Multiple sequence alignment - TraesCS3B01G438800

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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 TraesCS3B01G438800 chr3B 100.000 3228 0 0 1 3228 677997760 678000987 0.000000e+00 5962.0
1 TraesCS3B01G438800 chr3B 94.099 1237 43 12 1118 2338 654159389 654160611 0.000000e+00 1853.0
2 TraesCS3B01G438800 chr3B 91.225 604 22 15 535 1123 654153074 654153661 0.000000e+00 793.0
3 TraesCS3B01G438800 chr3B 95.161 124 5 1 364 487 244451524 244451402 9.140000e-46 195.0
4 TraesCS3B01G438800 chr3B 81.977 172 19 8 2603 2773 678023270 678023430 5.620000e-28 135.0
5 TraesCS3B01G438800 chr3A 89.066 2003 113 45 486 2440 649814307 649816251 0.000000e+00 2388.0
6 TraesCS3B01G438800 chr3A 89.535 258 18 3 2521 2778 649817210 649817458 5.200000e-83 318.0
7 TraesCS3B01G438800 chr3A 95.833 120 5 0 371 490 120804894 120804775 9.140000e-46 195.0
8 TraesCS3B01G438800 chr3A 81.218 197 15 10 74 250 649812984 649813178 4.340000e-29 139.0
9 TraesCS3B01G438800 chr3A 100.000 62 0 0 15 76 649812616 649812677 7.320000e-22 115.0
10 TraesCS3B01G438800 chr3D 90.069 1893 106 34 523 2364 515263052 515264913 0.000000e+00 2379.0
11 TraesCS3B01G438800 chr3D 94.958 119 4 2 2661 2778 515264915 515265032 5.500000e-43 185.0
12 TraesCS3B01G438800 chr6B 86.280 328 36 5 2876 3202 402179609 402179928 6.630000e-92 348.0
13 TraesCS3B01G438800 chr6B 94.958 119 6 0 369 487 365062947 365063065 1.530000e-43 187.0
14 TraesCS3B01G438800 chr6B 89.320 103 11 0 2772 2874 402179656 402179758 2.610000e-26 130.0
15 TraesCS3B01G438800 chr5A 87.892 223 21 5 2977 3197 677904601 677904819 1.150000e-64 257.0
16 TraesCS3B01G438800 chr5A 90.132 152 12 2 2877 3027 677902349 677902498 9.140000e-46 195.0
17 TraesCS3B01G438800 chr5A 83.408 223 21 4 2772 2993 677902697 677902904 3.290000e-45 193.0
18 TraesCS3B01G438800 chr5A 95.798 119 4 1 372 489 39114698 39114816 1.180000e-44 191.0
19 TraesCS3B01G438800 chr6A 97.436 117 3 0 371 487 117376356 117376240 1.960000e-47 200.0
20 TraesCS3B01G438800 chr7B 95.868 121 4 1 371 491 456489744 456489863 9.140000e-46 195.0
21 TraesCS3B01G438800 chr7B 97.436 39 1 0 3190 3228 394860388 394860426 2.080000e-07 67.6
22 TraesCS3B01G438800 chr7B 97.436 39 1 0 3190 3228 394908328 394908366 2.080000e-07 67.6
23 TraesCS3B01G438800 chr7B 95.349 43 0 2 3188 3228 702682009 702682051 2.080000e-07 67.6
24 TraesCS3B01G438800 chr4D 93.701 127 7 1 372 498 302003833 302003958 4.250000e-44 189.0
25 TraesCS3B01G438800 chr4D 93.478 46 2 1 3183 3228 393840411 393840455 2.080000e-07 67.6
26 TraesCS3B01G438800 chr2B 93.600 125 8 0 372 496 678549128 678549252 1.530000e-43 187.0
27 TraesCS3B01G438800 chr2B 95.238 42 1 1 3188 3228 749158195 749158154 7.480000e-07 65.8
28 TraesCS3B01G438800 chr1B 93.600 125 8 0 371 495 22196781 22196657 1.530000e-43 187.0
29 TraesCS3B01G438800 chr7D 95.349 43 1 1 3187 3228 303094451 303094409 2.080000e-07 67.6
30 TraesCS3B01G438800 chr6D 95.238 42 1 1 3188 3228 305004601 305004560 7.480000e-07 65.8
31 TraesCS3B01G438800 chr4B 93.333 45 1 2 3184 3228 381258390 381258432 7.480000e-07 65.8
32 TraesCS3B01G438800 chr1D 95.238 42 1 1 3187 3228 47331096 47331056 7.480000e-07 65.8


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 TraesCS3B01G438800 chr3B 677997760 678000987 3227 False 5962 5962 100.00000 1 3228 1 chr3B.!!$F3 3227
1 TraesCS3B01G438800 chr3B 654159389 654160611 1222 False 1853 1853 94.09900 1118 2338 1 chr3B.!!$F2 1220
2 TraesCS3B01G438800 chr3B 654153074 654153661 587 False 793 793 91.22500 535 1123 1 chr3B.!!$F1 588
3 TraesCS3B01G438800 chr3A 649812616 649817458 4842 False 740 2388 89.95475 15 2778 4 chr3A.!!$F1 2763
4 TraesCS3B01G438800 chr3D 515263052 515265032 1980 False 1282 2379 92.51350 523 2778 2 chr3D.!!$F1 2255
5 TraesCS3B01G438800 chr5A 677902349 677904819 2470 False 215 257 87.14400 2772 3197 3 chr5A.!!$F2 425

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
483 1831 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 3845 0.107654 GTTGCCTAGGTCAAGCGGAT 60.108 55.0 16.04 0.0 0.0 4.18 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
104 414 7.228706 GTGAAACTTATCCTTCTGTTCCTTGAA 59.771 37.037 0.00 0.00 0.00 2.69
105 415 7.944554 TGAAACTTATCCTTCTGTTCCTTGAAT 59.055 33.333 0.00 0.00 0.00 2.57
106 416 8.712228 AAACTTATCCTTCTGTTCCTTGAATT 57.288 30.769 0.00 0.00 0.00 2.17
107 417 7.693969 ACTTATCCTTCTGTTCCTTGAATTG 57.306 36.000 0.00 0.00 0.00 2.32
123 433 7.277539 TCCTTGAATTGTGTGTTGAATTTTGAC 59.722 33.333 0.00 0.00 0.00 3.18
126 436 7.776107 TGAATTGTGTGTTGAATTTTGACCTA 58.224 30.769 0.00 0.00 0.00 3.08
127 437 8.420222 TGAATTGTGTGTTGAATTTTGACCTAT 58.580 29.630 0.00 0.00 0.00 2.57
128 438 9.906660 GAATTGTGTGTTGAATTTTGACCTATA 57.093 29.630 0.00 0.00 0.00 1.31
135 445 8.349983 GTGTTGAATTTTGACCTATAACTGTGT 58.650 33.333 0.00 0.00 0.00 3.72
149 459 9.856488 CCTATAACTGTGTGACATGGTATATAC 57.144 37.037 4.14 4.14 0.00 1.47
165 491 8.644374 TGGTATATACATGCTGTATGAGTGTA 57.356 34.615 14.70 0.00 42.93 2.90
166 492 8.739972 TGGTATATACATGCTGTATGAGTGTAG 58.260 37.037 14.70 0.00 42.93 2.74
167 493 8.740906 GGTATATACATGCTGTATGAGTGTAGT 58.259 37.037 14.70 0.00 42.93 2.73
222 548 3.402628 TTGAGTGCTGAACTAAGGGTC 57.597 47.619 0.00 0.00 40.07 4.46
224 550 2.300152 TGAGTGCTGAACTAAGGGTCTG 59.700 50.000 0.00 0.00 40.07 3.51
264 1612 1.978580 GTGTACCCCATATCCCTCCAG 59.021 57.143 0.00 0.00 0.00 3.86
265 1613 0.984995 GTACCCCATATCCCTCCAGC 59.015 60.000 0.00 0.00 0.00 4.85
266 1614 0.178873 TACCCCATATCCCTCCAGCC 60.179 60.000 0.00 0.00 0.00 4.85
267 1615 1.151721 CCCCATATCCCTCCAGCCT 60.152 63.158 0.00 0.00 0.00 4.58
268 1616 1.204113 CCCCATATCCCTCCAGCCTC 61.204 65.000 0.00 0.00 0.00 4.70
269 1617 1.204113 CCCATATCCCTCCAGCCTCC 61.204 65.000 0.00 0.00 0.00 4.30
270 1618 0.474466 CCATATCCCTCCAGCCTCCA 60.474 60.000 0.00 0.00 0.00 3.86
271 1619 0.982704 CATATCCCTCCAGCCTCCAG 59.017 60.000 0.00 0.00 0.00 3.86
272 1620 0.178879 ATATCCCTCCAGCCTCCAGG 60.179 60.000 0.00 0.00 38.53 4.45
304 1652 2.818921 TGGGCATTTACCAGCATCTTT 58.181 42.857 0.00 0.00 33.23 2.52
326 1674 9.847224 TCTTTAACCTGTTTCTTCTTCAGTTAT 57.153 29.630 0.00 0.00 0.00 1.89
362 1710 2.872858 GCGTAGAGAAAATGATGACCCC 59.127 50.000 0.00 0.00 0.00 4.95
375 1723 5.871396 TGATGACCCCTAAACAGATACTC 57.129 43.478 0.00 0.00 0.00 2.59
376 1724 4.654262 TGATGACCCCTAAACAGATACTCC 59.346 45.833 0.00 0.00 0.00 3.85
378 1726 3.013648 TGACCCCTAAACAGATACTCCCT 59.986 47.826 0.00 0.00 0.00 4.20
380 1728 2.973406 CCCCTAAACAGATACTCCCTCC 59.027 54.545 0.00 0.00 0.00 4.30
381 1729 2.628657 CCCTAAACAGATACTCCCTCCG 59.371 54.545 0.00 0.00 0.00 4.63
382 1730 3.297736 CCTAAACAGATACTCCCTCCGT 58.702 50.000 0.00 0.00 0.00 4.69
383 1731 3.318557 CCTAAACAGATACTCCCTCCGTC 59.681 52.174 0.00 0.00 0.00 4.79
384 1732 1.777941 AACAGATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
385 1733 0.629596 ACAGATACTCCCTCCGTCCA 59.370 55.000 0.00 0.00 0.00 4.02
386 1734 1.006758 ACAGATACTCCCTCCGTCCAA 59.993 52.381 0.00 0.00 0.00 3.53
387 1735 2.108168 CAGATACTCCCTCCGTCCAAA 58.892 52.381 0.00 0.00 0.00 3.28
388 1736 2.500098 CAGATACTCCCTCCGTCCAAAA 59.500 50.000 0.00 0.00 0.00 2.44
389 1737 3.055385 CAGATACTCCCTCCGTCCAAAAA 60.055 47.826 0.00 0.00 0.00 1.94
390 1738 3.780850 AGATACTCCCTCCGTCCAAAAAT 59.219 43.478 0.00 0.00 0.00 1.82
391 1739 4.966805 AGATACTCCCTCCGTCCAAAAATA 59.033 41.667 0.00 0.00 0.00 1.40
392 1740 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
393 1741 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
394 1742 3.329814 ACTCCCTCCGTCCAAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
395 1743 3.681593 TCCCTCCGTCCAAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
396 1744 3.073356 TCCCTCCGTCCAAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
397 1745 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
398 1746 3.439129 CCTCCGTCCAAAAATACTTGTCC 59.561 47.826 0.00 0.00 0.00 4.02
399 1747 4.324267 CTCCGTCCAAAAATACTTGTCCT 58.676 43.478 0.00 0.00 0.00 3.85
400 1748 4.320870 TCCGTCCAAAAATACTTGTCCTC 58.679 43.478 0.00 0.00 0.00 3.71
401 1749 3.124636 CCGTCCAAAAATACTTGTCCTCG 59.875 47.826 0.00 0.00 0.00 4.63
402 1750 3.991773 CGTCCAAAAATACTTGTCCTCGA 59.008 43.478 0.00 0.00 0.00 4.04
403 1751 4.449743 CGTCCAAAAATACTTGTCCTCGAA 59.550 41.667 0.00 0.00 0.00 3.71
404 1752 5.049954 CGTCCAAAAATACTTGTCCTCGAAA 60.050 40.000 0.00 0.00 0.00 3.46
405 1753 6.348213 CGTCCAAAAATACTTGTCCTCGAAAT 60.348 38.462 0.00 0.00 0.00 2.17
406 1754 6.801862 GTCCAAAAATACTTGTCCTCGAAATG 59.198 38.462 0.00 0.00 0.00 2.32
407 1755 6.072175 TCCAAAAATACTTGTCCTCGAAATGG 60.072 38.462 0.00 0.00 0.00 3.16
408 1756 6.294508 CCAAAAATACTTGTCCTCGAAATGGT 60.295 38.462 0.00 0.00 0.00 3.55
409 1757 6.894339 AAAATACTTGTCCTCGAAATGGTT 57.106 33.333 0.00 0.00 0.00 3.67
410 1758 5.880054 AATACTTGTCCTCGAAATGGTTG 57.120 39.130 0.00 0.00 0.00 3.77
411 1759 3.208747 ACTTGTCCTCGAAATGGTTGT 57.791 42.857 0.00 0.00 0.00 3.32
412 1760 4.345859 ACTTGTCCTCGAAATGGTTGTA 57.654 40.909 0.00 0.00 0.00 2.41
413 1761 4.906618 ACTTGTCCTCGAAATGGTTGTAT 58.093 39.130 0.00 0.00 0.00 2.29
414 1762 4.935808 ACTTGTCCTCGAAATGGTTGTATC 59.064 41.667 0.00 0.00 0.00 2.24
415 1763 4.819105 TGTCCTCGAAATGGTTGTATCT 57.181 40.909 0.00 0.00 0.00 1.98
416 1764 5.925506 TGTCCTCGAAATGGTTGTATCTA 57.074 39.130 0.00 0.00 0.00 1.98
417 1765 5.902681 TGTCCTCGAAATGGTTGTATCTAG 58.097 41.667 0.00 0.00 0.00 2.43
418 1766 5.655090 TGTCCTCGAAATGGTTGTATCTAGA 59.345 40.000 0.00 0.00 0.00 2.43
419 1767 5.978322 GTCCTCGAAATGGTTGTATCTAGAC 59.022 44.000 0.00 0.00 0.00 2.59
420 1768 5.892119 TCCTCGAAATGGTTGTATCTAGACT 59.108 40.000 0.00 0.00 0.00 3.24
421 1769 6.380274 TCCTCGAAATGGTTGTATCTAGACTT 59.620 38.462 0.00 0.00 0.00 3.01
422 1770 7.558807 TCCTCGAAATGGTTGTATCTAGACTTA 59.441 37.037 0.00 0.00 0.00 2.24
423 1771 8.361139 CCTCGAAATGGTTGTATCTAGACTTAT 58.639 37.037 0.00 0.00 0.00 1.73
424 1772 9.751542 CTCGAAATGGTTGTATCTAGACTTATT 57.248 33.333 0.00 0.00 0.00 1.40
473 1821 6.494893 TCATTTTGAGGACAAGTATTTCCG 57.505 37.500 0.00 0.00 36.95 4.30
474 1822 5.414454 TCATTTTGAGGACAAGTATTTCCGG 59.586 40.000 0.00 0.00 36.95 5.14
475 1823 4.627284 TTTGAGGACAAGTATTTCCGGA 57.373 40.909 0.00 0.00 36.95 5.14
476 1824 3.604875 TGAGGACAAGTATTTCCGGAC 57.395 47.619 1.83 0.00 36.95 4.79
477 1825 2.094390 TGAGGACAAGTATTTCCGGACG 60.094 50.000 1.83 0.00 36.95 4.79
478 1826 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
479 1827 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
480 1828 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
481 1829 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
482 1830 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
483 1831 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
484 1832 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
485 1833 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
486 1834 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
487 1835 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
488 1836 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
489 1837 1.379576 CCGGACGGAGGGAGTACTT 60.380 63.158 4.40 0.00 37.50 2.24
490 1838 0.107017 CCGGACGGAGGGAGTACTTA 60.107 60.000 4.40 0.00 37.50 2.24
491 1839 1.020437 CGGACGGAGGGAGTACTTAC 58.980 60.000 0.00 0.00 0.00 2.34
492 1840 1.020437 GGACGGAGGGAGTACTTACG 58.980 60.000 0.00 0.00 0.00 3.18
493 1841 1.680249 GGACGGAGGGAGTACTTACGT 60.680 57.143 2.96 2.96 37.17 3.57
548 1896 6.429385 GCCTTAGATCACAGAAAATATCCAGG 59.571 42.308 0.00 0.00 0.00 4.45
709 2063 0.877071 CCAAAGGCTACAGCACACAG 59.123 55.000 3.24 0.00 44.36 3.66
787 2141 3.044305 GTGTCCTGTGTGCCGCTC 61.044 66.667 0.00 0.00 0.00 5.03
833 2187 1.593006 GTACGTGATGGCTGTGTATGC 59.407 52.381 0.00 0.00 0.00 3.14
899 2253 1.458588 ATTCCTCGCCTCCTCCTCC 60.459 63.158 0.00 0.00 0.00 4.30
934 2290 2.350804 CACTCCATCACAAGATTCGCAG 59.649 50.000 0.00 0.00 30.20 5.18
978 2353 0.178950 AGTGAGACTGAGACCAGCCA 60.179 55.000 0.00 0.00 44.16 4.75
1089 2475 4.748102 TCGATCTGCTTACTTTGACGTTTT 59.252 37.500 0.00 0.00 0.00 2.43
1283 2682 5.923684 CCTAGCTAGCTAGTTCATTAAGCAC 59.076 44.000 37.50 0.88 43.22 4.40
1284 2683 4.363999 AGCTAGCTAGTTCATTAAGCACG 58.636 43.478 17.69 0.00 38.75 5.34
1285 2684 4.098044 AGCTAGCTAGTTCATTAAGCACGA 59.902 41.667 17.69 0.00 38.75 4.35
1286 2685 4.442733 GCTAGCTAGTTCATTAAGCACGAG 59.557 45.833 21.62 0.00 38.75 4.18
1467 2878 4.424566 TCGCCAACGAGTACGGCC 62.425 66.667 9.97 0.00 45.12 6.13
1664 3084 3.197983 CGTTCCCTTCCCTTGTATCTTCT 59.802 47.826 0.00 0.00 0.00 2.85
1677 3097 7.601886 CCCTTGTATCTTCTCTTGCAGTATATG 59.398 40.741 0.00 0.00 0.00 1.78
1700 3125 2.661866 GAACTGACAGTGCGCGGT 60.662 61.111 9.33 1.67 0.00 5.68
1720 3148 4.448060 CGGTTGAGTTAAACAGAAGAGGAC 59.552 45.833 0.00 0.00 0.00 3.85
1763 3194 1.601759 GGGAGTGAAAGCAGCAGCA 60.602 57.895 3.17 0.00 45.49 4.41
1767 3198 0.815213 AGTGAAAGCAGCAGCAACGA 60.815 50.000 3.17 0.00 45.49 3.85
1896 3330 0.606944 AAATTAACGTGCGCCCCTCA 60.607 50.000 4.18 0.00 0.00 3.86
1912 3351 2.159338 CCCTCATCGCATCTTTGGTTTG 60.159 50.000 0.00 0.00 0.00 2.93
2333 3784 7.599621 TGTTGGATGAATGAACTGCTTTTATTG 59.400 33.333 0.00 0.00 0.00 1.90
2381 3832 1.807755 GCGATGAGCTGCTAACCATCA 60.808 52.381 22.08 9.34 44.04 3.07
2388 3839 3.758554 GAGCTGCTAACCATCAAGGAAAA 59.241 43.478 0.15 0.00 41.22 2.29
2415 3866 2.100631 CGCTTGACCTAGGCAACCG 61.101 63.158 9.30 12.96 37.17 4.44
2464 4100 3.634504 TGAACAAATCATGGGAGATGGG 58.365 45.455 0.00 0.00 31.50 4.00
2467 4103 2.176364 ACAAATCATGGGAGATGGGAGG 59.824 50.000 0.00 0.00 0.00 4.30
2487 4123 4.918588 AGGGATCCAAACAATAGAAACGT 58.081 39.130 15.23 0.00 0.00 3.99
2492 4128 7.094506 GGGATCCAAACAATAGAAACGTTAGTT 60.095 37.037 15.23 0.00 43.50 2.24
2493 4129 8.938906 GGATCCAAACAATAGAAACGTTAGTTA 58.061 33.333 6.95 0.00 40.18 2.24
2512 4148 9.043079 GTTAGTTAATTATTACAGGACTGAGGC 57.957 37.037 6.29 0.00 0.00 4.70
2517 4153 3.802948 ATTACAGGACTGAGGCTAACG 57.197 47.619 6.29 0.00 0.00 3.18
2521 4157 1.067821 CAGGACTGAGGCTAACGGATC 59.932 57.143 0.00 0.00 0.00 3.36
2526 4162 0.616395 TGAGGCTAACGGATCACCCA 60.616 55.000 0.00 0.00 34.14 4.51
2527 4163 0.539986 GAGGCTAACGGATCACCCAA 59.460 55.000 0.00 0.00 34.14 4.12
2546 4879 6.018751 CACCCAATCGATACACAAGAATACAG 60.019 42.308 0.00 0.00 0.00 2.74
2565 4898 2.341760 CAGCTCGAACGTTTACTGCTAC 59.658 50.000 0.46 0.00 0.00 3.58
2566 4899 1.652619 GCTCGAACGTTTACTGCTACC 59.347 52.381 0.46 0.00 0.00 3.18
2567 4900 2.923605 GCTCGAACGTTTACTGCTACCA 60.924 50.000 0.46 0.00 0.00 3.25
2568 4901 2.915463 CTCGAACGTTTACTGCTACCAG 59.085 50.000 0.46 0.00 44.80 4.00
2569 4902 1.389106 CGAACGTTTACTGCTACCAGC 59.611 52.381 0.46 0.00 43.02 4.85
2570 4903 1.389106 GAACGTTTACTGCTACCAGCG 59.611 52.381 0.46 0.00 46.26 5.18
2594 4927 2.528041 AAGTTCAGACGACCCAACTC 57.472 50.000 0.00 0.00 0.00 3.01
2595 4928 1.705873 AGTTCAGACGACCCAACTCT 58.294 50.000 0.00 0.00 0.00 3.24
2603 4936 2.801111 GACGACCCAACTCTTGTTTCTC 59.199 50.000 0.00 0.00 33.52 2.87
2608 4941 2.143925 CCAACTCTTGTTTCTCCGTCC 58.856 52.381 0.00 0.00 33.52 4.79
2620 4953 2.125202 CTCCGTCCGTGCCAAAAACC 62.125 60.000 0.00 0.00 0.00 3.27
2624 4957 0.594602 GTCCGTGCCAAAAACCCTAC 59.405 55.000 0.00 0.00 0.00 3.18
2628 4961 1.001815 CGTGCCAAAAACCCTACACAG 60.002 52.381 0.00 0.00 0.00 3.66
2629 4962 2.028876 GTGCCAAAAACCCTACACAGT 58.971 47.619 0.00 0.00 0.00 3.55
2653 4986 7.442969 AGTTAATCAGAGTCCTATCTACACTCG 59.557 40.741 0.00 0.00 41.32 4.18
2659 4992 4.465886 AGTCCTATCTACACTCGCTCAAT 58.534 43.478 0.00 0.00 0.00 2.57
2708 5041 2.081462 CACATCTTGCTGCTCATCACA 58.919 47.619 0.00 0.00 0.00 3.58
2774 5108 0.319555 TCGCCTTCTGGAACTGAACG 60.320 55.000 0.00 0.00 41.26 3.95
2775 5109 1.869690 GCCTTCTGGAACTGAACGC 59.130 57.895 0.00 0.00 41.26 4.84
2781 5115 5.300752 CCTTCTGGAACTGAACGCATATAT 58.699 41.667 0.00 0.00 41.26 0.86
2782 5116 5.760253 CCTTCTGGAACTGAACGCATATATT 59.240 40.000 0.00 0.00 41.26 1.28
2798 5132 8.076178 ACGCATATATTCTGTTTAAGCAAATCC 58.924 33.333 0.00 0.00 0.00 3.01
2815 5149 2.094659 CCAGTGCTACCGTGAAGCG 61.095 63.158 0.00 0.00 43.11 4.68
2818 5152 2.092882 GTGCTACCGTGAAGCGACC 61.093 63.158 0.00 0.00 43.11 4.79
2846 5330 4.279420 TGAGCTACTACATGCTACCTGATG 59.721 45.833 0.00 0.00 39.91 3.07
2851 5335 3.969976 ACTACATGCTACCTGATGACCAT 59.030 43.478 0.00 0.00 0.00 3.55
2896 5713 5.059833 ACTGACAAAAACAAAAAGGTGCAA 58.940 33.333 0.00 0.00 0.00 4.08
2897 5714 5.704978 ACTGACAAAAACAAAAAGGTGCAAT 59.295 32.000 0.00 0.00 0.00 3.56
2900 5717 4.217118 ACAAAAACAAAAAGGTGCAATGCA 59.783 33.333 2.72 2.72 35.60 3.96
2901 5718 5.159209 CAAAAACAAAAAGGTGCAATGCAA 58.841 33.333 10.44 0.00 41.47 4.08
2902 5719 5.382618 AAAACAAAAAGGTGCAATGCAAA 57.617 30.435 10.44 0.00 41.47 3.68
2936 5753 6.284459 GCTGGAAGTAAGCAACTCATATACT 58.716 40.000 0.00 0.00 40.52 2.12
2937 5754 6.422400 GCTGGAAGTAAGCAACTCATATACTC 59.578 42.308 0.00 0.00 40.52 2.59
2953 5770 8.365399 TCATATACTCTGTTTAAGCAAATCCG 57.635 34.615 0.00 0.00 0.00 4.18
2956 5773 4.142038 ACTCTGTTTAAGCAAATCCGGTT 58.858 39.130 0.00 0.00 0.00 4.44
2961 5778 4.456566 TGTTTAAGCAAATCCGGTTCTACC 59.543 41.667 0.00 0.00 34.05 3.18
2973 5790 2.067013 GGTTCTACCGTGAAGCAACTC 58.933 52.381 0.00 0.00 42.14 3.01
2978 7316 2.386661 ACCGTGAAGCAACTCCTATG 57.613 50.000 0.00 0.00 0.00 2.23
2995 7333 5.631119 TCCTATGAGCTACTACATGCTACA 58.369 41.667 0.00 0.00 39.91 2.74
2996 7334 6.249192 TCCTATGAGCTACTACATGCTACAT 58.751 40.000 0.00 0.00 39.91 2.29
3009 7347 1.764723 TGCTACATGATGACCAGGGAG 59.235 52.381 0.00 0.00 40.39 4.30
3056 7395 3.361977 CGTTTGGCACCTTCGGGG 61.362 66.667 0.00 0.00 40.03 5.73
3092 7431 9.018716 TGCGATACTTATTGCAAATATTGTTTG 57.981 29.630 1.71 1.83 46.95 2.93
3098 7437 9.369904 ACTTATTGCAAATATTGTTTGTCATCC 57.630 29.630 1.71 0.00 0.00 3.51
3101 7440 6.587206 TGCAAATATTGTTTGTCATCCTGA 57.413 33.333 7.57 0.00 0.00 3.86
3138 7477 9.615295 ACAAAATGCATGCTAATTTTTCATTTC 57.385 25.926 20.31 0.00 34.55 2.17
3140 7479 8.570068 AAATGCATGCTAATTTTTCATTTCCT 57.430 26.923 20.33 0.00 29.81 3.36
3143 7482 6.814644 TGCATGCTAATTTTTCATTTCCTCAG 59.185 34.615 20.33 0.00 0.00 3.35
3180 7519 6.017109 GTGTCATATGCCAACTAAATGTAGGG 60.017 42.308 0.00 0.00 0.00 3.53
3181 7520 6.126623 TGTCATATGCCAACTAAATGTAGGGA 60.127 38.462 0.00 0.00 0.00 4.20
3185 7524 8.950210 CATATGCCAACTAAATGTAGGGAATAG 58.050 37.037 0.00 0.00 31.33 1.73
3189 7528 8.058847 TGCCAACTAAATGTAGGGAATAGAAAT 58.941 33.333 0.00 0.00 0.00 2.17
3213 7552 8.904099 ATTTTAAGAAACTAGATGATACCCCG 57.096 34.615 0.00 0.00 0.00 5.73
3214 7553 4.338379 AAGAAACTAGATGATACCCCGC 57.662 45.455 0.00 0.00 0.00 6.13
3215 7554 2.296471 AGAAACTAGATGATACCCCGCG 59.704 50.000 0.00 0.00 0.00 6.46
3216 7555 0.317479 AACTAGATGATACCCCGCGC 59.683 55.000 0.00 0.00 0.00 6.86
3217 7556 1.154016 CTAGATGATACCCCGCGCG 60.154 63.158 25.67 25.67 0.00 6.86
3218 7557 1.863662 CTAGATGATACCCCGCGCGT 61.864 60.000 29.95 13.36 0.00 6.01
3219 7558 1.457823 TAGATGATACCCCGCGCGTT 61.458 55.000 29.95 14.98 0.00 4.84
3220 7559 2.587753 ATGATACCCCGCGCGTTG 60.588 61.111 29.95 21.02 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.552355 TGAGAGCTTGCAATTTTCATGTG 58.448 39.130 0.00 0.00 0.00 3.21
4 5 5.008619 TGTTTGAGAGCTTGCAATTTTCA 57.991 34.783 0.00 0.00 0.00 2.69
5 6 5.971895 TTGTTTGAGAGCTTGCAATTTTC 57.028 34.783 0.00 0.00 0.00 2.29
8 9 5.422145 ACTTTTGTTTGAGAGCTTGCAATT 58.578 33.333 0.00 0.00 0.00 2.32
10 11 4.082300 TGACTTTTGTTTGAGAGCTTGCAA 60.082 37.500 0.00 0.00 0.00 4.08
11 12 3.443329 TGACTTTTGTTTGAGAGCTTGCA 59.557 39.130 0.00 0.00 0.00 4.08
12 13 4.032703 TGACTTTTGTTTGAGAGCTTGC 57.967 40.909 0.00 0.00 0.00 4.01
13 14 6.183360 GGTTTTGACTTTTGTTTGAGAGCTTG 60.183 38.462 0.00 0.00 0.00 4.01
104 414 9.691362 GTTATAGGTCAAAATTCAACACACAAT 57.309 29.630 0.00 0.00 0.00 2.71
105 415 8.908903 AGTTATAGGTCAAAATTCAACACACAA 58.091 29.630 0.00 0.00 0.00 3.33
106 416 8.349245 CAGTTATAGGTCAAAATTCAACACACA 58.651 33.333 0.00 0.00 0.00 3.72
107 417 8.349983 ACAGTTATAGGTCAAAATTCAACACAC 58.650 33.333 0.00 0.00 0.00 3.82
123 433 9.856488 GTATATACCATGTCACACAGTTATAGG 57.144 37.037 1.02 0.00 0.00 2.57
126 436 9.710900 CATGTATATACCATGTCACACAGTTAT 57.289 33.333 10.38 0.00 0.00 1.89
127 437 7.655732 GCATGTATATACCATGTCACACAGTTA 59.344 37.037 10.38 0.00 0.00 2.24
128 438 6.483307 GCATGTATATACCATGTCACACAGTT 59.517 38.462 10.38 0.00 0.00 3.16
149 459 6.915544 AATGAACTACACTCATACAGCATG 57.084 37.500 0.00 0.00 35.61 4.06
181 507 6.454795 TCAAAGCGCCTTGAAAATATCTTTT 58.545 32.000 18.78 0.00 37.28 2.27
185 511 4.795278 CACTCAAAGCGCCTTGAAAATATC 59.205 41.667 21.07 0.00 34.96 1.63
188 514 2.863704 GCACTCAAAGCGCCTTGAAAAT 60.864 45.455 21.07 8.20 34.96 1.82
277 1625 0.252012 TGGTAAATGCCCAACCCTGG 60.252 55.000 0.00 0.00 43.10 4.45
278 1626 1.185315 CTGGTAAATGCCCAACCCTG 58.815 55.000 0.00 0.00 31.97 4.45
279 1627 0.614697 GCTGGTAAATGCCCAACCCT 60.615 55.000 0.00 0.00 31.97 4.34
326 1674 0.394938 TACGCAGAGCCAAACCAGAA 59.605 50.000 0.00 0.00 0.00 3.02
352 1700 5.308237 GGAGTATCTGTTTAGGGGTCATCAT 59.692 44.000 0.00 0.00 33.73 2.45
362 1710 3.318557 GGACGGAGGGAGTATCTGTTTAG 59.681 52.174 0.00 0.00 36.41 1.85
375 1723 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
376 1724 3.439129 GGACAAGTATTTTTGGACGGAGG 59.561 47.826 0.00 0.00 32.32 4.30
378 1726 4.320870 GAGGACAAGTATTTTTGGACGGA 58.679 43.478 0.00 0.00 32.32 4.69
380 1728 3.991773 TCGAGGACAAGTATTTTTGGACG 59.008 43.478 0.00 0.00 32.32 4.79
381 1729 5.934935 TTCGAGGACAAGTATTTTTGGAC 57.065 39.130 0.00 0.00 32.32 4.02
382 1730 6.072175 CCATTTCGAGGACAAGTATTTTTGGA 60.072 38.462 0.00 0.00 32.32 3.53
383 1731 6.092748 CCATTTCGAGGACAAGTATTTTTGG 58.907 40.000 0.00 0.00 32.32 3.28
384 1732 6.677913 ACCATTTCGAGGACAAGTATTTTTG 58.322 36.000 0.00 0.00 0.00 2.44
385 1733 6.894339 ACCATTTCGAGGACAAGTATTTTT 57.106 33.333 0.00 0.00 0.00 1.94
386 1734 6.264518 ACAACCATTTCGAGGACAAGTATTTT 59.735 34.615 0.00 0.00 0.00 1.82
387 1735 5.768164 ACAACCATTTCGAGGACAAGTATTT 59.232 36.000 0.00 0.00 0.00 1.40
388 1736 5.313712 ACAACCATTTCGAGGACAAGTATT 58.686 37.500 0.00 0.00 0.00 1.89
389 1737 4.906618 ACAACCATTTCGAGGACAAGTAT 58.093 39.130 0.00 0.00 0.00 2.12
390 1738 4.345859 ACAACCATTTCGAGGACAAGTA 57.654 40.909 0.00 0.00 0.00 2.24
391 1739 3.208747 ACAACCATTTCGAGGACAAGT 57.791 42.857 0.00 0.00 0.00 3.16
392 1740 5.178797 AGATACAACCATTTCGAGGACAAG 58.821 41.667 0.00 0.00 0.00 3.16
393 1741 5.160607 AGATACAACCATTTCGAGGACAA 57.839 39.130 0.00 0.00 0.00 3.18
394 1742 4.819105 AGATACAACCATTTCGAGGACA 57.181 40.909 0.00 0.00 0.00 4.02
395 1743 5.978322 GTCTAGATACAACCATTTCGAGGAC 59.022 44.000 0.00 0.00 0.00 3.85
396 1744 5.892119 AGTCTAGATACAACCATTTCGAGGA 59.108 40.000 0.00 0.00 0.00 3.71
397 1745 6.150396 AGTCTAGATACAACCATTTCGAGG 57.850 41.667 0.00 0.00 0.00 4.63
398 1746 9.751542 AATAAGTCTAGATACAACCATTTCGAG 57.248 33.333 0.00 0.00 0.00 4.04
447 1795 8.673711 CGGAAATACTTGTCCTCAAAATGAATA 58.326 33.333 0.00 0.00 32.87 1.75
448 1796 7.362920 CCGGAAATACTTGTCCTCAAAATGAAT 60.363 37.037 0.00 0.00 32.87 2.57
449 1797 6.072175 CCGGAAATACTTGTCCTCAAAATGAA 60.072 38.462 0.00 0.00 32.87 2.57
450 1798 5.414454 CCGGAAATACTTGTCCTCAAAATGA 59.586 40.000 0.00 0.00 32.87 2.57
451 1799 5.414454 TCCGGAAATACTTGTCCTCAAAATG 59.586 40.000 0.00 0.00 32.87 2.32
452 1800 5.414765 GTCCGGAAATACTTGTCCTCAAAAT 59.585 40.000 5.23 0.00 32.87 1.82
453 1801 4.758165 GTCCGGAAATACTTGTCCTCAAAA 59.242 41.667 5.23 0.00 32.87 2.44
454 1802 4.320870 GTCCGGAAATACTTGTCCTCAAA 58.679 43.478 5.23 0.00 32.87 2.69
455 1803 3.615592 CGTCCGGAAATACTTGTCCTCAA 60.616 47.826 5.23 0.00 0.00 3.02
456 1804 2.094390 CGTCCGGAAATACTTGTCCTCA 60.094 50.000 5.23 0.00 0.00 3.86
457 1805 2.537401 CGTCCGGAAATACTTGTCCTC 58.463 52.381 5.23 0.00 0.00 3.71
458 1806 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
459 1807 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
460 1808 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
461 1809 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
462 1810 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
463 1811 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
464 1812 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
465 1813 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
466 1814 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
467 1815 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
468 1816 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
469 1817 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
470 1818 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
471 1819 0.107017 TAAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
472 1820 1.020437 GTAAGTACTCCCTCCGTCCG 58.980 60.000 0.00 0.00 0.00 4.79
473 1821 1.020437 CGTAAGTACTCCCTCCGTCC 58.980 60.000 0.00 0.00 0.00 4.79
517 1865 3.257469 TCTGTGATCTAAGGCTGCTTG 57.743 47.619 0.00 0.00 0.00 4.01
531 1879 5.670792 ACGTACCTGGATATTTTCTGTGA 57.329 39.130 0.00 0.00 0.00 3.58
565 1913 0.249657 GCTACTCTTCCCCGAGCATG 60.250 60.000 0.00 0.00 34.35 4.06
570 1918 2.022754 GCTACAGCTACTCTTCCCCGA 61.023 57.143 0.00 0.00 38.21 5.14
727 2081 1.959226 GGCAGCGAACACCGAAAGA 60.959 57.895 0.00 0.00 41.76 2.52
787 2141 2.350772 CGTTTGCCACTTCTTAGCAAGG 60.351 50.000 0.00 0.00 46.30 3.61
899 2253 1.768077 GAGTGGGATGGGAGGAGGG 60.768 68.421 0.00 0.00 0.00 4.30
934 2290 1.841103 GATGGGAGGAGGAGGAGGC 60.841 68.421 0.00 0.00 0.00 4.70
991 2366 1.741706 CAGAATCACCATGGAGCACAC 59.258 52.381 21.47 5.17 0.00 3.82
992 2367 1.951895 GCAGAATCACCATGGAGCACA 60.952 52.381 21.47 0.00 0.00 4.57
1043 2422 1.524008 GGTGGTGCTTCCTTTTCCGG 61.524 60.000 0.00 0.00 37.07 5.14
1044 2423 0.821711 TGGTGGTGCTTCCTTTTCCG 60.822 55.000 0.80 0.00 37.07 4.30
1045 2424 0.961753 CTGGTGGTGCTTCCTTTTCC 59.038 55.000 0.80 0.00 37.07 3.13
1046 2425 1.692411 ACTGGTGGTGCTTCCTTTTC 58.308 50.000 0.80 0.00 37.07 2.29
1047 2426 2.031870 GAACTGGTGGTGCTTCCTTTT 58.968 47.619 0.80 0.00 37.07 2.27
1048 2427 1.692411 GAACTGGTGGTGCTTCCTTT 58.308 50.000 0.80 0.00 37.07 3.11
1053 2432 0.687354 AGATCGAACTGGTGGTGCTT 59.313 50.000 0.00 0.00 0.00 3.91
1214 2603 2.678934 CTCCCAGGACGTTCCGGA 60.679 66.667 0.00 0.00 42.75 5.14
1269 2668 3.119602 ACTCGCTCGTGCTTAATGAACTA 60.120 43.478 7.97 0.00 36.97 2.24
1270 2669 2.263077 CTCGCTCGTGCTTAATGAACT 58.737 47.619 7.97 0.00 36.97 3.01
1271 2670 1.993370 ACTCGCTCGTGCTTAATGAAC 59.007 47.619 7.97 0.00 36.97 3.18
1272 2671 2.363788 ACTCGCTCGTGCTTAATGAA 57.636 45.000 7.97 0.00 36.97 2.57
1291 2690 2.507886 AGAGAGATGGGAGAGAGACGAA 59.492 50.000 0.00 0.00 0.00 3.85
1347 2758 2.671177 CGAACTTGTCAGGCAGCGG 61.671 63.158 0.00 0.00 0.00 5.52
1348 2759 1.956170 ACGAACTTGTCAGGCAGCG 60.956 57.895 0.00 0.00 0.00 5.18
1467 2878 3.129502 CCTGCCGAGGTGCATGTG 61.130 66.667 0.00 0.00 41.16 3.21
1664 3084 4.716784 AGTTCCAGGACATATACTGCAAGA 59.283 41.667 0.00 0.00 35.10 3.02
1677 3097 0.946221 CGCACTGTCAGTTCCAGGAC 60.946 60.000 1.67 0.00 34.16 3.85
1700 3125 5.068723 ACTCGTCCTCTTCTGTTTAACTCAA 59.931 40.000 0.00 0.00 0.00 3.02
1752 3180 1.887242 TCGTCGTTGCTGCTGCTTT 60.887 52.632 17.00 0.00 40.48 3.51
1831 3262 1.059584 TCTTCTTGGTGCCCAGGTGA 61.060 55.000 3.82 2.18 33.81 4.02
1896 3330 5.009610 AGTTGTTACAAACCAAAGATGCGAT 59.990 36.000 0.00 0.00 0.00 4.58
1912 3351 2.711885 GACACGGCAAACAGTTGTTAC 58.288 47.619 0.00 0.00 37.25 2.50
2124 3563 3.282745 AAGCAGATGTCGCCGACGT 62.283 57.895 12.49 12.49 41.18 4.34
2306 3757 5.534207 AAAGCAGTTCATTCATCCAACAA 57.466 34.783 0.00 0.00 0.00 2.83
2388 3839 3.610911 CCTAGGTCAAGCGGATCTTTTT 58.389 45.455 0.00 0.00 38.22 1.94
2393 3844 0.178068 TTGCCTAGGTCAAGCGGATC 59.822 55.000 11.31 0.00 0.00 3.36
2394 3845 0.107654 GTTGCCTAGGTCAAGCGGAT 60.108 55.000 16.04 0.00 0.00 4.18
2395 3846 1.295423 GTTGCCTAGGTCAAGCGGA 59.705 57.895 16.04 0.00 0.00 5.54
2396 3847 1.745489 GGTTGCCTAGGTCAAGCGG 60.745 63.158 23.11 0.00 33.19 5.52
2397 3848 3.890674 GGTTGCCTAGGTCAAGCG 58.109 61.111 23.11 0.00 33.19 4.68
2398 3849 1.019805 GTCGGTTGCCTAGGTCAAGC 61.020 60.000 25.53 25.53 38.24 4.01
2415 3866 2.741486 TAGTTGGGTGGCGCTTGGTC 62.741 60.000 7.64 0.00 0.00 4.02
2464 4100 4.941873 ACGTTTCTATTGTTTGGATCCCTC 59.058 41.667 9.90 0.00 0.00 4.30
2467 4103 7.373778 ACTAACGTTTCTATTGTTTGGATCC 57.626 36.000 5.91 4.20 0.00 3.36
2487 4123 8.989131 AGCCTCAGTCCTGTAATAATTAACTAA 58.011 33.333 0.00 0.00 0.00 2.24
2492 4128 7.431249 CGTTAGCCTCAGTCCTGTAATAATTA 58.569 38.462 0.00 0.00 0.00 1.40
2493 4129 6.281405 CGTTAGCCTCAGTCCTGTAATAATT 58.719 40.000 0.00 0.00 0.00 1.40
2494 4130 5.221461 CCGTTAGCCTCAGTCCTGTAATAAT 60.221 44.000 0.00 0.00 0.00 1.28
2495 4131 4.098960 CCGTTAGCCTCAGTCCTGTAATAA 59.901 45.833 0.00 0.00 0.00 1.40
2496 4132 3.635373 CCGTTAGCCTCAGTCCTGTAATA 59.365 47.826 0.00 0.00 0.00 0.98
2497 4133 2.431057 CCGTTAGCCTCAGTCCTGTAAT 59.569 50.000 0.00 0.00 0.00 1.89
2498 4134 1.822990 CCGTTAGCCTCAGTCCTGTAA 59.177 52.381 0.00 0.00 0.00 2.41
2499 4135 1.005097 TCCGTTAGCCTCAGTCCTGTA 59.995 52.381 0.00 0.00 0.00 2.74
2500 4136 0.251653 TCCGTTAGCCTCAGTCCTGT 60.252 55.000 0.00 0.00 0.00 4.00
2501 4137 1.067821 GATCCGTTAGCCTCAGTCCTG 59.932 57.143 0.00 0.00 0.00 3.86
2508 4144 0.539986 TTGGGTGATCCGTTAGCCTC 59.460 55.000 1.27 0.00 38.76 4.70
2512 4148 2.882927 TCGATTGGGTGATCCGTTAG 57.117 50.000 0.00 0.00 38.76 2.34
2517 4153 3.469008 TGTGTATCGATTGGGTGATCC 57.531 47.619 1.71 0.00 0.00 3.36
2521 4157 5.815222 TGTATTCTTGTGTATCGATTGGGTG 59.185 40.000 1.71 0.00 0.00 4.61
2526 4162 5.687730 CGAGCTGTATTCTTGTGTATCGATT 59.312 40.000 1.71 0.00 0.00 3.34
2527 4163 5.008712 TCGAGCTGTATTCTTGTGTATCGAT 59.991 40.000 2.16 2.16 31.28 3.59
2546 4879 1.652619 GGTAGCAGTAAACGTTCGAGC 59.347 52.381 0.00 4.00 0.00 5.03
2565 4898 0.868406 GTCTGAACTTTGGTCGCTGG 59.132 55.000 0.00 0.00 0.00 4.85
2566 4899 0.508641 CGTCTGAACTTTGGTCGCTG 59.491 55.000 0.00 0.00 0.00 5.18
2567 4900 0.387929 TCGTCTGAACTTTGGTCGCT 59.612 50.000 0.00 0.00 0.00 4.93
2568 4901 0.507358 GTCGTCTGAACTTTGGTCGC 59.493 55.000 0.00 0.00 0.00 5.19
2569 4902 1.137513 GGTCGTCTGAACTTTGGTCG 58.862 55.000 0.00 0.00 0.00 4.79
2570 4903 1.202604 TGGGTCGTCTGAACTTTGGTC 60.203 52.381 0.00 0.00 30.37 4.02
2594 4927 1.566018 GGCACGGACGGAGAAACAAG 61.566 60.000 0.00 0.00 0.00 3.16
2595 4928 1.595929 GGCACGGACGGAGAAACAA 60.596 57.895 0.00 0.00 0.00 2.83
2603 4936 2.333581 GGTTTTTGGCACGGACGG 59.666 61.111 0.00 0.00 0.00 4.79
2608 4941 1.001815 CTGTGTAGGGTTTTTGGCACG 60.002 52.381 0.00 0.00 0.00 5.34
2620 4953 5.923733 AGGACTCTGATTAACTGTGTAGG 57.076 43.478 0.00 0.00 0.00 3.18
2624 4957 8.132362 GTGTAGATAGGACTCTGATTAACTGTG 58.868 40.741 0.00 0.00 0.00 3.66
2628 4961 7.577979 CGAGTGTAGATAGGACTCTGATTAAC 58.422 42.308 0.00 0.00 35.04 2.01
2629 4962 6.205076 GCGAGTGTAGATAGGACTCTGATTAA 59.795 42.308 0.00 0.00 35.04 1.40
2653 4986 1.821332 CCTCGGAGGCCAATTGAGC 60.821 63.158 11.83 8.64 0.00 4.26
2659 4992 4.344865 GGCAACCTCGGAGGCCAA 62.345 66.667 23.84 0.00 45.70 4.52
2706 5039 0.956633 CACAGCCTCATGCAACTTGT 59.043 50.000 0.00 0.00 44.83 3.16
2708 5041 1.962144 GCACAGCCTCATGCAACTT 59.038 52.632 0.00 0.00 44.83 2.66
2774 5108 9.403110 CTGGATTTGCTTAAACAGAATATATGC 57.597 33.333 0.00 0.00 30.57 3.14
2781 5115 4.870363 GCACTGGATTTGCTTAAACAGAA 58.130 39.130 0.00 0.00 37.00 3.02
2782 5116 4.503741 GCACTGGATTTGCTTAAACAGA 57.496 40.909 0.00 0.00 37.00 3.41
2798 5132 1.080772 TCGCTTCACGGTAGCACTG 60.081 57.895 4.00 0.00 43.89 3.66
2807 5141 0.249073 CTCATAGGGGTCGCTTCACG 60.249 60.000 0.00 0.00 45.62 4.35
2815 5149 3.056465 GCATGTAGTAGCTCATAGGGGTC 60.056 52.174 0.00 0.00 0.00 4.46
2818 5152 4.158764 GGTAGCATGTAGTAGCTCATAGGG 59.841 50.000 0.00 0.00 42.05 3.53
2846 5330 5.179555 GCGATAATAAGGTTTCTCCATGGTC 59.820 44.000 12.58 0.00 39.02 4.02
2851 5335 6.984474 CAGTTAGCGATAATAAGGTTTCTCCA 59.016 38.462 0.00 0.00 39.02 3.86
2906 5723 5.068987 TGAGTTGCTTACTTCCAGCATTTTT 59.931 36.000 0.00 0.00 46.62 1.94
2913 5730 7.651304 CAGAGTATATGAGTTGCTTACTTCCAG 59.349 40.741 0.00 0.00 37.17 3.86
2936 5753 4.394729 AGAACCGGATTTGCTTAAACAGA 58.605 39.130 9.46 0.00 0.00 3.41
2937 5754 4.766404 AGAACCGGATTTGCTTAAACAG 57.234 40.909 9.46 0.00 0.00 3.16
2953 5770 2.067013 GAGTTGCTTCACGGTAGAACC 58.933 52.381 0.00 0.00 34.05 3.62
2956 5773 1.629043 AGGAGTTGCTTCACGGTAGA 58.371 50.000 0.00 0.00 0.00 2.59
2961 5778 1.929836 GCTCATAGGAGTTGCTTCACG 59.070 52.381 6.23 0.00 43.37 4.35
2973 5790 5.966742 TGTAGCATGTAGTAGCTCATAGG 57.033 43.478 0.00 0.00 42.05 2.57
2978 7316 5.861251 GTCATCATGTAGCATGTAGTAGCTC 59.139 44.000 8.68 0.00 42.05 4.09
2995 7333 2.277008 AGGTTCTCCCTGGTCATCAT 57.723 50.000 0.00 0.00 44.08 2.45
2996 7334 2.044793 AAGGTTCTCCCTGGTCATCA 57.955 50.000 0.00 0.00 45.47 3.07
3026 7365 5.885912 AGGTGCCAAACGAGTTTATGATTAT 59.114 36.000 0.50 0.00 0.00 1.28
3033 7372 1.868498 CGAAGGTGCCAAACGAGTTTA 59.132 47.619 0.50 0.00 0.00 2.01
3056 7395 5.565259 GCAATAAGTATCGCATGTTACATGC 59.435 40.000 32.97 32.97 41.35 4.06
3112 7451 9.615295 GAAATGAAAAATTAGCATGCATTTTGT 57.385 25.926 22.35 13.51 35.40 2.83
3113 7452 9.068008 GGAAATGAAAAATTAGCATGCATTTTG 57.932 29.630 22.35 0.00 35.40 2.44
3138 7477 6.992063 ATGACACAATAGTTTTAGCTGAGG 57.008 37.500 0.00 0.00 0.00 3.86
3140 7479 7.012327 GGCATATGACACAATAGTTTTAGCTGA 59.988 37.037 6.97 0.00 0.00 4.26
3143 7482 7.026631 TGGCATATGACACAATAGTTTTAGC 57.973 36.000 7.32 0.00 0.00 3.09
3153 7492 6.832520 ACATTTAGTTGGCATATGACACAA 57.167 33.333 11.87 7.26 29.05 3.33
3189 7528 6.764560 GCGGGGTATCATCTAGTTTCTTAAAA 59.235 38.462 0.00 0.00 0.00 1.52
3191 7530 5.508489 CGCGGGGTATCATCTAGTTTCTTAA 60.508 44.000 0.00 0.00 0.00 1.85
3197 7536 0.317479 GCGCGGGGTATCATCTAGTT 59.683 55.000 8.83 0.00 0.00 2.24
3198 7537 1.863662 CGCGCGGGGTATCATCTAGT 61.864 60.000 24.84 0.00 0.00 2.57
3199 7538 1.154016 CGCGCGGGGTATCATCTAG 60.154 63.158 24.84 0.00 0.00 2.43
3200 7539 1.457823 AACGCGCGGGGTATCATCTA 61.458 55.000 35.22 0.00 0.00 1.98
3201 7540 2.792947 AACGCGCGGGGTATCATCT 61.793 57.895 35.22 5.42 0.00 2.90
3202 7541 2.279918 AACGCGCGGGGTATCATC 60.280 61.111 35.22 0.00 0.00 2.92
3203 7542 2.587753 CAACGCGCGGGGTATCAT 60.588 61.111 35.22 7.19 0.00 2.45


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

AutoCloner maintained by Alex Coulton.