Multiple sequence alignment - TraesCS5A01G199500

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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 TraesCS5A01G199500 chr5A 100.000 3627 0 0 3199 6825 404234683 404231057 0.000000e+00 6698.0
1 TraesCS5A01G199500 chr5A 100.000 2945 0 0 1 2945 404237881 404234937 0.000000e+00 5439.0
2 TraesCS5A01G199500 chr5A 89.610 154 13 3 5556 5706 206730372 206730525 6.990000e-45 193.0
3 TraesCS5A01G199500 chr5A 73.814 485 91 27 4938 5398 404311564 404311092 7.080000e-35 159.0
4 TraesCS5A01G199500 chr5D 93.912 2579 71 23 1 2539 310707842 310705310 0.000000e+00 3814.0
5 TraesCS5A01G199500 chr5D 95.036 2357 63 18 3199 5544 310704692 310702379 0.000000e+00 3655.0
6 TraesCS5A01G199500 chr5D 84.870 694 54 23 6135 6810 310698371 310697711 0.000000e+00 652.0
7 TraesCS5A01G199500 chr5D 95.226 398 11 6 2551 2945 310705326 310704934 2.090000e-174 623.0
8 TraesCS5A01G199500 chr5D 85.955 356 15 12 5722 6057 310698746 310698406 1.410000e-91 348.0
9 TraesCS5A01G199500 chr5D 80.212 283 38 14 4065 4334 310704646 310704369 5.400000e-46 196.0
10 TraesCS5A01G199500 chr5D 74.104 502 90 30 4938 5412 311308098 311307610 3.270000e-38 171.0
11 TraesCS5A01G199500 chr5D 82.540 126 10 8 2499 2622 248589492 248589377 4.360000e-17 100.0
12 TraesCS5A01G199500 chr5B 92.789 2510 116 23 3622 6102 356722802 356720329 0.000000e+00 3572.0
13 TraesCS5A01G199500 chr5B 91.906 1878 78 22 656 2500 356725493 356723657 0.000000e+00 2558.0
14 TraesCS5A01G199500 chr5B 87.694 707 43 17 6118 6810 356720254 356719578 0.000000e+00 784.0
15 TraesCS5A01G199500 chr5B 94.355 372 18 3 284 654 356725989 356725620 9.930000e-158 568.0
16 TraesCS5A01G199500 chr5B 94.277 332 17 1 3199 3530 356723136 356722807 2.200000e-139 507.0
17 TraesCS5A01G199500 chr5B 91.753 291 11 6 2660 2940 356723496 356723209 6.420000e-105 392.0
18 TraesCS5A01G199500 chr5B 79.359 281 42 13 4065 4334 356723091 356722816 4.200000e-42 183.0
19 TraesCS5A01G199500 chr5B 74.074 486 88 28 4938 5398 357104246 357103774 1.520000e-36 165.0
20 TraesCS5A01G199500 chr5B 86.207 116 9 5 2499 2614 477078549 477078441 1.200000e-22 119.0
21 TraesCS5A01G199500 chr5B 84.746 118 7 8 2499 2614 549974394 549974286 2.600000e-19 108.0
22 TraesCS5A01G199500 chr2D 88.608 158 14 3 5553 5708 153795164 153795009 9.040000e-44 189.0
23 TraesCS5A01G199500 chr2D 88.608 158 14 3 5553 5708 153800820 153800665 9.040000e-44 189.0
24 TraesCS5A01G199500 chr2D 87.425 167 16 5 5546 5708 556927104 556926939 3.250000e-43 187.0
25 TraesCS5A01G199500 chr4D 88.125 160 16 3 5551 5708 508222920 508222762 3.250000e-43 187.0
26 TraesCS5A01G199500 chr6D 86.905 168 19 3 5555 5719 90112237 90112404 1.170000e-42 185.0
27 TraesCS5A01G199500 chr6A 86.550 171 20 3 5555 5722 108947865 108947695 1.170000e-42 185.0
28 TraesCS5A01G199500 chr3D 88.050 159 16 3 5553 5708 549066788 549066946 1.170000e-42 185.0
29 TraesCS5A01G199500 chr7D 100.000 71 0 0 4334 4404 88599799 88599869 1.540000e-26 132.0
30 TraesCS5A01G199500 chr2A 98.630 73 1 0 4334 4406 335849758 335849686 5.560000e-26 130.0
31 TraesCS5A01G199500 chr2A 84.874 119 11 6 2498 2614 510433001 510433114 5.590000e-21 113.0
32 TraesCS5A01G199500 chr2A 81.301 123 12 9 2499 2621 761415477 761415588 9.430000e-14 89.8
33 TraesCS5A01G199500 chrUn 98.592 71 1 0 4334 4404 414708564 414708494 7.190000e-25 126.0
34 TraesCS5A01G199500 chrUn 98.592 71 1 0 4334 4404 428084445 428084515 7.190000e-25 126.0
35 TraesCS5A01G199500 chrUn 98.592 71 1 0 4334 4404 433990636 433990566 7.190000e-25 126.0
36 TraesCS5A01G199500 chrUn 82.759 116 12 7 2499 2614 284001398 284001291 5.630000e-16 97.1
37 TraesCS5A01G199500 chr1D 98.592 71 1 0 4334 4404 254528053 254527983 7.190000e-25 126.0
38 TraesCS5A01G199500 chr1D 98.592 71 1 0 4334 4404 311400516 311400586 7.190000e-25 126.0
39 TraesCS5A01G199500 chr6B 85.345 116 9 7 2499 2614 408625464 408625571 5.590000e-21 113.0
40 TraesCS5A01G199500 chr2B 81.452 124 15 6 2498 2614 794355336 794355214 2.030000e-15 95.3


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 TraesCS5A01G199500 chr5A 404231057 404237881 6824 True 6068.500000 6698 100.000000 1 6825 2 chr5A.!!$R2 6824
1 TraesCS5A01G199500 chr5D 310697711 310707842 10131 True 1548.000000 3814 89.201833 1 6810 6 chr5D.!!$R3 6809
2 TraesCS5A01G199500 chr5B 356719578 356725989 6411 True 1223.428571 3572 90.304714 284 6810 7 chr5B.!!$R4 6526

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
77 78 0.109781 CGAGCCCCATGTTTGTTTCG 60.110 55.000 0.00 0.00 0.00 3.46 F
319 322 0.251341 ATCACCCCACAGTGGAAAGC 60.251 55.000 22.37 0.00 40.96 3.51 F
1934 2104 0.178932 TGACTGGTAGACCTGGCAGT 60.179 55.000 14.43 3.93 46.37 4.40 F
2175 2347 1.010935 CGCGACAATGAGCAGTGAGT 61.011 55.000 0.00 0.00 0.00 3.41 F
2344 2516 3.826729 GGATTGGCTTTGAAAGTAGTGGT 59.173 43.478 6.81 0.00 0.00 4.16 F
2898 3186 5.465935 TGCATTTCAAGAATTCCGTTTACC 58.534 37.500 0.65 0.00 0.00 2.85 F
3503 3798 0.178975 AGGTTCACCAATTCCGCCAA 60.179 50.000 0.00 0.00 38.89 4.52 F
3519 3814 1.619654 CCAATTCAGGTGTCTGCCAA 58.380 50.000 0.00 0.00 40.69 4.52 F
3522 3817 2.559668 CAATTCAGGTGTCTGCCAATGT 59.440 45.455 0.00 0.00 40.69 2.71 F
4873 5195 0.621571 AGCTACATCCAAGCCAGGGA 60.622 55.000 0.00 0.00 41.02 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2053 1.776662 ATAGAGAGGCGTACCAAGCA 58.223 50.000 0.00 0.00 39.06 3.91 R
2104 2276 1.318576 GCGCAATAACCCCAAGCTAT 58.681 50.000 0.30 0.00 0.00 2.97 R
2750 3038 0.664761 CCAGCTGCCAAATGGATACG 59.335 55.000 8.66 0.00 42.51 3.06 R
3209 3503 2.138596 AATGCTGAACCAAACTTGCG 57.861 45.000 0.00 0.00 0.00 4.85 R
3503 3798 2.224843 TGACATTGGCAGACACCTGAAT 60.225 45.455 0.00 0.00 43.02 2.57 R
4503 4822 0.390124 ACATTGCAAACCCACAGCTG 59.610 50.000 13.48 13.48 0.00 4.24 R
4626 4945 0.868406 CCTGTGCTGACTTTTCGTCC 59.132 55.000 0.00 0.00 42.13 4.79 R
4757 5076 1.301677 CCTCTCTTTGCCGTTGCTCC 61.302 60.000 0.00 0.00 38.71 4.70 R
5465 5791 2.096614 CGGATTCACGTGTGTTTACCAC 60.097 50.000 16.51 0.00 44.78 4.16 R
6702 10760 0.400213 TTGTCCCACCCAAGTAGCAG 59.600 55.000 0.00 0.00 0.00 4.24 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
64 65 0.744771 CCTACAAGAAAGGCGAGCCC 60.745 60.000 10.95 0.00 36.58 5.19
77 78 0.109781 CGAGCCCCATGTTTGTTTCG 60.110 55.000 0.00 0.00 0.00 3.46
124 125 3.518634 TTGGTGTCTTTTGGTTTGCTC 57.481 42.857 0.00 0.00 0.00 4.26
164 165 3.961849 TGGTAATGCTTATTGGCTGTCA 58.038 40.909 0.00 0.00 0.00 3.58
230 232 5.069318 TCTTACACCATTTGAGTTCATGCA 58.931 37.500 0.00 0.00 0.00 3.96
231 233 3.928727 ACACCATTTGAGTTCATGCAG 57.071 42.857 0.00 0.00 0.00 4.41
232 234 3.225104 ACACCATTTGAGTTCATGCAGT 58.775 40.909 0.00 0.00 0.00 4.40
233 235 3.005050 ACACCATTTGAGTTCATGCAGTG 59.995 43.478 0.00 0.00 0.00 3.66
234 236 2.559668 ACCATTTGAGTTCATGCAGTGG 59.440 45.455 0.00 0.00 0.00 4.00
235 237 2.559668 CCATTTGAGTTCATGCAGTGGT 59.440 45.455 0.00 0.00 0.00 4.16
236 238 3.006110 CCATTTGAGTTCATGCAGTGGTT 59.994 43.478 0.00 0.00 0.00 3.67
237 239 4.501915 CCATTTGAGTTCATGCAGTGGTTT 60.502 41.667 0.00 0.00 0.00 3.27
238 240 5.278907 CCATTTGAGTTCATGCAGTGGTTTA 60.279 40.000 0.00 0.00 0.00 2.01
239 241 5.843673 TTTGAGTTCATGCAGTGGTTTAA 57.156 34.783 0.00 0.00 0.00 1.52
240 242 4.829064 TGAGTTCATGCAGTGGTTTAAC 57.171 40.909 0.00 0.00 0.00 2.01
241 243 4.460263 TGAGTTCATGCAGTGGTTTAACT 58.540 39.130 0.00 0.00 0.00 2.24
243 245 3.569701 AGTTCATGCAGTGGTTTAACTGG 59.430 43.478 6.48 0.00 46.34 4.00
244 246 3.222173 TCATGCAGTGGTTTAACTGGT 57.778 42.857 6.48 0.00 46.34 4.00
245 247 4.359434 TCATGCAGTGGTTTAACTGGTA 57.641 40.909 6.48 0.00 46.34 3.25
246 248 4.323417 TCATGCAGTGGTTTAACTGGTAG 58.677 43.478 6.48 0.00 46.34 3.18
247 249 2.500229 TGCAGTGGTTTAACTGGTAGC 58.500 47.619 6.48 0.00 46.34 3.58
248 250 2.158740 TGCAGTGGTTTAACTGGTAGCA 60.159 45.455 6.48 0.00 46.34 3.49
249 251 3.081804 GCAGTGGTTTAACTGGTAGCAT 58.918 45.455 6.48 0.00 46.34 3.79
250 252 3.119849 GCAGTGGTTTAACTGGTAGCATG 60.120 47.826 6.48 0.00 46.34 4.06
251 253 3.081804 AGTGGTTTAACTGGTAGCATGC 58.918 45.455 10.51 10.51 0.00 4.06
252 254 3.081804 GTGGTTTAACTGGTAGCATGCT 58.918 45.455 25.99 25.99 0.00 3.79
272 274 3.184986 GCTGTGGTTTATTTTGCTGCTTG 59.815 43.478 0.00 0.00 0.00 4.01
280 282 7.384660 TGGTTTATTTTGCTGCTTGAATTAGTG 59.615 33.333 0.00 0.00 0.00 2.74
282 284 9.405587 GTTTATTTTGCTGCTTGAATTAGTGTA 57.594 29.630 0.00 0.00 0.00 2.90
319 322 0.251341 ATCACCCCACAGTGGAAAGC 60.251 55.000 22.37 0.00 40.96 3.51
333 336 2.499289 TGGAAAGCTGCAAACTTCCAAA 59.501 40.909 16.69 0.30 0.00 3.28
352 355 7.922505 TCCAAATTAACATTTCTGAAACGTG 57.077 32.000 4.73 3.69 29.41 4.49
357 360 3.609103 ACATTTCTGAAACGTGTGCTC 57.391 42.857 4.73 0.00 0.00 4.26
530 533 9.802039 AAACCTATTGTGTTTGATTAGGTTAGA 57.198 29.630 11.82 0.00 43.28 2.10
531 534 9.975218 AACCTATTGTGTTTGATTAGGTTAGAT 57.025 29.630 10.18 0.00 42.56 1.98
537 540 7.007723 TGTGTTTGATTAGGTTAGATTTGGGT 58.992 34.615 0.00 0.00 0.00 4.51
538 541 7.040062 TGTGTTTGATTAGGTTAGATTTGGGTG 60.040 37.037 0.00 0.00 0.00 4.61
539 542 7.175990 GTGTTTGATTAGGTTAGATTTGGGTGA 59.824 37.037 0.00 0.00 0.00 4.02
580 584 3.130340 AGATTTGCATAAAACCGCCGATT 59.870 39.130 0.00 0.00 0.00 3.34
640 644 8.699749 GTTTACATGAGTTTTTATTCTGGTTGC 58.300 33.333 0.00 0.00 0.00 4.17
803 934 5.738619 TTCTCAGGCTGTTATGACTTGTA 57.261 39.130 15.27 0.00 0.00 2.41
1038 1169 1.737735 CTCGCATCAACGACCAGCA 60.738 57.895 0.00 0.00 37.09 4.41
1444 1588 9.899661 ATAATAGTGTGTATGTGCCTCTTTTTA 57.100 29.630 0.00 0.00 0.00 1.52
1454 1598 4.072839 GTGCCTCTTTTTAGCTACAGGTT 58.927 43.478 0.00 0.00 0.00 3.50
1622 1766 1.134098 GTGGTATGTACTGGGCTGCAT 60.134 52.381 0.50 0.00 0.00 3.96
1644 1788 6.347888 GCATGTCATTTATGCTTGCAACTTTT 60.348 34.615 0.00 0.00 45.64 2.27
1710 1854 8.342270 AGAAAAGTGGTACCCTAGTTAGAGATA 58.658 37.037 10.07 0.00 0.00 1.98
1832 2002 7.009179 TGAATTGGAGATAATAGGCCTACAG 57.991 40.000 16.61 0.00 0.00 2.74
1842 2012 2.677228 GCCTACAGCCATGGTGGT 59.323 61.111 14.67 14.13 40.46 4.16
1852 2022 1.257055 CCATGGTGGTTTGGGCGATT 61.257 55.000 2.57 0.00 31.35 3.34
1853 2023 0.607620 CATGGTGGTTTGGGCGATTT 59.392 50.000 0.00 0.00 0.00 2.17
1854 2024 0.607620 ATGGTGGTTTGGGCGATTTG 59.392 50.000 0.00 0.00 0.00 2.32
1855 2025 1.291906 GGTGGTTTGGGCGATTTGG 59.708 57.895 0.00 0.00 0.00 3.28
1856 2026 1.291906 GTGGTTTGGGCGATTTGGG 59.708 57.895 0.00 0.00 0.00 4.12
1857 2027 1.910772 TGGTTTGGGCGATTTGGGG 60.911 57.895 0.00 0.00 0.00 4.96
1858 2028 2.655073 GGTTTGGGCGATTTGGGGG 61.655 63.158 0.00 0.00 0.00 5.40
1883 2053 1.214992 GGGGGATTGGTGGAGAGGTT 61.215 60.000 0.00 0.00 0.00 3.50
1891 2061 0.690762 GGTGGAGAGGTTGCTTGGTA 59.309 55.000 0.00 0.00 0.00 3.25
1934 2104 0.178932 TGACTGGTAGACCTGGCAGT 60.179 55.000 14.43 3.93 46.37 4.40
2098 2270 8.904834 TGTGAGATCTAGAGGTATTTCTGTTAC 58.095 37.037 0.00 0.00 0.00 2.50
2175 2347 1.010935 CGCGACAATGAGCAGTGAGT 61.011 55.000 0.00 0.00 0.00 3.41
2190 2362 4.393155 AGTCGCTTCCGCCATGCA 62.393 61.111 0.00 0.00 0.00 3.96
2300 2472 6.825721 GGAAGAGTGACATTCAGGTAATTCAT 59.174 38.462 0.40 0.00 0.00 2.57
2301 2473 7.337942 GGAAGAGTGACATTCAGGTAATTCATT 59.662 37.037 0.40 0.00 0.00 2.57
2344 2516 3.826729 GGATTGGCTTTGAAAGTAGTGGT 59.173 43.478 6.81 0.00 0.00 4.16
2479 2651 9.170890 AGTAGGATTGGATTGGAACTGATAATA 57.829 33.333 0.00 0.00 0.00 0.98
2495 2667 6.944862 ACTGATAATAATCCCCATTCTTCTGC 59.055 38.462 0.00 0.00 0.00 4.26
2522 2694 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2523 2695 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2524 2696 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2525 2697 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2526 2698 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2527 2699 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
2528 2700 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2529 2701 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
2530 2702 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
2531 2703 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
2532 2704 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2572 2744 8.997621 TTTGAGCGTTTAGATCACTAAAGTAT 57.002 30.769 0.00 0.00 45.95 2.12
2574 2746 8.997621 TGAGCGTTTAGATCACTAAAGTATTT 57.002 30.769 0.00 0.00 45.42 1.40
2575 2747 8.869897 TGAGCGTTTAGATCACTAAAGTATTTG 58.130 33.333 0.00 0.00 45.42 2.32
2577 2749 8.656849 AGCGTTTAGATCACTAAAGTATTTGTG 58.343 33.333 0.00 0.00 45.42 3.33
2579 2751 9.741168 CGTTTAGATCACTAAAGTATTTGTGTG 57.259 33.333 0.00 0.00 45.42 3.82
2582 2754 9.990360 TTAGATCACTAAAGTATTTGTGTGTGA 57.010 29.630 0.00 0.00 41.33 3.58
2586 2758 9.719355 ATCACTAAAGTATTTGTGTGTGATACA 57.281 29.630 0.00 0.00 40.49 2.29
2731 3019 8.806177 TTAAATGCAGCAATTTATCTATGCAG 57.194 30.769 0.00 0.00 45.76 4.41
2750 3038 6.139048 TGCAGGAAAGTTAACCTTGTTTAC 57.861 37.500 0.88 0.00 33.91 2.01
2898 3186 5.465935 TGCATTTCAAGAATTCCGTTTACC 58.534 37.500 0.65 0.00 0.00 2.85
3503 3798 0.178975 AGGTTCACCAATTCCGCCAA 60.179 50.000 0.00 0.00 38.89 4.52
3519 3814 1.619654 CCAATTCAGGTGTCTGCCAA 58.380 50.000 0.00 0.00 40.69 4.52
3522 3817 2.559668 CAATTCAGGTGTCTGCCAATGT 59.440 45.455 0.00 0.00 40.69 2.71
3541 3836 7.415989 GCCAATGTCAGTATTGTTGATGAGAAT 60.416 37.037 0.00 0.00 36.54 2.40
3931 4227 8.084073 TGCACTTCTCTTTTTATGAAGAATTGG 58.916 33.333 8.65 0.00 39.42 3.16
4179 4495 5.244755 TGTACAGCTTAATGTCAATGCAGA 58.755 37.500 0.00 0.00 34.56 4.26
4217 4533 9.256228 AGAAATATGGTCAGAGTACTACAGAAA 57.744 33.333 0.00 0.00 0.00 2.52
4420 4739 5.573282 CGATGAAGTTGTTGACGAGAATAGT 59.427 40.000 0.00 0.00 0.00 2.12
4503 4822 4.018324 AGAGGACCATTTAAGGGAAAGGAC 60.018 45.833 1.56 0.00 30.11 3.85
4569 4888 2.810852 CTGGAAAGTCCTCTCTGCAAAC 59.189 50.000 0.00 0.00 37.46 2.93
4626 4945 4.024048 GTGTGAACCTACAGTTGAACATGG 60.024 45.833 0.00 0.00 39.40 3.66
4757 5076 5.614324 TGGACAGTAGATGGGTTTCATAG 57.386 43.478 0.00 0.00 35.97 2.23
4867 5189 3.119388 TGAATTGCAAGCTACATCCAAGC 60.119 43.478 4.94 0.00 40.40 4.01
4873 5195 0.621571 AGCTACATCCAAGCCAGGGA 60.622 55.000 0.00 0.00 41.02 4.20
5144 5468 7.119699 TGTTTAACTCCAGCTCATTCAGTATTG 59.880 37.037 0.00 0.00 0.00 1.90
5317 5641 4.170292 CAGAATGGTGGAGCTCTTTTTG 57.830 45.455 14.64 2.56 0.00 2.44
5442 5766 4.023291 TGCCAGGTTTGTTCTTCTCTTTT 58.977 39.130 0.00 0.00 0.00 2.27
5443 5767 4.466015 TGCCAGGTTTGTTCTTCTCTTTTT 59.534 37.500 0.00 0.00 0.00 1.94
5502 5833 1.778334 TCCGTGTCGATTGTCTTGTG 58.222 50.000 0.00 0.00 0.00 3.33
5574 5905 6.193504 AGTAGTACTCCCTCCGTTTCTAAAT 58.806 40.000 0.00 0.00 0.00 1.40
5610 5942 8.867112 TTAGAGATTCAATACGGACAACATAC 57.133 34.615 0.00 0.00 0.00 2.39
5615 5947 3.698539 TCAATACGGACAACATACGGGTA 59.301 43.478 0.00 0.00 0.00 3.69
5656 5988 3.825014 AGTGCAGATTCACTCATTTTGCT 59.175 39.130 0.00 0.00 43.28 3.91
5659 5991 4.278919 TGCAGATTCACTCATTTTGCTTCA 59.721 37.500 0.00 0.00 0.00 3.02
5710 6045 7.910441 AGACTTATATCTAGAAGCGGAGTAC 57.090 40.000 0.00 0.00 0.00 2.73
5715 6050 3.251479 TCTAGAAGCGGAGTACGTACA 57.749 47.619 26.55 2.62 46.52 2.90
5717 6052 4.948847 TCTAGAAGCGGAGTACGTACATA 58.051 43.478 26.55 6.22 46.52 2.29
5718 6053 5.545588 TCTAGAAGCGGAGTACGTACATAT 58.454 41.667 26.55 7.09 46.52 1.78
5729 9679 6.637254 GGAGTACGTACATATGAGTCAATGTG 59.363 42.308 26.55 13.16 36.96 3.21
5749 9703 4.795795 TGTGCTTTGTGTTGTTCAAATACG 59.204 37.500 0.00 0.00 34.88 3.06
5782 9736 5.065090 TGAATTACTGATGCTGTGTATGTGC 59.935 40.000 0.00 0.00 0.00 4.57
5820 9774 2.281070 CGCTGCTCAAGGTGGTGT 60.281 61.111 0.00 0.00 0.00 4.16
5836 9790 3.437049 GTGGTGTGTAGATTGGAAGAAGC 59.563 47.826 0.00 0.00 0.00 3.86
5859 9813 4.079850 CCTCTGAGCTGCCGCAGT 62.080 66.667 21.29 8.55 39.54 4.40
5860 9814 2.047465 CTCTGAGCTGCCGCAGTT 60.047 61.111 21.29 16.04 39.54 3.16
5866 9820 4.395583 GCTGCCGCAGTTGCTGAC 62.396 66.667 21.29 0.00 39.32 3.51
5954 9928 2.476519 GGTTCGTTGAACTTTTGACGCA 60.477 45.455 9.32 0.00 41.70 5.24
5970 9944 1.072331 ACGCAATCTTGGACTTGGACT 59.928 47.619 0.00 0.00 0.00 3.85
5972 9946 2.554032 CGCAATCTTGGACTTGGACTTT 59.446 45.455 0.00 0.00 0.00 2.66
5973 9947 3.365364 CGCAATCTTGGACTTGGACTTTC 60.365 47.826 0.00 0.00 0.00 2.62
6049 10023 3.042560 GCGGTGCCAGCTTTTCTT 58.957 55.556 0.00 0.00 0.00 2.52
6050 10024 1.363807 GCGGTGCCAGCTTTTCTTT 59.636 52.632 0.00 0.00 0.00 2.52
6063 10037 9.208022 GCCAGCTTTTCTTTTATCTTGTAAAAT 57.792 29.630 0.00 0.00 0.00 1.82
6099 10073 6.090493 AGACTTAAGTATCTTTCCGCGTTTTC 59.910 38.462 8.42 0.00 0.00 2.29
6102 10076 2.921754 AGTATCTTTCCGCGTTTTCTCG 59.078 45.455 4.92 0.00 0.00 4.04
6103 10077 2.074547 ATCTTTCCGCGTTTTCTCGA 57.925 45.000 4.92 0.00 0.00 4.04
6104 10078 1.855513 TCTTTCCGCGTTTTCTCGAA 58.144 45.000 4.92 0.00 0.00 3.71
6105 10079 2.203401 TCTTTCCGCGTTTTCTCGAAA 58.797 42.857 4.92 4.81 0.00 3.46
6106 10080 2.803956 TCTTTCCGCGTTTTCTCGAAAT 59.196 40.909 4.92 0.00 0.00 2.17
6107 10081 3.989167 TCTTTCCGCGTTTTCTCGAAATA 59.011 39.130 4.92 0.00 0.00 1.40
6108 10082 4.628333 TCTTTCCGCGTTTTCTCGAAATAT 59.372 37.500 4.92 0.00 0.00 1.28
6109 10083 5.806502 TCTTTCCGCGTTTTCTCGAAATATA 59.193 36.000 4.92 0.00 0.00 0.86
6110 10084 6.310956 TCTTTCCGCGTTTTCTCGAAATATAA 59.689 34.615 4.92 0.00 0.00 0.98
6112 10086 5.342433 TCCGCGTTTTCTCGAAATATAAGA 58.658 37.500 4.92 0.00 0.00 2.10
6113 10087 5.981315 TCCGCGTTTTCTCGAAATATAAGAT 59.019 36.000 4.92 0.00 0.00 2.40
6152 10185 3.251571 GGAGGTAGTAGTTGCGTGAAAG 58.748 50.000 0.00 0.00 0.00 2.62
6154 10187 2.028385 AGGTAGTAGTTGCGTGAAAGGG 60.028 50.000 0.00 0.00 0.00 3.95
6163 10196 2.269241 GTGAAAGGGAGGGAGGCG 59.731 66.667 0.00 0.00 0.00 5.52
6179 10212 1.812571 AGGCGTCCACAAAAGCATAAG 59.187 47.619 0.00 0.00 0.00 1.73
6197 10230 5.007430 GCATAAGTCTGGTGATGTGAGATTG 59.993 44.000 0.00 0.00 0.00 2.67
6210 10244 0.984230 GAGATTGGTGTCCTGGGTCA 59.016 55.000 0.00 0.00 0.00 4.02
6226 10260 2.035832 GGGTCAATGTTTGGTTGGACAG 59.964 50.000 0.00 0.00 0.00 3.51
6230 10264 1.238439 ATGTTTGGTTGGACAGCTCG 58.762 50.000 0.00 0.00 0.00 5.03
6263 10297 4.396478 ACACGGATCGATCTGGAGTATATG 59.604 45.833 32.19 22.61 37.50 1.78
6363 10402 6.038714 GCTTGGGATTTCCTGATAACAACTAG 59.961 42.308 0.00 0.00 36.20 2.57
6416 10458 9.627123 TCTTTCTTTTCTTTCCTTGTGAAGATA 57.373 29.630 0.00 0.00 33.63 1.98
6417 10459 9.670719 CTTTCTTTTCTTTCCTTGTGAAGATAC 57.329 33.333 0.00 0.00 33.63 2.24
6418 10460 7.421530 TCTTTTCTTTCCTTGTGAAGATACG 57.578 36.000 0.00 0.00 33.63 3.06
6441 10483 1.006813 ATGGAGCAACCCCACCATTA 58.993 50.000 0.00 0.00 39.69 1.90
6538 10591 2.184167 CAACGAACACCAACGGCCT 61.184 57.895 0.00 0.00 0.00 5.19
6540 10593 1.033202 AACGAACACCAACGGCCTTT 61.033 50.000 0.00 0.00 0.00 3.11
6585 10638 1.916697 GCAAGCAAGGGAGAAGCGAC 61.917 60.000 0.00 0.00 0.00 5.19
6587 10640 2.788191 AAGCAAGGGAGAAGCGACGG 62.788 60.000 0.00 0.00 0.00 4.79
6619 10677 2.806608 GCCATCGCCATGATTCATTT 57.193 45.000 0.00 0.00 34.13 2.32
6620 10678 2.669364 GCCATCGCCATGATTCATTTC 58.331 47.619 0.00 0.00 34.13 2.17
6621 10679 2.919387 GCCATCGCCATGATTCATTTCG 60.919 50.000 0.00 3.95 34.13 3.46
6682 10740 1.154413 CACGTTTCGGTGATGCTGC 60.154 57.895 0.00 0.00 40.38 5.25
6688 10746 3.490759 CGGTGATGCTGCGGTGAC 61.491 66.667 0.00 0.00 0.00 3.67
6747 10805 1.214062 CTTCTCGCGCTCCTCAACT 59.786 57.895 5.56 0.00 0.00 3.16
6751 10809 1.347817 CTCGCGCTCCTCAACTCAAC 61.348 60.000 5.56 0.00 0.00 3.18
6752 10810 1.373497 CGCGCTCCTCAACTCAACT 60.373 57.895 5.56 0.00 0.00 3.16
6810 10874 7.095187 GCAAGTTGCGAGGCTAATAATAATAGT 60.095 37.037 12.95 0.00 31.71 2.12
6811 10875 9.419297 CAAGTTGCGAGGCTAATAATAATAGTA 57.581 33.333 0.00 0.00 0.00 1.82
6812 10876 9.991906 AAGTTGCGAGGCTAATAATAATAGTAA 57.008 29.630 0.00 0.00 0.00 2.24
6813 10877 9.420551 AGTTGCGAGGCTAATAATAATAGTAAC 57.579 33.333 0.00 0.00 0.00 2.50
6814 10878 9.199982 GTTGCGAGGCTAATAATAATAGTAACA 57.800 33.333 0.00 0.00 0.00 2.41
6815 10879 8.981724 TGCGAGGCTAATAATAATAGTAACAG 57.018 34.615 0.00 0.00 0.00 3.16
6816 10880 7.544566 TGCGAGGCTAATAATAATAGTAACAGC 59.455 37.037 0.00 0.00 0.00 4.40
6817 10881 7.544566 GCGAGGCTAATAATAATAGTAACAGCA 59.455 37.037 0.00 0.00 0.00 4.41
6818 10882 9.587772 CGAGGCTAATAATAATAGTAACAGCAT 57.412 33.333 0.00 0.47 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.269084 CACAATCATTACTGTTACAGAAAAGCG 59.731 37.037 20.07 8.27 35.18 4.68
64 65 5.643777 ACTAGATCTTCCGAAACAAACATGG 59.356 40.000 0.00 0.00 0.00 3.66
124 125 0.750182 AAACACACCAAGGTCGTGGG 60.750 55.000 18.98 3.52 43.56 4.61
164 165 7.221838 GTGCACATTGTGTTTTTAGTGTAACAT 59.778 33.333 17.64 0.00 36.72 2.71
230 232 3.081804 GCATGCTACCAGTTAAACCACT 58.918 45.455 11.37 0.00 0.00 4.00
231 233 3.081804 AGCATGCTACCAGTTAAACCAC 58.918 45.455 21.21 0.00 0.00 4.16
232 234 3.081061 CAGCATGCTACCAGTTAAACCA 58.919 45.455 22.19 0.00 0.00 3.67
233 235 3.081804 ACAGCATGCTACCAGTTAAACC 58.918 45.455 22.19 0.00 42.53 3.27
234 236 3.119849 CCACAGCATGCTACCAGTTAAAC 60.120 47.826 22.19 0.00 42.53 2.01
235 237 3.081061 CCACAGCATGCTACCAGTTAAA 58.919 45.455 22.19 0.00 42.53 1.52
236 238 2.039746 ACCACAGCATGCTACCAGTTAA 59.960 45.455 22.19 0.00 42.53 2.01
237 239 1.628340 ACCACAGCATGCTACCAGTTA 59.372 47.619 22.19 0.00 42.53 2.24
238 240 0.401738 ACCACAGCATGCTACCAGTT 59.598 50.000 22.19 0.00 42.53 3.16
239 241 0.401738 AACCACAGCATGCTACCAGT 59.598 50.000 22.19 11.52 42.53 4.00
240 242 1.538047 AAACCACAGCATGCTACCAG 58.462 50.000 22.19 10.78 42.53 4.00
241 243 2.869101 TAAACCACAGCATGCTACCA 57.131 45.000 22.19 0.00 42.53 3.25
242 244 4.718940 AAATAAACCACAGCATGCTACC 57.281 40.909 22.19 0.00 42.53 3.18
243 245 4.327087 GCAAAATAAACCACAGCATGCTAC 59.673 41.667 22.19 0.00 42.53 3.58
244 246 4.220382 AGCAAAATAAACCACAGCATGCTA 59.780 37.500 22.19 2.63 42.53 3.49
245 247 3.007182 AGCAAAATAAACCACAGCATGCT 59.993 39.130 16.30 16.30 42.53 3.79
246 248 3.123959 CAGCAAAATAAACCACAGCATGC 59.876 43.478 10.51 10.51 42.53 4.06
247 249 3.123959 GCAGCAAAATAAACCACAGCATG 59.876 43.478 0.00 0.00 46.00 4.06
248 250 3.007182 AGCAGCAAAATAAACCACAGCAT 59.993 39.130 0.00 0.00 0.00 3.79
249 251 2.364970 AGCAGCAAAATAAACCACAGCA 59.635 40.909 0.00 0.00 0.00 4.41
250 252 3.030668 AGCAGCAAAATAAACCACAGC 57.969 42.857 0.00 0.00 0.00 4.40
251 253 4.619973 TCAAGCAGCAAAATAAACCACAG 58.380 39.130 0.00 0.00 0.00 3.66
252 254 4.662468 TCAAGCAGCAAAATAAACCACA 57.338 36.364 0.00 0.00 0.00 4.17
289 291 6.465751 CCACTGTGGGGTGATGTACATATTAT 60.466 42.308 19.23 0.00 39.34 1.28
319 322 8.277713 CAGAAATGTTAATTTGGAAGTTTGCAG 58.722 33.333 0.00 0.00 36.10 4.41
333 336 6.017109 AGAGCACACGTTTCAGAAATGTTAAT 60.017 34.615 16.80 4.68 38.51 1.40
349 352 5.295292 AGAAATGGAAATGATAGAGCACACG 59.705 40.000 0.00 0.00 0.00 4.49
352 355 8.388484 ACATAGAAATGGAAATGATAGAGCAC 57.612 34.615 0.00 0.00 37.43 4.40
429 432 5.757320 GCACTACAGACTATGAATGCTTGAT 59.243 40.000 0.00 0.00 34.15 2.57
528 531 6.537355 CAGACATATATGGTCACCCAAATCT 58.463 40.000 16.96 3.89 46.04 2.40
529 532 5.182001 GCAGACATATATGGTCACCCAAATC 59.818 44.000 16.96 1.69 46.04 2.17
530 533 5.072741 GCAGACATATATGGTCACCCAAAT 58.927 41.667 16.96 0.00 46.04 2.32
531 534 4.460263 GCAGACATATATGGTCACCCAAA 58.540 43.478 16.96 0.00 46.04 3.28
534 537 2.639839 AGGCAGACATATATGGTCACCC 59.360 50.000 16.96 13.61 37.74 4.61
537 540 3.580022 CTGGAGGCAGACATATATGGTCA 59.420 47.826 16.96 3.05 37.74 4.02
538 541 3.834813 TCTGGAGGCAGACATATATGGTC 59.165 47.826 16.96 11.30 35.50 4.02
539 542 3.861846 TCTGGAGGCAGACATATATGGT 58.138 45.455 16.96 2.89 0.00 3.55
624 628 9.685828 TTGTAATACTGCAACCAGAATAAAAAC 57.314 29.630 0.00 0.00 41.77 2.43
733 864 4.479619 CAGATGAGTAAAACAAAGCTGGC 58.520 43.478 0.00 0.00 0.00 4.85
1038 1169 4.576463 GGATCAGAAACGCCATGAATTACT 59.424 41.667 0.00 0.00 0.00 2.24
1454 1598 4.601084 TCCAACTTTTTACAGGTCCACAA 58.399 39.130 0.00 0.00 0.00 3.33
1622 1766 6.538021 ACAAAAAGTTGCAAGCATAAATGACA 59.462 30.769 0.00 0.00 38.39 3.58
1832 2002 4.067913 CGCCCAAACCACCATGGC 62.068 66.667 13.04 0.00 42.67 4.40
1883 2053 1.776662 ATAGAGAGGCGTACCAAGCA 58.223 50.000 0.00 0.00 39.06 3.91
1934 2104 5.106876 TGATGAAATTCTCTCTCCATGCA 57.893 39.130 0.00 0.00 0.00 3.96
2098 2270 5.505654 CGCAATAACCCCAAGCTATGTAAAG 60.506 44.000 0.00 0.00 0.00 1.85
2104 2276 1.318576 GCGCAATAACCCCAAGCTAT 58.681 50.000 0.30 0.00 0.00 2.97
2300 2472 8.635765 ATCCAGCTTATGTCTTCACTTTTAAA 57.364 30.769 0.00 0.00 0.00 1.52
2301 2473 8.514594 CAATCCAGCTTATGTCTTCACTTTTAA 58.485 33.333 0.00 0.00 0.00 1.52
2479 2651 3.525199 AGTACTGCAGAAGAATGGGGATT 59.475 43.478 23.35 0.00 0.00 3.01
2495 2667 4.796038 TTTCTTTACGGAGGGAGTACTG 57.204 45.455 0.00 0.00 0.00 2.74
2544 2716 9.601217 ACTTTAGTGATCTAAACGCTCAAATAT 57.399 29.630 0.00 0.00 40.05 1.28
2545 2717 8.997621 ACTTTAGTGATCTAAACGCTCAAATA 57.002 30.769 0.00 0.00 40.05 1.40
2546 2718 7.907214 ACTTTAGTGATCTAAACGCTCAAAT 57.093 32.000 0.00 0.00 40.05 2.32
2547 2719 8.997621 ATACTTTAGTGATCTAAACGCTCAAA 57.002 30.769 0.00 0.00 40.05 2.69
2548 2720 8.997621 AATACTTTAGTGATCTAAACGCTCAA 57.002 30.769 0.00 0.00 40.05 3.02
2549 2721 8.869897 CAAATACTTTAGTGATCTAAACGCTCA 58.130 33.333 0.00 0.00 40.05 4.26
2583 2755 8.636213 CCCTCCGTAAAGAAATATAAGAGTGTA 58.364 37.037 0.00 0.00 0.00 2.90
2586 2758 7.564292 ACTCCCTCCGTAAAGAAATATAAGAGT 59.436 37.037 0.00 0.00 0.00 3.24
2731 3019 7.173047 TGGATACGTAAACAAGGTTAACTTTCC 59.827 37.037 5.42 0.00 36.82 3.13
2750 3038 0.664761 CCAGCTGCCAAATGGATACG 59.335 55.000 8.66 0.00 42.51 3.06
2801 3089 7.501559 AGCATGATGATAGCATTGAAAGTAAGT 59.498 33.333 0.00 0.00 34.11 2.24
3209 3503 2.138596 AATGCTGAACCAAACTTGCG 57.861 45.000 0.00 0.00 0.00 4.85
3252 3547 6.259829 AGTGGGCAAAACATTACAAATGAAAC 59.740 34.615 6.64 0.00 0.00 2.78
3390 3685 6.548251 ACTGGCCTTCTCTTCTATAGTTCTAC 59.452 42.308 3.32 0.00 0.00 2.59
3430 3725 4.778842 ACTGCGTATCTTTTGAATAGCG 57.221 40.909 0.00 0.00 0.00 4.26
3503 3798 2.224843 TGACATTGGCAGACACCTGAAT 60.225 45.455 0.00 0.00 43.02 2.57
3519 3814 8.797350 TTCATTCTCATCAACAATACTGACAT 57.203 30.769 0.00 0.00 0.00 3.06
3522 3817 9.106070 CATCTTCATTCTCATCAACAATACTGA 57.894 33.333 0.00 0.00 0.00 3.41
3541 3836 5.958380 ACTACTCCTTGTATCACCATCTTCA 59.042 40.000 0.00 0.00 0.00 3.02
3806 4101 8.349568 GGATAACTTCCTTTTATGGACAACTT 57.650 34.615 0.00 0.00 41.78 2.66
3964 4260 3.731431 TCTCCTAGGCCATTAGGTTCAA 58.269 45.455 15.82 0.00 40.91 2.69
4063 4359 7.933033 ACCATTGTAAATGAAAGCTTGACAAAT 59.067 29.630 0.00 0.00 0.00 2.32
4097 4413 8.738645 AATATTTCACTAGATTGAGAACCCAC 57.261 34.615 0.00 0.00 0.00 4.61
4157 4473 5.122239 TGTCTGCATTGACATTAAGCTGTAC 59.878 40.000 4.76 0.00 41.43 2.90
4179 4495 6.873997 TGACCATATTTCTGAAGATACGTGT 58.126 36.000 0.00 0.00 0.00 4.49
4217 4533 2.592102 TCAGCTTCATTGGCCTTCTT 57.408 45.000 3.32 0.00 0.00 2.52
4420 4739 5.945191 TGCAATACTTCTGGAATCAACATCA 59.055 36.000 0.00 0.00 0.00 3.07
4503 4822 0.390124 ACATTGCAAACCCACAGCTG 59.610 50.000 13.48 13.48 0.00 4.24
4626 4945 0.868406 CCTGTGCTGACTTTTCGTCC 59.132 55.000 0.00 0.00 42.13 4.79
4707 5026 5.495640 AGCAAAAACAAATCCAGGTTCAAA 58.504 33.333 0.00 0.00 0.00 2.69
4714 5033 5.759273 TCCAATGAAGCAAAAACAAATCCAG 59.241 36.000 0.00 0.00 0.00 3.86
4757 5076 1.301677 CCTCTCTTTGCCGTTGCTCC 61.302 60.000 0.00 0.00 38.71 4.70
4867 5189 6.149308 GCATCCAAAGTTTTATTTTTCCCTGG 59.851 38.462 0.00 0.00 0.00 4.45
4873 5195 9.786105 CTGTTTTGCATCCAAAGTTTTATTTTT 57.214 25.926 0.00 0.00 41.58 1.94
5144 5468 9.994432 CAGGAAGATAAACTTATTTCATGTCAC 57.006 33.333 0.00 0.00 39.13 3.67
5317 5641 2.926200 CGTGTCATCATCCAACAGAGAC 59.074 50.000 0.00 0.00 0.00 3.36
5465 5791 2.096614 CGGATTCACGTGTGTTTACCAC 60.097 50.000 16.51 0.00 44.78 4.16
5502 5833 4.767409 AGGAGCCTAAAACTGGAAAACATC 59.233 41.667 0.00 0.00 0.00 3.06
5558 5889 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
5559 5890 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
5682 6014 7.502895 ACTCCGCTTCTAGATATAAGTCTTTCA 59.497 37.037 0.00 0.00 0.00 2.69
5683 6015 7.878036 ACTCCGCTTCTAGATATAAGTCTTTC 58.122 38.462 0.00 0.00 0.00 2.62
5696 6031 5.407691 TCATATGTACGTACTCCGCTTCTAG 59.592 44.000 25.12 5.88 41.42 2.43
5710 6045 5.973651 AAGCACATTGACTCATATGTACG 57.026 39.130 1.90 0.00 33.42 3.67
5715 6050 6.016024 ACAACACAAAGCACATTGACTCATAT 60.016 34.615 4.22 0.00 34.38 1.78
5717 6052 4.098349 ACAACACAAAGCACATTGACTCAT 59.902 37.500 4.22 0.00 34.38 2.90
5718 6053 3.443329 ACAACACAAAGCACATTGACTCA 59.557 39.130 4.22 0.00 34.38 3.41
5729 9679 5.966503 TGTACGTATTTGAACAACACAAAGC 59.033 36.000 0.00 0.00 39.90 3.51
5749 9703 6.094048 ACAGCATCAGTAATTCAACCATGTAC 59.906 38.462 0.00 0.00 0.00 2.90
5782 9736 3.046087 CACTGTGACAGGCAGCGG 61.046 66.667 17.92 0.00 37.47 5.52
5820 9774 4.256920 GAGCAAGCTTCTTCCAATCTACA 58.743 43.478 0.00 0.00 0.00 2.74
5859 9813 2.948315 TGCAACATGTACAAGTCAGCAA 59.052 40.909 21.45 10.58 0.00 3.91
5860 9814 2.549329 CTGCAACATGTACAAGTCAGCA 59.451 45.455 21.95 21.95 0.00 4.41
5866 9820 2.159787 GCTCGACTGCAACATGTACAAG 60.160 50.000 0.00 0.00 0.00 3.16
5954 9928 5.053978 AGTGAAAGTCCAAGTCCAAGATT 57.946 39.130 0.00 0.00 0.00 2.40
5970 9944 6.370442 CCATACATTGACCGAGTTAAGTGAAA 59.630 38.462 0.00 0.00 0.00 2.69
5972 9946 5.186215 TCCATACATTGACCGAGTTAAGTGA 59.814 40.000 0.00 0.00 0.00 3.41
5973 9947 5.416083 TCCATACATTGACCGAGTTAAGTG 58.584 41.667 0.00 0.00 0.00 3.16
6020 9994 4.557942 CACCGCCAATGTGCTTTC 57.442 55.556 0.00 0.00 0.00 2.62
6071 10045 4.735822 CGCGGAAAGATACTTAAGTCTCAG 59.264 45.833 19.67 9.38 0.00 3.35
6080 10054 3.367025 CGAGAAAACGCGGAAAGATACTT 59.633 43.478 12.47 0.00 0.00 2.24
6091 10065 6.637365 ACATCTTATATTTCGAGAAAACGCG 58.363 36.000 3.53 3.53 33.56 6.01
6106 10080 9.146984 CCGCCTCGAAATATAAAACATCTTATA 57.853 33.333 0.00 0.00 0.00 0.98
6107 10081 7.876068 TCCGCCTCGAAATATAAAACATCTTAT 59.124 33.333 0.00 0.00 0.00 1.73
6108 10082 7.211573 TCCGCCTCGAAATATAAAACATCTTA 58.788 34.615 0.00 0.00 0.00 2.10
6109 10083 6.053005 TCCGCCTCGAAATATAAAACATCTT 58.947 36.000 0.00 0.00 0.00 2.40
6110 10084 5.607477 TCCGCCTCGAAATATAAAACATCT 58.393 37.500 0.00 0.00 0.00 2.90
6112 10086 4.755123 CCTCCGCCTCGAAATATAAAACAT 59.245 41.667 0.00 0.00 0.00 2.71
6113 10087 4.124238 CCTCCGCCTCGAAATATAAAACA 58.876 43.478 0.00 0.00 0.00 2.83
6154 10187 0.955919 CTTTTGTGGACGCCTCCCTC 60.956 60.000 0.00 0.00 35.34 4.30
6163 10196 3.821033 ACCAGACTTATGCTTTTGTGGAC 59.179 43.478 0.00 0.00 0.00 4.02
6168 10201 5.181811 TCACATCACCAGACTTATGCTTTTG 59.818 40.000 0.00 0.00 0.00 2.44
6179 10212 3.005554 CACCAATCTCACATCACCAGAC 58.994 50.000 0.00 0.00 0.00 3.51
6197 10230 1.613437 CAAACATTGACCCAGGACACC 59.387 52.381 0.00 0.00 0.00 4.16
6210 10244 1.608590 CGAGCTGTCCAACCAAACATT 59.391 47.619 0.00 0.00 0.00 2.71
6226 10260 2.580470 CGTGTCGCCATCATCGAGC 61.580 63.158 0.00 0.00 36.56 5.03
6230 10264 1.278172 CGATCCGTGTCGCCATCATC 61.278 60.000 0.00 0.00 34.56 2.92
6263 10297 1.664965 GTGACACAGACCAGGCGTC 60.665 63.158 0.00 0.00 42.32 5.19
6339 10378 7.112779 ACTAGTTGTTATCAGGAAATCCCAAG 58.887 38.462 0.00 0.00 37.41 3.61
6406 10448 3.733988 GCTCCATCGTCGTATCTTCACAA 60.734 47.826 0.00 0.00 0.00 3.33
6416 10458 2.264794 GGGTTGCTCCATCGTCGT 59.735 61.111 0.00 0.00 38.11 4.34
6417 10459 2.511600 GGGGTTGCTCCATCGTCG 60.512 66.667 1.43 0.00 38.11 5.12
6418 10460 1.745489 GTGGGGTTGCTCCATCGTC 60.745 63.158 0.00 0.00 36.58 4.20
6441 10483 2.264794 GTCGACCGGAGCAATGGT 59.735 61.111 9.46 0.00 42.42 3.55
6538 10591 2.122901 AAGCCAGGGCAAGCCAAA 60.123 55.556 13.63 0.00 44.88 3.28
6547 10600 2.444700 CTTGCAAAGCCAAGCCAGGG 62.445 60.000 0.00 0.00 36.98 4.45
6571 10624 2.815647 GCCGTCGCTTCTCCCTTG 60.816 66.667 0.00 0.00 0.00 3.61
6572 10625 4.436998 CGCCGTCGCTTCTCCCTT 62.437 66.667 0.00 0.00 0.00 3.95
6574 10627 4.856607 CTCGCCGTCGCTTCTCCC 62.857 72.222 0.00 0.00 35.26 4.30
6575 10628 4.856607 CCTCGCCGTCGCTTCTCC 62.857 72.222 0.00 0.00 35.26 3.71
6576 10629 4.856607 CCCTCGCCGTCGCTTCTC 62.857 72.222 0.00 0.00 35.26 2.87
6617 10675 2.616842 GAGAGCAAGGAACCAAACGAAA 59.383 45.455 0.00 0.00 0.00 3.46
6618 10676 2.218603 GAGAGCAAGGAACCAAACGAA 58.781 47.619 0.00 0.00 0.00 3.85
6619 10677 1.542547 GGAGAGCAAGGAACCAAACGA 60.543 52.381 0.00 0.00 0.00 3.85
6620 10678 0.875059 GGAGAGCAAGGAACCAAACG 59.125 55.000 0.00 0.00 0.00 3.60
6621 10679 1.248486 GGGAGAGCAAGGAACCAAAC 58.752 55.000 0.00 0.00 0.00 2.93
6702 10760 0.400213 TTGTCCCACCCAAGTAGCAG 59.600 55.000 0.00 0.00 0.00 4.24
6708 10766 1.001181 CAAGCATTTGTCCCACCCAAG 59.999 52.381 0.00 0.00 0.00 3.61
6709 10767 1.047002 CAAGCATTTGTCCCACCCAA 58.953 50.000 0.00 0.00 0.00 4.12
6710 10768 1.470996 GCAAGCATTTGTCCCACCCA 61.471 55.000 0.00 0.00 36.65 4.51
6747 10805 3.557898 GGCAGGATTGAGTTGAGAGTTGA 60.558 47.826 0.00 0.00 0.00 3.18
6751 10809 1.407989 GGGGCAGGATTGAGTTGAGAG 60.408 57.143 0.00 0.00 0.00 3.20
6752 10810 0.620556 GGGGCAGGATTGAGTTGAGA 59.379 55.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.