCGATGGCTATAT 59.310 50.000 0.00 0.00 41.76 0.86
38 39 2.092323 CTCCGATGTCCGATGGCTATA 58.908 52.381 0.00 0.00 41.76 1.31
39 40 0.891373 CTCCGATGTCCGATGGCTAT 59.109 55.000 0.00 0.00 41.76 2.97
40 41 1.179174 CCTCCGATGTCCGATGGCTA 61.179 60.000 0.00 0.00 41.76 3.93
41 42 2.502492 CCTCCGATGTCCGATGGCT 61.502 63.158 0.00 0.00 41.76 4.75
42 43 1.461091 TACCTCCGATGTCCGATGGC 61.461 60.000 0.00 0.00 41.76 4.40
43 44 0.314302 GTACCTCCGATGTCCGATGG 59.686 60.000 0.00 0.00 41.76 3.51
44 45 0.314302 GGTACCTCCGATGTCCGATG 59.686 60.000 4.06 0.00 41.76 3.84
45 46 2.729692 GGTACCTCCGATGTCCGAT 58.270 57.895 4.06 0.00 41.76 4.18
46 47 4.247781 GGTACCTCCGATGTCCGA 57.752 61.111 4.06 0.00 41.76 4.55
74 75 4.586235 GGATCCGTGGCCCATGGG 62.586 72.222 27.87 27.87 40.65 4.00
75 76 4.586235 GGGATCCGTGGCCCATGG 62.586 72.222 16.45 16.45 44.07 3.66
76 77 4.586235 GGGGATCCGTGGCCCATG 62.586 72.222 5.45 0.00 46.57 3.66
80 81 3.768833 TAGAGGGGGATCCGTGGCC 62.769 68.421 5.45 0.00 41.52 5.36
81 82 2.122989 TAGAGGGGGATCCGTGGC 60.123 66.667 5.45 0.00 41.52 5.01
82 83 0.828343 GTCTAGAGGGGGATCCGTGG 60.828 65.000 5.45 0.00 41.52 4.94
83 84 1.173444 CGTCTAGAGGGGGATCCGTG 61.173 65.000 5.45 0.00 41.52 4.94
84 85 1.150992 CGTCTAGAGGGGGATCCGT 59.849 63.158 5.45 0.00 41.52 4.69
85 86 2.269529 GCGTCTAGAGGGGGATCCG 61.270 68.421 14.00 2.91 41.52 4.18
86 87 1.909287 GGCGTCTAGAGGGGGATCC 60.909 68.421 14.00 1.92 0.00 3.36
87 88 0.404812 TAGGCGTCTAGAGGGGGATC 59.595 60.000 14.00 0.00 0.00 3.36
88 89 0.112801 GTAGGCGTCTAGAGGGGGAT 59.887 60.000 14.00 0.00 0.00 3.85
89 90 1.535685 GTAGGCGTCTAGAGGGGGA 59.464 63.158 14.00 0.00 0.00 4.81
90 91 1.531128 GGTAGGCGTCTAGAGGGGG 60.531 68.421 14.00 0.00 0.00 5.40
91 92 0.106116 AAGGTAGGCGTCTAGAGGGG 60.106 60.000 14.00 0.00 0.00 4.79
92 93 1.033574 CAAGGTAGGCGTCTAGAGGG 58.966 60.000 14.00 0.60 0.00 4.30
93 94 0.386113 GCAAGGTAGGCGTCTAGAGG 59.614 60.000 8.10 8.10 0.00 3.69
94 95 1.103803 TGCAAGGTAGGCGTCTAGAG 58.896 55.000 0.00 0.00 0.00 2.43
95 96 1.476891 CTTGCAAGGTAGGCGTCTAGA 59.523 52.381 19.14 0.00 0.00 2.43
96 97 1.471676 CCTTGCAAGGTAGGCGTCTAG 60.472 57.143 33.46 6.91 41.41 2.43
97 98 0.535335 CCTTGCAAGGTAGGCGTCTA 59.465 55.000 33.46 0.00 41.41 2.59
98 99 1.296715 CCTTGCAAGGTAGGCGTCT 59.703 57.895 33.46 0.00 41.41 4.18
99 100 1.745489 CCCTTGCAAGGTAGGCGTC 60.745 63.158 37.09 0.00 44.98 5.19
100 101 2.351276 CCCTTGCAAGGTAGGCGT 59.649 61.111 37.09 0.00 44.98 5.68
101 102 2.040544 CACCCTTGCAAGGTAGGCG 61.041 63.158 37.09 25.88 44.98 5.52
102 103 4.002797 CACCCTTGCAAGGTAGGC 57.997 61.111 37.09 0.00 44.98 3.93
112 113 1.604378 CCTCCTGTAGGCACCCTTG 59.396 63.158 0.00 0.00 38.97 3.61
113 114 4.153957 CCTCCTGTAGGCACCCTT 57.846 61.111 0.00 0.00 38.97 3.95
130 131 1.406860 CCAAGAGAGGCCCTAGGAGC 61.407 65.000 11.48 12.06 0.00 4.70
131 132 2.833244 CCAAGAGAGGCCCTAGGAG 58.167 63.158 11.48 1.06 0.00 3.69
167 168 4.365514 TTTTGCATCACTAGAGGACCAA 57.634 40.909 0.00 0.00 0.00 3.67
169 170 4.072131 TGTTTTTGCATCACTAGAGGACC 58.928 43.478 0.00 0.00 0.00 4.46
215 217 3.163616 TGACCATACAAAAAGTCCCCC 57.836 47.619 0.00 0.00 0.00 5.40
216 218 5.738619 AAATGACCATACAAAAAGTCCCC 57.261 39.130 0.00 0.00 0.00 4.81
268 270 6.909550 TTATTCAGTGCCCATTTACAGTTT 57.090 33.333 0.00 0.00 0.00 2.66
271 273 7.285401 ACCTATTTATTCAGTGCCCATTTACAG 59.715 37.037 0.00 0.00 0.00 2.74
317 319 9.248291 CTATCATGTAAGTTTGCAAAGTTTGTT 57.752 29.630 31.33 21.30 33.79 2.83
319 321 8.801715 ACTATCATGTAAGTTTGCAAAGTTTG 57.198 30.769 31.33 24.07 33.79 2.93
327 329 6.483307 TCATGGCTACTATCATGTAAGTTTGC 59.517 38.462 7.78 11.31 40.94 3.68
328 330 8.437360 TTCATGGCTACTATCATGTAAGTTTG 57.563 34.615 7.78 4.25 40.94 2.93
339 341 7.496529 TTTTGTATGCTTCATGGCTACTATC 57.503 36.000 0.00 0.00 0.00 2.08
343 345 9.533253 AATAATTTTTGTATGCTTCATGGCTAC 57.467 29.630 0.00 0.00 0.00 3.58
354 356 8.828644 TCCAATGCATCAATAATTTTTGTATGC 58.171 29.630 23.09 23.09 38.79 3.14
379 382 5.968528 ATGGATAGGTCTTGATACGTCTC 57.031 43.478 0.00 0.00 0.00 3.36
411 414 6.208599 CCACATAACCTACTCAACAATTTGGT 59.791 38.462 0.78 0.00 33.06 3.67
412 415 6.620678 CCACATAACCTACTCAACAATTTGG 58.379 40.000 0.78 0.00 33.06 3.28
463 466 3.128415 TGCCATCGATGTGGTACAAAATG 59.872 43.478 23.27 5.22 44.16 2.32
469 472 1.665679 CACTTGCCATCGATGTGGTAC 59.334 52.381 23.27 8.36 41.47 3.34
503 506 6.384015 TCATCACTCTAGAGAAATAGGCCAAA 59.616 38.462 26.57 0.00 0.00 3.28
537 540 0.179062 ATCTTGCAGGACGATGAGCC 60.179 55.000 0.00 0.00 0.00 4.70
618 622 0.522286 CGCGGCTATCAGATCGCTAG 60.522 60.000 11.85 6.14 45.11 3.42
721 739 9.393249 CTTCAATTTTGCACGTCTAATTTAAGA 57.607 29.630 0.00 0.00 29.26 2.10
731 749 6.019961 TGTCATTTTCTTCAATTTTGCACGTC 60.020 34.615 0.00 0.00 0.00 4.34
734 752 7.462731 TGTTGTCATTTTCTTCAATTTTGCAC 58.537 30.769 0.00 0.00 0.00 4.57
790 888 8.353684 ACTAGACCAACTCTAATTCGTCATATG 58.646 37.037 0.00 0.00 30.58 1.78
803 901 5.575157 TGAGAGATTCACTAGACCAACTCT 58.425 41.667 0.00 5.08 36.42 3.24
937 1509 2.420687 GCTTCCATCTCATCTTCCCGTT 60.421 50.000 0.00 0.00 0.00 4.44
1030 1602 2.660556 AGGAGAGGAGAGGAGGGTTTTA 59.339 50.000 0.00 0.00 0.00 1.52
1228 1805 1.887198 ACGGCGAAGAAGAAGAGAAGA 59.113 47.619 16.62 0.00 0.00 2.87
1229 1806 1.989165 CACGGCGAAGAAGAAGAGAAG 59.011 52.381 16.62 0.00 0.00 2.85
1231 1808 1.200252 CTCACGGCGAAGAAGAAGAGA 59.800 52.381 16.62 0.00 0.00 3.10
1232 1809 1.623359 CTCACGGCGAAGAAGAAGAG 58.377 55.000 16.62 3.64 0.00 2.85
1318 1895 5.279910 GGGAGAAGAATGATCTGATCGGATT 60.280 44.000 18.14 3.50 35.59 3.01
1327 1904 0.249657 GCGCGGGAGAAGAATGATCT 60.250 55.000 8.83 0.00 37.57 2.75
1442 2024 3.631227 GCTAAGAAGAAGCAAGCATCCAT 59.369 43.478 0.00 0.00 39.83 3.41
1443 2025 3.012518 GCTAAGAAGAAGCAAGCATCCA 58.987 45.455 0.00 0.00 39.83 3.41
1444 2026 2.357323 GGCTAAGAAGAAGCAAGCATCC 59.643 50.000 0.00 0.00 41.93 3.51
1445 2027 3.012518 TGGCTAAGAAGAAGCAAGCATC 58.987 45.455 0.00 0.00 41.93 3.91
1446 2028 2.751806 GTGGCTAAGAAGAAGCAAGCAT 59.248 45.455 0.00 0.00 41.93 3.79
1447 2029 2.154462 GTGGCTAAGAAGAAGCAAGCA 58.846 47.619 0.00 0.00 41.93 3.91
1448 2030 1.129437 CGTGGCTAAGAAGAAGCAAGC 59.871 52.381 0.00 0.00 41.93 4.01
1449 2031 1.129437 GCGTGGCTAAGAAGAAGCAAG 59.871 52.381 0.00 0.00 41.93 4.01
1450 2032 1.156736 GCGTGGCTAAGAAGAAGCAA 58.843 50.000 0.00 0.00 41.93 3.91
1451 2033 1.014044 CGCGTGGCTAAGAAGAAGCA 61.014 55.000 0.00 0.00 41.93 3.91
1452 2034 1.014564 ACGCGTGGCTAAGAAGAAGC 61.015 55.000 12.93 0.00 39.33 3.86
1453 2035 0.716108 CACGCGTGGCTAAGAAGAAG 59.284 55.000 31.15 0.00 0.00 2.85
1517 2099 3.275338 GCCCGACATGCTGCTAGC 61.275 66.667 8.10 8.10 42.82 3.42
1539 2121 3.394606 ACTCCCCGCCATTAAATATCACT 59.605 43.478 0.00 0.00 0.00 3.41
1600 2183 5.614324 ACTTGCAGATACTAGCATGGTTA 57.386 39.130 1.12 0.00 40.94 2.85
1617 2200 3.924073 CCCGGCAATTAAAAACTACTTGC 59.076 43.478 0.00 0.00 41.04 4.01
1676 2259 6.404734 GGAACAAAAGCATTAGTATGGACAGG 60.405 42.308 0.00 0.00 32.15 4.00
1692 2275 8.678199 AGACAAAGTAGAGAAAAGGAACAAAAG 58.322 33.333 0.00 0.00 0.00 2.27
1834 2417 2.162208 GCATCGTTTGATTCTTGCTCCA 59.838 45.455 0.00 0.00 30.49 3.86
2015 2598 1.613255 CCCTTTCTTGGCGGCTTTCTA 60.613 52.381 11.43 0.00 0.00 2.10
2064 2647 6.316140 GGAGGCTTTTTGTCTTGAAACATTTT 59.684 34.615 0.00 0.00 0.00 1.82
2290 2873 3.443045 CGATGCGCCCTGCCTTTT 61.443 61.111 4.18 0.00 45.60 2.27
2419 3002 9.078452 TGCATAGCAACATTCCCATACTGAATG 62.078 40.741 10.53 10.53 42.91 2.67
2420 3003 5.242393 GCATAGCAACATTCCCATACTGAAT 59.758 40.000 0.00 0.00 32.77 2.57
2550 3133 7.039313 ACAAAACCTATCACAGAAAAGTTCC 57.961 36.000 0.00 0.00 0.00 3.62
2561 3144 8.896320 ATTTAAAACCCAACAAAACCTATCAC 57.104 30.769 0.00 0.00 0.00 3.06
2623 3206 9.606631 AGTATGTTTCAGGCAAAATTAACAAAA 57.393 25.926 0.00 0.00 0.00 2.44
2647 3230 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2648 3231 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2649 3232 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2650 3233 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2651 3234 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2659 3242 9.694137 GGTGATCTAAACGCTCTTATATTAGTT 57.306 33.333 0.00 0.00 0.00 2.24
2660 3243 8.857098 TGGTGATCTAAACGCTCTTATATTAGT 58.143 33.333 0.00 0.00 0.00 2.24
2661 3244 9.130312 GTGGTGATCTAAACGCTCTTATATTAG 57.870 37.037 0.00 0.00 0.00 1.73
2662 3245 8.857098 AGTGGTGATCTAAACGCTCTTATATTA 58.143 33.333 0.00 0.00 0.00 0.98
2663 3246 7.727181 AGTGGTGATCTAAACGCTCTTATATT 58.273 34.615 0.00 0.00 0.00 1.28
2664 3247 7.291411 AGTGGTGATCTAAACGCTCTTATAT 57.709 36.000 0.00 0.00 0.00 0.86
2665 3248 6.710597 AGTGGTGATCTAAACGCTCTTATA 57.289 37.500 0.00 0.00 0.00 0.98
2666 3249 5.599999 AGTGGTGATCTAAACGCTCTTAT 57.400 39.130 0.00 0.00 0.00 1.73
2667 3250 5.401531 AAGTGGTGATCTAAACGCTCTTA 57.598 39.130 0.00 0.00 0.00 2.10
2668 3251 3.963428 AGTGGTGATCTAAACGCTCTT 57.037 42.857 0.00 0.00 0.00 2.85
2669 3252 3.963428 AAGTGGTGATCTAAACGCTCT 57.037 42.857 0.00 0.00 0.00 4.09
2670 3253 5.062308 CACTAAAGTGGTGATCTAAACGCTC 59.938 44.000 2.01 0.00 42.10 5.03
2671 3254 4.929808 CACTAAAGTGGTGATCTAAACGCT 59.070 41.667 2.01 0.00 42.10 5.07
2672 3255 5.178809 AACACTAAAGTGGTGATCTAAACGC 59.821 40.000 14.30 0.00 45.59 4.84
2673 3256 6.780706 AACACTAAAGTGGTGATCTAAACG 57.219 37.500 14.30 0.00 45.59 3.60
2701 3284 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
2702 3285 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
2703 3286 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
2704 3287 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
2705 3288 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2706 3289 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2707 3290 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2708 3291 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2709 3292 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2710 3293 9.592196 AATGTACTCCCTCCGTAAACTAATATA 57.408 33.333 0.00 0.00 0.00 0.86
2711 3294 8.488308 AATGTACTCCCTCCGTAAACTAATAT 57.512 34.615 0.00 0.00 0.00 1.28
2712 3295 7.902920 AATGTACTCCCTCCGTAAACTAATA 57.097 36.000 0.00 0.00 0.00 0.98
2713 3296 6.803366 AATGTACTCCCTCCGTAAACTAAT 57.197 37.500 0.00 0.00 0.00 1.73
2714 3297 7.118723 TCTAATGTACTCCCTCCGTAAACTAA 58.881 38.462 0.00 0.00 0.00 2.24
2715 3298 6.662755 TCTAATGTACTCCCTCCGTAAACTA 58.337 40.000 0.00 0.00 0.00 2.24
2716 3299 5.513233 TCTAATGTACTCCCTCCGTAAACT 58.487 41.667 0.00 0.00 0.00 2.66
2717 3300 5.841957 TCTAATGTACTCCCTCCGTAAAC 57.158 43.478 0.00 0.00 0.00 2.01
2718 3301 5.954150 ACTTCTAATGTACTCCCTCCGTAAA 59.046 40.000 0.00 0.00 0.00 2.01
2719 3302 5.513233 ACTTCTAATGTACTCCCTCCGTAA 58.487 41.667 0.00 0.00 0.00 3.18
2720 3303 5.121380 ACTTCTAATGTACTCCCTCCGTA 57.879 43.478 0.00 0.00 0.00 4.02
2721 3304 3.978610 ACTTCTAATGTACTCCCTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
2722 3305 5.768662 TCATACTTCTAATGTACTCCCTCCG 59.231 44.000 0.00 0.00 0.00 4.63
2723 3306 6.550108 TGTCATACTTCTAATGTACTCCCTCC 59.450 42.308 0.00 0.00 0.00 4.30
2724 3307 7.285858 ACTGTCATACTTCTAATGTACTCCCTC 59.714 40.741 0.00 0.00 0.00 4.30
2725 3308 7.126733 ACTGTCATACTTCTAATGTACTCCCT 58.873 38.462 0.00 0.00 0.00 4.20
2726 3309 7.349412 ACTGTCATACTTCTAATGTACTCCC 57.651 40.000 0.00 0.00 0.00 4.30
2727 3310 8.251721 ACAACTGTCATACTTCTAATGTACTCC 58.748 37.037 0.00 0.00 0.00 3.85
2765 3348 7.944729 AACAAAGCTCATGTCAATAAGGTAT 57.055 32.000 5.66 0.00 0.00 2.73
2776 3359 5.648092 GGGTTCACTATAACAAAGCTCATGT 59.352 40.000 0.00 0.00 0.00 3.21
2822 5460 8.091449 CCAAAGGTACCATAAATAAGCAAAACA 58.909 33.333 15.94 0.00 0.00 2.83
3080 5718 3.216800 AGAGCAAAGTTTCTGCACATCA 58.783 40.909 2.54 0.00 42.48 3.07
3221 5869 9.748708 CCATGAAAAGAAGTTTGTAAGATTCAA 57.251 29.630 0.00 0.00 0.00 2.69
3356 6004 2.552155 CCAGTACCAAAGCTTGTAGCCA 60.552 50.000 0.00 0.00 43.77 4.75
3392 6040 2.936032 GGCTCCCCAGTGGAAGGT 60.936 66.667 11.95 0.00 44.57 3.50
3521 6169 4.157246 TCCTGGTAAAGCACTTAGACTCA 58.843 43.478 0.00 0.00 0.00 3.41
3575 6223 1.597854 CGAGCAACCTTCTGCACCA 60.598 57.895 0.00 0.00 45.18 4.17
3680 6328 2.899303 GGAAACCATCCTCTTCCCAA 57.101 50.000 0.00 0.00 45.56 4.12
4027 6675 1.114627 GACCAATTTGCCATCCTCCC 58.885 55.000 0.00 0.00 0.00 4.30
4040 6688 2.355108 CCTCTGTGAACCGATGACCAAT 60.355 50.000 0.00 0.00 0.00 3.16
4117 6765 6.183360 GCCACAACATTCTAACCATCGAATAA 60.183 38.462 0.00 0.00 0.00 1.40
4130 6778 1.167851 CGATGTGGCCACAACATTCT 58.832 50.000 40.48 24.42 45.41 2.40
4492 7158 6.231211 ACGAAGTGGAAAAACTGTGATATCT 58.769 36.000 3.98 0.00 42.51 1.98
4655 7321 2.595238 AGTGGAGGTGTAGAACTCGTT 58.405 47.619 0.00 0.00 34.58 3.85
4750 7416 7.860613 TCATTTTGTTGTGTGTGTAGTCTATG 58.139 34.615 0.00 0.00 0.00 2.23
4765 7431 6.282930 AGGGTTCACTCATTTCATTTTGTTG 58.717 36.000 0.00 0.00 0.00 3.33
4774 7440 9.886132 TTTTAGAGTATAGGGTTCACTCATTTC 57.114 33.333 4.01 0.00 40.94 2.17
4776 7442 8.487028 CCTTTTAGAGTATAGGGTTCACTCATT 58.513 37.037 4.01 0.00 40.94 2.57
4777 7443 7.419172 GCCTTTTAGAGTATAGGGTTCACTCAT 60.419 40.741 4.01 0.00 40.94 2.90
4778 7444 6.127140 GCCTTTTAGAGTATAGGGTTCACTCA 60.127 42.308 4.01 0.00 40.94 3.41
4779 7445 6.282167 GCCTTTTAGAGTATAGGGTTCACTC 58.718 44.000 0.00 0.00 39.19 3.51
4781 7447 5.048507 CGCCTTTTAGAGTATAGGGTTCAC 58.951 45.833 0.00 0.00 0.00 3.18
4782 7448 4.713321 ACGCCTTTTAGAGTATAGGGTTCA 59.287 41.667 0.00 0.00 0.00 3.18
4783 7449 5.273674 ACGCCTTTTAGAGTATAGGGTTC 57.726 43.478 0.00 0.00 0.00 3.62
4784 7450 5.688814 AACGCCTTTTAGAGTATAGGGTT 57.311 39.130 0.00 0.00 0.00 4.11
4785 7451 5.046087 ACAAACGCCTTTTAGAGTATAGGGT 60.046 40.000 0.00 0.00 0.00 4.34
4786 7452 5.425630 ACAAACGCCTTTTAGAGTATAGGG 58.574 41.667 0.00 0.00 0.00 3.53
4798 7464 6.708949 ACATTCGGATATATACAAACGCCTTT 59.291 34.615 0.00 0.00 0.00 3.11
4804 7470 7.754027 AGCGACTACATTCGGATATATACAAAC 59.246 37.037 0.00 0.00 39.50 2.93
4805 7471 7.823665 AGCGACTACATTCGGATATATACAAA 58.176 34.615 0.00 0.00 39.50 2.83
4806 7472 7.387119 AGCGACTACATTCGGATATATACAA 57.613 36.000 0.00 0.00 39.50 2.41
4813 7480 5.353400 CCACTATAGCGACTACATTCGGATA 59.647 44.000 0.00 0.00 39.50 2.59
4828 7495 6.492087 AGTCCTTGTAGAGATTCCACTATAGC 59.508 42.308 0.00 0.00 0.00 2.97
4829 7496 8.472007 AAGTCCTTGTAGAGATTCCACTATAG 57.528 38.462 0.00 0.00 0.00 1.31
4846 7513 6.071840 CCTCCGTTCCTAGATATAAGTCCTTG 60.072 46.154 0.00 0.00 0.00 3.61
4859 7526 5.322754 TCAATATACTCCCTCCGTTCCTAG 58.677 45.833 0.00 0.00 0.00 3.02
4901 7568 2.712466 GCGAAACACGTTGCTAAGTTTC 59.288 45.455 13.87 13.87 43.76 2.78
4956 7623 2.447443 AGCGGTGAGATGACTTCAGTA 58.553 47.619 0.00 0.00 0.00 2.74
4964 7637 3.797039 CCAGAATTTAGCGGTGAGATGA 58.203 45.455 0.00 0.00 0.00 2.92
5015 7688 5.876651 AATTTCTAATTCTTCATGGGGGC 57.123 39.130 0.00 0.00 0.00 5.80
5286 7960 1.951209 TGGGCAGGTAGATCTTGTGA 58.049 50.000 0.00 0.00 0.00 3.58
5321 7995 7.559590 AGGTGCAGAGTTATTGAAATGATAC 57.440 36.000 0.00 0.00 0.00 2.24
5532 8215 1.865865 TTCGACAGTGAACAGGAAGC 58.134 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.