Multiple sequence alignment - TraesCS7D01G268400

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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 TraesCS7D01G268400 chr7D 100.000 4460 0 0 1 4460 252245107 252240648 0.000000e+00 8237
1 TraesCS7D01G268400 chr7D 90.361 83 7 1 1757 1838 122836267 122836349 1.700000e-19 108
2 TraesCS7D01G268400 chr7A 92.439 1878 111 20 2596 4460 268864154 268866013 0.000000e+00 2652
3 TraesCS7D01G268400 chr7A 87.125 1701 112 41 59 1708 268861418 268863062 0.000000e+00 1829
4 TraesCS7D01G268400 chr7A 87.910 670 58 13 1916 2578 268863518 268864171 0.000000e+00 767
5 TraesCS7D01G268400 chr7A 95.833 72 3 0 3763 3834 268865233 268865304 2.820000e-22 117
6 TraesCS7D01G268400 chr7B 91.640 1878 107 25 2596 4460 228918602 228916762 0.000000e+00 2553
7 TraesCS7D01G268400 chr7B 90.426 1807 85 27 1 1758 228921626 228919859 0.000000e+00 2298
8 TraesCS7D01G268400 chr7B 89.139 488 45 4 1926 2410 228919283 228918801 6.380000e-168 601
9 TraesCS7D01G268400 chr7B 88.000 150 12 3 2429 2578 228918728 228918585 5.930000e-39 172
10 TraesCS7D01G268400 chr7B 94.444 72 4 0 3763 3834 228917536 228917465 1.310000e-20 111
11 TraesCS7D01G268400 chr5B 78.112 466 71 23 1099 1538 486368914 486368454 2.640000e-67 267
12 TraesCS7D01G268400 chr5B 89.773 88 5 1 1755 1838 440023745 440023832 4.720000e-20 110
13 TraesCS7D01G268400 chr5D 77.897 466 72 23 1099 1538 405398873 405398413 1.230000e-65 261
14 TraesCS7D01G268400 chr4B 90.909 88 4 1 1757 1840 277407906 277407993 1.010000e-21 115
15 TraesCS7D01G268400 chr4B 89.655 87 6 2 1754 1840 498374454 498374537 1.700000e-19 108
16 TraesCS7D01G268400 chr4B 89.655 87 5 1 1756 1838 613320184 613320098 1.700000e-19 108
17 TraesCS7D01G268400 chr4A 90.698 86 4 1 1757 1838 670849337 670849252 1.310000e-20 111
18 TraesCS7D01G268400 chr3A 88.298 94 7 3 1750 1840 9230351 9230259 4.720000e-20 110
19 TraesCS7D01G268400 chr4D 89.655 87 6 2 1754 1840 402527925 402528008 1.700000e-19 108
20 TraesCS7D01G268400 chr4D 89.655 87 5 1 1756 1838 483109751 483109665 1.700000e-19 108


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 TraesCS7D01G268400 chr7D 252240648 252245107 4459 True 8237.00 8237 100.00000 1 4460 1 chr7D.!!$R1 4459
1 TraesCS7D01G268400 chr7A 268861418 268866013 4595 False 1341.25 2652 90.82675 59 4460 4 chr7A.!!$F1 4401
2 TraesCS7D01G268400 chr7B 228916762 228921626 4864 True 1147.00 2553 90.72980 1 4460 5 chr7B.!!$R1 4459

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
702 758 0.107410 TGTCCGGAAAATAGGCGCAT 60.107 50.0 5.23 3.98 0.00 4.73 F
1503 1566 0.319555 ACGCAAAGCTCGCAGAACTA 60.320 50.0 8.63 0.00 28.07 2.24 F
2642 3235 0.321671 TAGTGGTCTTGCACCTGAGC 59.678 55.0 0.00 0.00 46.98 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2526 3119 0.034186 TGGAGGTGATGGCATTGTCC 60.034 55.0 0.00 6.43 0.00 4.02 R
3217 3815 0.251787 ATTGGCTGGTTCCCTCCAAC 60.252 55.0 11.89 0.00 38.70 3.77 R
3503 4104 0.242555 CCGGTGGGGATTTTCGTTTG 59.757 55.0 0.00 0.00 38.47 2.93 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
200 221 8.268850 AGAATCGCAACATAAGTTCTTTACAT 57.731 30.769 0.00 0.00 35.28 2.29
201 222 8.730680 AGAATCGCAACATAAGTTCTTTACATT 58.269 29.630 0.00 0.00 35.28 2.71
206 227 9.901724 CGCAACATAAGTTCTTTACATTAGTAG 57.098 33.333 0.00 0.00 35.28 2.57
256 278 4.035843 CCCCCACGAGAAGTAGCT 57.964 61.111 0.00 0.00 0.00 3.32
260 282 2.100989 CCCCACGAGAAGTAGCTTAGT 58.899 52.381 0.00 0.00 0.00 2.24
271 293 9.440784 CGAGAAGTAGCTTAGTATAAACTTGAG 57.559 37.037 0.00 0.00 37.15 3.02
488 515 2.238521 TGCCCTTCAACATGACTTTCC 58.761 47.619 0.00 0.00 0.00 3.13
490 517 2.489722 GCCCTTCAACATGACTTTCCTC 59.510 50.000 0.00 0.00 0.00 3.71
507 534 1.363744 CTCTACCGTCCGTTACTCGT 58.636 55.000 0.00 0.00 37.94 4.18
536 563 5.847111 ACGTGTATGAGGATAAGCTTACA 57.153 39.130 8.70 2.45 0.00 2.41
578 605 8.341903 TGTTTGCGTCATGTTTTCCTATATATG 58.658 33.333 0.00 0.00 0.00 1.78
601 649 2.936919 TGCACTGTTTCACTCTCCAT 57.063 45.000 0.00 0.00 0.00 3.41
613 661 4.965814 TCACTCTCCATGAGATAAATGCC 58.034 43.478 0.00 0.00 45.39 4.40
615 663 5.840693 TCACTCTCCATGAGATAAATGCCTA 59.159 40.000 0.00 0.00 45.39 3.93
637 691 9.908152 GCCTAGTTGTTGTTGTAAATAGAAATT 57.092 29.630 0.00 0.00 28.78 1.82
683 739 2.301346 CAGGCTCCTTCACTGTTTGTT 58.699 47.619 0.00 0.00 0.00 2.83
702 758 0.107410 TGTCCGGAAAATAGGCGCAT 60.107 50.000 5.23 3.98 0.00 4.73
795 852 1.756538 CCAAGGTGGTTGCTGTTCTTT 59.243 47.619 0.00 0.00 34.45 2.52
798 855 3.018423 AGGTGGTTGCTGTTCTTTCTT 57.982 42.857 0.00 0.00 0.00 2.52
799 856 2.952310 AGGTGGTTGCTGTTCTTTCTTC 59.048 45.455 0.00 0.00 0.00 2.87
801 858 2.952310 GTGGTTGCTGTTCTTTCTTCCT 59.048 45.455 0.00 0.00 0.00 3.36
804 861 1.512926 TGCTGTTCTTTCTTCCTCGC 58.487 50.000 0.00 0.00 0.00 5.03
805 862 0.440371 GCTGTTCTTTCTTCCTCGCG 59.560 55.000 0.00 0.00 0.00 5.87
806 863 1.784525 CTGTTCTTTCTTCCTCGCGT 58.215 50.000 5.77 0.00 0.00 6.01
833 890 4.425577 ACCAGAAAAATGTTGCGATCTC 57.574 40.909 0.00 0.00 0.00 2.75
857 914 3.744426 ACGGGTTTGTTTAGATCTTGTCG 59.256 43.478 0.00 0.00 0.00 4.35
859 916 4.143179 CGGGTTTGTTTAGATCTTGTCGTC 60.143 45.833 0.00 0.00 0.00 4.20
882 939 1.856265 GCAGTGCCTTCCAAACCTCG 61.856 60.000 2.85 0.00 0.00 4.63
918 975 2.611518 GTTCCTGACCACATTCTCTCG 58.388 52.381 0.00 0.00 0.00 4.04
948 1005 1.202722 TCCAAGAAGAACGTTGGACCC 60.203 52.381 5.00 0.00 45.93 4.46
1205 1265 3.417224 CGACGACCACGACCTCGA 61.417 66.667 0.78 0.00 43.02 4.04
1207 1267 3.319926 GACGACCACGACCTCGACC 62.320 68.421 0.78 0.00 43.02 4.79
1503 1566 0.319555 ACGCAAAGCTCGCAGAACTA 60.320 50.000 8.63 0.00 28.07 2.24
1536 1599 3.118408 ACCCAAAGAAGGCAAAAAGGTTC 60.118 43.478 0.00 0.00 0.00 3.62
1539 1602 0.673985 AGAAGGCAAAAAGGTTCGGC 59.326 50.000 0.00 0.00 0.00 5.54
1585 1648 7.826252 CGAAATTCCATCAGTAGGATTATCCAT 59.174 37.037 14.30 1.50 39.61 3.41
1594 1657 8.267620 TCAGTAGGATTATCCATTGTTCATCT 57.732 34.615 14.30 0.00 39.61 2.90
1595 1658 8.152898 TCAGTAGGATTATCCATTGTTCATCTG 58.847 37.037 14.30 7.77 39.61 2.90
1597 1660 8.153550 AGTAGGATTATCCATTGTTCATCTGAC 58.846 37.037 14.30 0.00 39.61 3.51
1663 1736 6.854496 TTTACGGCTGTTATATGGATGAAC 57.146 37.500 1.99 0.00 0.00 3.18
1731 1804 5.931441 ACAGAACATTAGAAGACAACTGC 57.069 39.130 0.00 0.00 0.00 4.40
1732 1805 5.368145 ACAGAACATTAGAAGACAACTGCA 58.632 37.500 0.00 0.00 0.00 4.41
1733 1806 6.000219 ACAGAACATTAGAAGACAACTGCAT 59.000 36.000 0.00 0.00 0.00 3.96
1734 1807 6.072838 ACAGAACATTAGAAGACAACTGCATG 60.073 38.462 0.00 0.00 0.00 4.06
1772 1845 9.822185 GTTTATAAATTACTCCCTCCGTAAAGA 57.178 33.333 0.31 0.00 31.36 2.52
1784 1857 7.600065 TCCCTCCGTAAAGAAATATAAGATCG 58.400 38.462 0.00 0.00 0.00 3.69
1842 1915 8.834749 ATTTCTTTACAGAGGAAGTACAACTC 57.165 34.615 0.00 0.00 0.00 3.01
1843 1916 6.971726 TCTTTACAGAGGAAGTACAACTCA 57.028 37.500 12.15 0.00 33.76 3.41
1844 1917 7.540474 TCTTTACAGAGGAAGTACAACTCAT 57.460 36.000 12.15 4.70 33.76 2.90
1845 1918 7.378966 TCTTTACAGAGGAAGTACAACTCATG 58.621 38.462 12.15 9.90 33.76 3.07
1846 1919 4.543590 ACAGAGGAAGTACAACTCATGG 57.456 45.455 12.15 5.70 33.76 3.66
1847 1920 4.160329 ACAGAGGAAGTACAACTCATGGA 58.840 43.478 12.15 0.00 33.76 3.41
1848 1921 4.593206 ACAGAGGAAGTACAACTCATGGAA 59.407 41.667 12.15 0.00 33.76 3.53
1849 1922 4.932200 CAGAGGAAGTACAACTCATGGAAC 59.068 45.833 12.15 0.00 33.76 3.62
1874 1947 1.173913 GTGTTTGATGTGCCCCTACC 58.826 55.000 0.00 0.00 0.00 3.18
1881 1954 1.198759 ATGTGCCCCTACCAACGAGT 61.199 55.000 0.00 0.00 0.00 4.18
1885 1958 1.005805 TGCCCCTACCAACGAGTACTA 59.994 52.381 0.00 0.00 0.00 1.82
1890 1963 4.488879 CCCTACCAACGAGTACTAACAAC 58.511 47.826 0.00 0.00 0.00 3.32
1893 1966 6.404074 CCCTACCAACGAGTACTAACAACTAG 60.404 46.154 0.00 0.00 0.00 2.57
1938 2472 5.475220 TCCAATGTGGTGTGTTTATAAGGTG 59.525 40.000 0.00 0.00 39.03 4.00
1945 2479 7.285629 TGTGGTGTGTTTATAAGGTGAAAATCA 59.714 33.333 0.00 0.00 0.00 2.57
1962 2496 4.627611 AATCACTCGGATGAAAATGCTG 57.372 40.909 0.00 0.00 36.02 4.41
1966 2500 1.065102 CTCGGATGAAAATGCTGCCTG 59.935 52.381 0.00 0.00 0.00 4.85
1967 2501 1.097232 CGGATGAAAATGCTGCCTGA 58.903 50.000 0.00 0.00 0.00 3.86
1993 2529 3.951979 AGTAAGCTAAATGCACGATGC 57.048 42.857 0.00 0.00 45.94 3.91
2007 2543 2.667969 CACGATGCGATCTGAAGAACAA 59.332 45.455 0.00 0.00 0.00 2.83
2014 2550 4.694982 TGCGATCTGAAGAACAAGCAAATA 59.305 37.500 0.00 0.00 0.00 1.40
2018 2554 7.253552 GCGATCTGAAGAACAAGCAAATATTTG 60.254 37.037 21.54 21.54 41.03 2.32
2057 2593 5.279356 GCTAGCCGTATATAGTTGGTCCTTT 60.279 44.000 2.29 0.00 0.00 3.11
2062 2598 6.094464 GCCGTATATAGTTGGTCCTTTTGTTT 59.906 38.462 0.00 0.00 0.00 2.83
2064 2600 7.120138 CCGTATATAGTTGGTCCTTTTGTTTGT 59.880 37.037 0.00 0.00 0.00 2.83
2070 2606 6.394809 AGTTGGTCCTTTTGTTTGTAAAGTG 58.605 36.000 0.00 0.00 32.06 3.16
2075 2611 6.206498 GTCCTTTTGTTTGTAAAGTGCCTAG 58.794 40.000 0.00 0.00 32.06 3.02
2078 2614 6.475402 CCTTTTGTTTGTAAAGTGCCTAGTTG 59.525 38.462 0.00 0.00 32.06 3.16
2094 2630 7.010275 GTGCCTAGTTGTCTATGTTTACTTAGC 59.990 40.741 0.00 0.00 0.00 3.09
2325 2861 7.961325 TTAAAAATGTGGAAGAAAATCCTGC 57.039 32.000 0.00 0.00 40.35 4.85
2338 2874 6.019108 AGAAAATCCTGCCCTATCTGTTTTT 58.981 36.000 0.00 0.00 0.00 1.94
2358 2895 0.392461 TCGGCACCTGTAATCCTTGC 60.392 55.000 0.00 0.00 0.00 4.01
2362 2899 2.945668 GGCACCTGTAATCCTTGCTTAG 59.054 50.000 0.00 0.00 33.55 2.18
2367 2904 3.118738 CCTGTAATCCTTGCTTAGACGGT 60.119 47.826 0.00 0.00 0.00 4.83
2376 2913 5.125097 TCCTTGCTTAGACGGTAAGAACTAG 59.875 44.000 10.19 0.00 0.00 2.57
2468 3060 7.708752 CCTCTCCTGTAGATTTCATGTAGTTTC 59.291 40.741 0.00 0.00 32.41 2.78
2501 3093 8.991026 CATAATGAAAGAAAATTGTCCAAGCAA 58.009 29.630 0.00 0.00 0.00 3.91
2507 3100 6.165700 AGAAAATTGTCCAAGCAAGTCATT 57.834 33.333 0.00 0.00 0.00 2.57
2508 3101 6.218746 AGAAAATTGTCCAAGCAAGTCATTC 58.781 36.000 0.00 0.00 0.00 2.67
2514 3107 3.753272 GTCCAAGCAAGTCATTCAGCTAA 59.247 43.478 0.00 0.00 36.07 3.09
2522 3115 5.049129 GCAAGTCATTCAGCTAACTTCAACT 60.049 40.000 0.00 0.00 29.78 3.16
2526 3119 4.756642 TCATTCAGCTAACTTCAACTGGTG 59.243 41.667 0.00 0.00 0.00 4.17
2540 3133 0.813184 CTGGTGGACAATGCCATCAC 59.187 55.000 5.72 0.00 43.90 3.06
2542 3135 0.323725 GGTGGACAATGCCATCACCT 60.324 55.000 6.13 0.00 43.14 4.00
2571 3164 5.435686 TTGTGTCAGGTAGCTTTATCCAT 57.564 39.130 0.00 0.00 0.00 3.41
2572 3165 5.023533 TGTGTCAGGTAGCTTTATCCATC 57.976 43.478 0.00 0.00 0.00 3.51
2573 3166 4.716784 TGTGTCAGGTAGCTTTATCCATCT 59.283 41.667 0.00 0.00 0.00 2.90
2574 3167 5.189736 TGTGTCAGGTAGCTTTATCCATCTT 59.810 40.000 0.00 0.00 0.00 2.40
2575 3168 5.525378 GTGTCAGGTAGCTTTATCCATCTTG 59.475 44.000 0.00 0.00 0.00 3.02
2576 3169 5.189736 TGTCAGGTAGCTTTATCCATCTTGT 59.810 40.000 0.00 0.00 0.00 3.16
2577 3170 6.116126 GTCAGGTAGCTTTATCCATCTTGTT 58.884 40.000 0.00 0.00 0.00 2.83
2578 3171 6.258947 GTCAGGTAGCTTTATCCATCTTGTTC 59.741 42.308 0.00 0.00 0.00 3.18
2579 3172 5.235186 CAGGTAGCTTTATCCATCTTGTTCG 59.765 44.000 0.00 0.00 0.00 3.95
2580 3173 5.104900 AGGTAGCTTTATCCATCTTGTTCGT 60.105 40.000 0.00 0.00 0.00 3.85
2581 3174 5.234543 GGTAGCTTTATCCATCTTGTTCGTC 59.765 44.000 0.00 0.00 0.00 4.20
2582 3175 3.865745 AGCTTTATCCATCTTGTTCGTCG 59.134 43.478 0.00 0.00 0.00 5.12
2583 3176 3.544244 GCTTTATCCATCTTGTTCGTCGC 60.544 47.826 0.00 0.00 0.00 5.19
2584 3177 2.951457 TATCCATCTTGTTCGTCGCA 57.049 45.000 0.00 0.00 0.00 5.10
2585 3178 2.093306 ATCCATCTTGTTCGTCGCAA 57.907 45.000 0.00 0.00 0.00 4.85
2586 3179 1.872388 TCCATCTTGTTCGTCGCAAA 58.128 45.000 0.00 0.00 0.00 3.68
2587 3180 2.214347 TCCATCTTGTTCGTCGCAAAA 58.786 42.857 0.00 0.00 0.00 2.44
2588 3181 2.614520 TCCATCTTGTTCGTCGCAAAAA 59.385 40.909 0.00 0.00 0.00 1.94
2632 3225 2.239681 AGCTGCTAGGTAGTGGTCTT 57.760 50.000 0.00 0.00 0.00 3.01
2636 3229 1.275291 TGCTAGGTAGTGGTCTTGCAC 59.725 52.381 0.00 0.00 36.98 4.57
2639 3232 0.687354 AGGTAGTGGTCTTGCACCTG 59.313 55.000 0.00 0.00 46.98 4.00
2642 3235 0.321671 TAGTGGTCTTGCACCTGAGC 59.678 55.000 0.00 0.00 46.98 4.26
2666 3259 3.823873 CCCACTGTTATGGCTAACAACAA 59.176 43.478 9.65 0.00 44.95 2.83
2672 3265 6.428159 ACTGTTATGGCTAACAACAAAGAGAG 59.572 38.462 9.65 0.00 44.95 3.20
2673 3266 6.530120 TGTTATGGCTAACAACAAAGAGAGA 58.470 36.000 6.96 0.00 43.22 3.10
2705 3298 2.011046 GCTTGATCTGACTGAGGGTGC 61.011 57.143 0.00 0.00 0.00 5.01
2711 3304 1.000506 TCTGACTGAGGGTGCGTTAAC 59.999 52.381 0.00 0.00 0.00 2.01
2723 3316 3.486108 GGTGCGTTAACTATGAGTCGATG 59.514 47.826 3.71 0.00 0.00 3.84
2724 3317 4.348656 GTGCGTTAACTATGAGTCGATGA 58.651 43.478 3.71 0.00 0.00 2.92
2725 3318 4.796830 GTGCGTTAACTATGAGTCGATGAA 59.203 41.667 3.71 0.00 0.00 2.57
2727 3320 6.019801 GTGCGTTAACTATGAGTCGATGAATT 60.020 38.462 3.71 0.00 0.00 2.17
2729 3322 7.865889 TGCGTTAACTATGAGTCGATGAATTAT 59.134 33.333 3.71 0.00 0.00 1.28
2730 3323 8.156553 GCGTTAACTATGAGTCGATGAATTATG 58.843 37.037 3.71 0.00 0.00 1.90
2731 3324 8.156553 CGTTAACTATGAGTCGATGAATTATGC 58.843 37.037 3.71 0.00 0.00 3.14
2732 3325 8.978539 GTTAACTATGAGTCGATGAATTATGCA 58.021 33.333 0.00 0.00 0.00 3.96
2733 3326 9.710900 TTAACTATGAGTCGATGAATTATGCAT 57.289 29.630 3.79 3.79 0.00 3.96
2734 3327 7.824704 ACTATGAGTCGATGAATTATGCATC 57.175 36.000 0.19 3.08 38.95 3.91
2735 3328 7.381323 ACTATGAGTCGATGAATTATGCATCA 58.619 34.615 13.11 0.00 41.66 3.07
2736 3329 5.912360 TGAGTCGATGAATTATGCATCAC 57.088 39.130 13.11 9.83 41.66 3.06
2764 3357 2.876581 AGCTAACCTTGTTCCCTTTGG 58.123 47.619 0.00 0.00 0.00 3.28
2771 3364 1.136110 CTTGTTCCCTTTGGCACGTTT 59.864 47.619 0.00 0.00 29.21 3.60
2777 3370 2.099427 TCCCTTTGGCACGTTTGTAAAC 59.901 45.455 0.00 0.00 35.59 2.01
2796 3389 1.375268 GGCACAGAGAGACACTGCC 60.375 63.158 0.00 0.00 38.74 4.85
2809 3402 2.759973 CTGCCGGGCTCTCTACCA 60.760 66.667 21.46 0.00 0.00 3.25
2878 3471 5.801380 TCCACTTACAAGATGGTAAAGTCC 58.199 41.667 0.00 0.00 33.18 3.85
2895 3488 5.733620 AAGTCCGTAATTCCAGTTACTCA 57.266 39.130 0.00 0.00 33.44 3.41
2913 3506 7.775561 AGTTACTCATTGTCTTTCACCTTCTTT 59.224 33.333 0.00 0.00 0.00 2.52
2934 3527 5.885230 TTGTTCTGCCATGAATGTAAGAG 57.115 39.130 0.00 0.00 0.00 2.85
2961 3556 2.030027 TGTTCACCATGAGGGAGACT 57.970 50.000 0.00 0.00 41.15 3.24
2963 3558 1.065854 GTTCACCATGAGGGAGACTGG 60.066 57.143 0.00 0.00 41.15 4.00
2965 3560 1.307343 ACCATGAGGGAGACTGGGG 60.307 63.158 0.00 0.00 41.15 4.96
2966 3561 2.074948 CCATGAGGGAGACTGGGGG 61.075 68.421 0.00 0.00 40.01 5.40
2967 3562 1.003442 CATGAGGGAGACTGGGGGA 59.997 63.158 0.00 0.00 0.00 4.81
2968 3563 0.621571 CATGAGGGAGACTGGGGGAA 60.622 60.000 0.00 0.00 0.00 3.97
2969 3564 0.327000 ATGAGGGAGACTGGGGGAAG 60.327 60.000 0.00 0.00 0.00 3.46
2970 3565 1.690985 GAGGGAGACTGGGGGAAGG 60.691 68.421 0.00 0.00 0.00 3.46
2971 3566 2.125225 GGGAGACTGGGGGAAGGT 59.875 66.667 0.00 0.00 0.00 3.50
2972 3567 2.301738 GGGAGACTGGGGGAAGGTG 61.302 68.421 0.00 0.00 0.00 4.00
2973 3568 1.229529 GGAGACTGGGGGAAGGTGA 60.230 63.158 0.00 0.00 0.00 4.02
2974 3569 0.621862 GGAGACTGGGGGAAGGTGAT 60.622 60.000 0.00 0.00 0.00 3.06
2975 3570 1.290134 GAGACTGGGGGAAGGTGATT 58.710 55.000 0.00 0.00 0.00 2.57
2976 3571 2.478292 GAGACTGGGGGAAGGTGATTA 58.522 52.381 0.00 0.00 0.00 1.75
2980 3575 3.954258 GACTGGGGGAAGGTGATTAATTG 59.046 47.826 0.00 0.00 0.00 2.32
2987 3582 6.192044 GGGGAAGGTGATTAATTGAAAGGTA 58.808 40.000 0.00 0.00 0.00 3.08
2990 3585 8.050930 GGGAAGGTGATTAATTGAAAGGTACTA 58.949 37.037 0.00 0.00 38.49 1.82
3006 3601 9.606631 GAAAGGTACTATGAACTTCTTGATCAT 57.393 33.333 0.00 0.00 38.49 2.45
3016 3614 1.564207 TCTTGATCATCTTGAGCGCG 58.436 50.000 0.00 0.00 35.14 6.86
3027 3625 0.459411 TTGAGCGCGCTAGCACATAA 60.459 50.000 36.69 16.71 45.49 1.90
3035 3633 2.032178 GCGCTAGCACATAAAAGAAGGG 59.968 50.000 16.45 0.00 44.35 3.95
3036 3634 2.614057 CGCTAGCACATAAAAGAAGGGG 59.386 50.000 16.45 0.00 0.00 4.79
3038 3636 4.270008 GCTAGCACATAAAAGAAGGGGAA 58.730 43.478 10.63 0.00 0.00 3.97
3040 3638 5.393135 GCTAGCACATAAAAGAAGGGGAAAC 60.393 44.000 10.63 0.00 0.00 2.78
3046 3644 7.228507 GCACATAAAAGAAGGGGAAACAATTTT 59.771 33.333 0.00 0.00 0.00 1.82
3061 3659 7.861872 GGAAACAATTTTTCATGACCATTTTGG 59.138 33.333 0.00 0.00 45.02 3.28
3077 3675 2.847959 TTGGGGTTTTTCGTCGAAAC 57.152 45.000 19.59 10.30 36.51 2.78
3086 3684 4.398549 TTTTCGTCGAAACCTTAGCATG 57.601 40.909 19.59 0.00 30.83 4.06
3568 4169 1.306633 GGGTGGATTCAGGGGGTTC 59.693 63.158 0.00 0.00 0.00 3.62
3670 4274 3.253677 TCAGTTGTCGAGTCTTCCTTCTC 59.746 47.826 0.00 0.00 0.00 2.87
3677 4281 4.920927 GTCGAGTCTTCCTTCTCAAGAAAG 59.079 45.833 0.00 0.00 31.60 2.62
3682 4286 7.522399 CGAGTCTTCCTTCTCAAGAAAGAGTTA 60.522 40.741 0.00 0.00 36.97 2.24
3683 4287 7.438564 AGTCTTCCTTCTCAAGAAAGAGTTAC 58.561 38.462 0.00 0.00 36.97 2.50
3707 4311 1.837439 CTTATGGGGTCTACAGGTGCA 59.163 52.381 0.00 0.00 0.00 4.57
3740 4344 6.385649 TGAAGGAAAATGTTACCAACTCAC 57.614 37.500 0.00 0.00 0.00 3.51
3757 4361 2.537625 CTCACGCAGATTCTTCGGATTC 59.462 50.000 10.37 0.00 0.00 2.52
3788 4393 0.249398 GGTCTACAGGTGCGGATGTT 59.751 55.000 0.00 0.00 0.00 2.71
3804 4409 4.685628 CGGATGTTTGTTGAAGGAAAATGG 59.314 41.667 0.00 0.00 0.00 3.16
3902 4507 3.873361 TGCTGCTCCATTTCTTAATCTCG 59.127 43.478 0.00 0.00 0.00 4.04
3998 4603 2.957491 TTTGGTGACTGGCAAGTTTG 57.043 45.000 0.00 0.00 36.52 2.93
4069 4674 7.646922 GCAGCATATTCATAGAAGAAACAAAGG 59.353 37.037 0.00 0.00 0.00 3.11
4091 4696 7.145932 AGGCAATCTGTCAAGTGTAATTTAC 57.854 36.000 0.00 0.00 0.00 2.01
4093 4698 7.230510 AGGCAATCTGTCAAGTGTAATTTACAA 59.769 33.333 10.73 0.00 40.93 2.41
4121 4726 7.973944 AGTGTTTTTCAAAAGACTCACCAATAC 59.026 33.333 8.60 0.00 45.82 1.89
4166 4774 2.234661 TGCACAAACCACATGTTTTGGA 59.765 40.909 21.30 7.41 44.80 3.53
4336 4947 4.083802 GCGAGCAAATCTGACACTTAACTT 60.084 41.667 0.00 0.00 0.00 2.66
4337 4948 5.560953 GCGAGCAAATCTGACACTTAACTTT 60.561 40.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 6.729690 TTGGTCAAATTTGAGAACTGGATT 57.270 33.333 21.05 0.00 37.98 3.01
133 140 7.977293 TGATCAATGGACATGCTTGAATTTTAG 59.023 33.333 6.60 0.00 33.03 1.85
271 293 5.390567 GGACACGACATTAACTGATTTCCAC 60.391 44.000 0.00 0.00 0.00 4.02
281 303 8.071368 TCAGTTTTTAATGGACACGACATTAAC 58.929 33.333 9.39 3.20 45.35 2.01
480 507 1.171308 CGGACGGTAGAGGAAAGTCA 58.829 55.000 0.00 0.00 33.84 3.41
481 508 1.172175 ACGGACGGTAGAGGAAAGTC 58.828 55.000 0.00 0.00 0.00 3.01
482 509 1.625511 AACGGACGGTAGAGGAAAGT 58.374 50.000 0.00 0.00 0.00 2.66
485 512 2.359900 GAGTAACGGACGGTAGAGGAA 58.640 52.381 0.00 0.00 0.00 3.36
507 534 3.992943 ATCCTCATACACGTTTTGGGA 57.007 42.857 0.00 0.00 0.00 4.37
536 563 4.259610 CGCAAACACGTTTTACTTGCAATT 60.260 37.500 0.00 0.00 41.92 2.32
578 605 3.128589 TGGAGAGTGAAACAGTGCAAAAC 59.871 43.478 0.00 0.00 41.43 2.43
601 649 6.714810 ACAACAACAACTAGGCATTTATCTCA 59.285 34.615 0.00 0.00 0.00 3.27
615 663 9.248291 CAGCAATTTCTATTTACAACAACAACT 57.752 29.630 0.00 0.00 0.00 3.16
637 691 3.051210 CAGGGACACTCGTCAGCA 58.949 61.111 0.00 0.00 44.54 4.41
638 692 2.433318 GCAGGGACACTCGTCAGC 60.433 66.667 0.00 0.00 44.54 4.26
683 739 0.107410 ATGCGCCTATTTTCCGGACA 60.107 50.000 1.83 0.00 0.00 4.02
702 758 1.300971 GCTTGCAGATTGGACTCGCA 61.301 55.000 0.00 0.00 0.00 5.10
795 852 2.552743 CTGGTATATCACGCGAGGAAGA 59.447 50.000 15.93 2.47 0.00 2.87
798 855 2.265589 TCTGGTATATCACGCGAGGA 57.734 50.000 15.93 10.85 0.00 3.71
799 856 3.364889 TTTCTGGTATATCACGCGAGG 57.635 47.619 15.93 4.29 0.00 4.63
801 858 5.113383 ACATTTTTCTGGTATATCACGCGA 58.887 37.500 15.93 0.00 0.00 5.87
804 861 5.676744 CGCAACATTTTTCTGGTATATCACG 59.323 40.000 0.00 0.00 0.00 4.35
805 862 6.781138 TCGCAACATTTTTCTGGTATATCAC 58.219 36.000 0.00 0.00 0.00 3.06
806 863 6.993786 TCGCAACATTTTTCTGGTATATCA 57.006 33.333 0.00 0.00 0.00 2.15
833 890 5.061808 CGACAAGATCTAAACAAACCCGTAG 59.938 44.000 0.00 0.00 0.00 3.51
857 914 1.032014 TTGGAAGGCACTGCAAAGAC 58.968 50.000 2.82 0.00 40.86 3.01
859 916 1.538849 GGTTTGGAAGGCACTGCAAAG 60.539 52.381 2.82 0.00 40.86 2.77
898 955 2.231478 TCGAGAGAATGTGGTCAGGAAC 59.769 50.000 0.00 0.00 37.03 3.62
918 975 3.858238 CGTTCTTCTTGGATTACGGAGTC 59.142 47.826 0.00 0.00 43.93 3.36
954 1011 4.974645 TTAGATTATCCCTCCACGCAAT 57.025 40.909 0.00 0.00 0.00 3.56
998 1055 2.202987 CCGGAGACCTGCTCATGC 60.203 66.667 0.00 0.00 45.81 4.06
1503 1566 1.961277 CTTTGGGTCGACAAGCGCT 60.961 57.895 18.91 2.64 40.61 5.92
1536 1599 3.810310 AGAAGAGAACATAAGAGGCCG 57.190 47.619 0.00 0.00 0.00 6.13
1645 1718 6.942532 TCTTTGTTCATCCATATAACAGCC 57.057 37.500 0.00 0.00 34.80 4.85
1663 1736 6.145048 GCATTTCAGACCACTTTCATTCTTTG 59.855 38.462 0.00 0.00 0.00 2.77
1676 1749 4.206375 TCTTTTGACAGCATTTCAGACCA 58.794 39.130 0.00 0.00 0.00 4.02
1708 1781 6.521162 TGCAGTTGTCTTCTAATGTTCTGTA 58.479 36.000 0.00 0.00 0.00 2.74
1710 1783 5.929697 TGCAGTTGTCTTCTAATGTTCTG 57.070 39.130 0.00 0.00 0.00 3.02
1725 1798 6.506500 AACTTTAATCTCCTCATGCAGTTG 57.493 37.500 0.00 0.00 0.00 3.16
1726 1799 8.814038 ATAAACTTTAATCTCCTCATGCAGTT 57.186 30.769 0.00 0.00 0.00 3.16
1727 1800 9.905713 TTATAAACTTTAATCTCCTCATGCAGT 57.094 29.630 0.00 0.00 0.00 4.40
1816 1889 9.924650 GAGTTGTACTTCCTCTGTAAAGAAATA 57.075 33.333 0.00 0.00 0.00 1.40
1818 1891 7.788026 TGAGTTGTACTTCCTCTGTAAAGAAA 58.212 34.615 0.00 0.00 0.00 2.52
1819 1892 7.356089 TGAGTTGTACTTCCTCTGTAAAGAA 57.644 36.000 0.00 0.00 0.00 2.52
1821 1894 6.591834 CCATGAGTTGTACTTCCTCTGTAAAG 59.408 42.308 0.00 0.00 0.00 1.85
1823 1896 5.778241 TCCATGAGTTGTACTTCCTCTGTAA 59.222 40.000 0.00 0.00 0.00 2.41
1825 1898 4.160329 TCCATGAGTTGTACTTCCTCTGT 58.840 43.478 0.00 0.00 0.00 3.41
1826 1899 4.808414 TCCATGAGTTGTACTTCCTCTG 57.192 45.455 0.00 0.00 0.00 3.35
1827 1900 4.593206 TGTTCCATGAGTTGTACTTCCTCT 59.407 41.667 0.00 0.00 0.00 3.69
1828 1901 4.691216 GTGTTCCATGAGTTGTACTTCCTC 59.309 45.833 0.00 0.00 0.00 3.71
1829 1902 4.102524 TGTGTTCCATGAGTTGTACTTCCT 59.897 41.667 0.00 0.00 0.00 3.36
1830 1903 4.385825 TGTGTTCCATGAGTTGTACTTCC 58.614 43.478 0.00 0.00 0.00 3.46
1831 1904 5.163953 CGATGTGTTCCATGAGTTGTACTTC 60.164 44.000 0.00 0.00 32.56 3.01
1832 1905 4.690748 CGATGTGTTCCATGAGTTGTACTT 59.309 41.667 0.00 0.00 32.56 2.24
1833 1906 4.245660 CGATGTGTTCCATGAGTTGTACT 58.754 43.478 0.00 0.00 32.56 2.73
1834 1907 3.994392 ACGATGTGTTCCATGAGTTGTAC 59.006 43.478 0.00 0.00 32.56 2.90
1835 1908 3.993736 CACGATGTGTTCCATGAGTTGTA 59.006 43.478 0.00 0.00 32.56 2.41
1836 1909 2.807967 CACGATGTGTTCCATGAGTTGT 59.192 45.455 0.00 0.00 32.56 3.32
1837 1910 2.807967 ACACGATGTGTTCCATGAGTTG 59.192 45.455 0.00 0.00 45.08 3.16
1838 1911 3.126001 ACACGATGTGTTCCATGAGTT 57.874 42.857 0.00 0.00 45.08 3.01
1839 1912 2.839486 ACACGATGTGTTCCATGAGT 57.161 45.000 0.00 0.00 45.08 3.41
1851 1924 0.171007 GGGGCACATCAAACACGATG 59.829 55.000 0.00 0.00 46.78 3.84
1852 1925 0.038166 AGGGGCACATCAAACACGAT 59.962 50.000 0.00 0.00 0.00 3.73
1853 1926 0.687920 TAGGGGCACATCAAACACGA 59.312 50.000 0.00 0.00 0.00 4.35
1859 1932 0.322098 CGTTGGTAGGGGCACATCAA 60.322 55.000 0.00 0.00 0.00 2.57
1867 1940 3.091545 TGTTAGTACTCGTTGGTAGGGG 58.908 50.000 0.00 0.00 0.00 4.79
1915 1988 5.475220 TCACCTTATAAACACACCACATTGG 59.525 40.000 0.00 0.00 45.02 3.16
1916 1989 6.567687 TCACCTTATAAACACACCACATTG 57.432 37.500 0.00 0.00 0.00 2.82
1917 1990 7.589958 TTTCACCTTATAAACACACCACATT 57.410 32.000 0.00 0.00 0.00 2.71
1918 1991 7.589958 TTTTCACCTTATAAACACACCACAT 57.410 32.000 0.00 0.00 0.00 3.21
1919 1992 7.285629 TGATTTTCACCTTATAAACACACCACA 59.714 33.333 0.00 0.00 0.00 4.17
1920 1993 7.593644 GTGATTTTCACCTTATAAACACACCAC 59.406 37.037 0.00 0.00 41.37 4.16
1938 2472 5.514204 CAGCATTTTCATCCGAGTGATTTTC 59.486 40.000 0.00 0.00 0.00 2.29
1945 2479 1.098050 GGCAGCATTTTCATCCGAGT 58.902 50.000 0.00 0.00 0.00 4.18
1962 2496 5.278022 GCATTTAGCTTACTTATGGTCAGGC 60.278 44.000 0.00 0.00 41.15 4.85
1966 2500 5.522460 TCGTGCATTTAGCTTACTTATGGTC 59.478 40.000 0.00 0.00 45.94 4.02
1967 2501 5.424757 TCGTGCATTTAGCTTACTTATGGT 58.575 37.500 0.00 0.00 45.94 3.55
1993 2529 8.100863 CAAATATTTGCTTGTTCTTCAGATCG 57.899 34.615 14.96 0.00 0.00 3.69
2033 2569 3.762823 AGGACCAACTATATACGGCTAGC 59.237 47.826 6.04 6.04 0.00 3.42
2037 2573 5.121105 ACAAAAGGACCAACTATATACGGC 58.879 41.667 0.00 0.00 0.00 5.68
2043 2579 9.411189 ACTTTACAAACAAAAGGACCAACTATA 57.589 29.630 0.00 0.00 38.09 1.31
2044 2580 8.194769 CACTTTACAAACAAAAGGACCAACTAT 58.805 33.333 0.00 0.00 38.09 2.12
2050 2586 4.116961 GGCACTTTACAAACAAAAGGACC 58.883 43.478 0.00 0.00 38.09 4.46
2057 2593 5.883673 AGACAACTAGGCACTTTACAAACAA 59.116 36.000 0.00 0.00 41.75 2.83
2062 2598 6.354794 ACATAGACAACTAGGCACTTTACA 57.645 37.500 0.00 0.00 41.75 2.41
2064 2600 8.591072 AGTAAACATAGACAACTAGGCACTTTA 58.409 33.333 0.00 0.00 41.75 1.85
2070 2606 6.479331 GGCTAAGTAAACATAGACAACTAGGC 59.521 42.308 0.00 0.00 34.28 3.93
2075 2611 6.403878 TGGAGGCTAAGTAAACATAGACAAC 58.596 40.000 1.44 0.00 28.02 3.32
2078 2614 9.780186 AATTATGGAGGCTAAGTAAACATAGAC 57.220 33.333 0.00 0.00 0.00 2.59
2094 2630 8.737175 CAAATCCTATCACATGAATTATGGAGG 58.263 37.037 0.00 0.00 41.25 4.30
2338 2874 1.948611 GCAAGGATTACAGGTGCCGAA 60.949 52.381 0.00 0.00 0.00 4.30
2353 2890 4.189639 AGTTCTTACCGTCTAAGCAAGG 57.810 45.455 0.00 0.00 0.00 3.61
2358 2895 6.756299 AGTTCCTAGTTCTTACCGTCTAAG 57.244 41.667 0.00 0.00 0.00 2.18
2362 2899 6.507958 AGTTAGTTCCTAGTTCTTACCGTC 57.492 41.667 0.00 0.00 0.00 4.79
2397 2934 9.340695 CAAACTTTTGTGCATAATATTCTTCGA 57.659 29.630 0.00 0.00 33.59 3.71
2398 2935 8.586273 CCAAACTTTTGTGCATAATATTCTTCG 58.414 33.333 0.00 0.00 36.45 3.79
2407 2944 3.986572 CGCATCCAAACTTTTGTGCATAA 59.013 39.130 14.24 0.00 39.01 1.90
2411 2948 1.139163 CCGCATCCAAACTTTTGTGC 58.861 50.000 7.06 7.06 37.03 4.57
2413 2950 2.890311 TGATCCGCATCCAAACTTTTGT 59.110 40.909 1.21 0.00 36.45 2.83
2415 2952 3.676873 GCATGATCCGCATCCAAACTTTT 60.677 43.478 0.00 0.00 34.15 2.27
2416 2953 2.159198 GCATGATCCGCATCCAAACTTT 60.159 45.455 0.00 0.00 34.15 2.66
2417 2954 1.406539 GCATGATCCGCATCCAAACTT 59.593 47.619 0.00 0.00 34.15 2.66
2418 2955 1.027357 GCATGATCCGCATCCAAACT 58.973 50.000 0.00 0.00 34.15 2.66
2478 3070 7.049754 ACTTGCTTGGACAATTTTCTTTCATT 58.950 30.769 0.00 0.00 0.00 2.57
2479 3071 6.585416 ACTTGCTTGGACAATTTTCTTTCAT 58.415 32.000 0.00 0.00 0.00 2.57
2480 3072 5.976458 ACTTGCTTGGACAATTTTCTTTCA 58.024 33.333 0.00 0.00 0.00 2.69
2481 3073 6.042143 TGACTTGCTTGGACAATTTTCTTTC 58.958 36.000 0.00 0.00 0.00 2.62
2484 3076 5.796424 ATGACTTGCTTGGACAATTTTCT 57.204 34.783 0.00 0.00 0.00 2.52
2501 3093 4.999950 CCAGTTGAAGTTAGCTGAATGACT 59.000 41.667 0.00 0.00 31.40 3.41
2507 3100 2.703536 TCCACCAGTTGAAGTTAGCTGA 59.296 45.455 0.00 0.00 31.40 4.26
2508 3101 2.808543 GTCCACCAGTTGAAGTTAGCTG 59.191 50.000 0.00 0.00 0.00 4.24
2514 3107 1.956477 GCATTGTCCACCAGTTGAAGT 59.044 47.619 0.00 0.00 0.00 3.01
2522 3115 0.611618 GGTGATGGCATTGTCCACCA 60.612 55.000 23.77 5.16 44.83 4.17
2526 3119 0.034186 TGGAGGTGATGGCATTGTCC 60.034 55.000 0.00 6.43 0.00 4.02
2540 3133 2.276732 ACCTGACACAAACATGGAGG 57.723 50.000 0.00 0.00 32.23 4.30
2542 3135 2.371841 AGCTACCTGACACAAACATGGA 59.628 45.455 0.00 0.00 0.00 3.41
2589 3182 8.246871 GCTAACAAGATGGATAAAGCTTCTTTT 58.753 33.333 0.00 0.00 0.00 2.27
2590 3183 7.613411 AGCTAACAAGATGGATAAAGCTTCTTT 59.387 33.333 0.00 0.00 35.64 2.52
2591 3184 7.066766 CAGCTAACAAGATGGATAAAGCTTCTT 59.933 37.037 0.00 0.00 36.97 2.52
2592 3185 6.541641 CAGCTAACAAGATGGATAAAGCTTCT 59.458 38.462 0.00 0.00 36.97 2.85
2593 3186 6.723282 CAGCTAACAAGATGGATAAAGCTTC 58.277 40.000 0.00 0.00 36.97 3.86
2594 3187 5.067023 GCAGCTAACAAGATGGATAAAGCTT 59.933 40.000 0.00 0.00 36.97 3.74
2595 3188 4.578105 GCAGCTAACAAGATGGATAAAGCT 59.422 41.667 0.00 0.00 39.54 3.74
2596 3189 4.578105 AGCAGCTAACAAGATGGATAAAGC 59.422 41.667 0.00 0.00 0.00 3.51
2597 3190 6.426328 CCTAGCAGCTAACAAGATGGATAAAG 59.574 42.308 3.09 0.00 0.00 1.85
2598 3191 6.126768 ACCTAGCAGCTAACAAGATGGATAAA 60.127 38.462 3.09 0.00 0.00 1.40
2599 3192 5.366768 ACCTAGCAGCTAACAAGATGGATAA 59.633 40.000 3.09 0.00 0.00 1.75
2600 3193 4.901849 ACCTAGCAGCTAACAAGATGGATA 59.098 41.667 3.09 0.00 0.00 2.59
2601 3194 3.713764 ACCTAGCAGCTAACAAGATGGAT 59.286 43.478 3.09 0.00 0.00 3.41
2602 3195 3.107601 ACCTAGCAGCTAACAAGATGGA 58.892 45.455 3.09 0.00 0.00 3.41
2603 3196 3.550437 ACCTAGCAGCTAACAAGATGG 57.450 47.619 3.09 1.89 0.00 3.51
2604 3197 5.046529 CACTACCTAGCAGCTAACAAGATG 58.953 45.833 3.09 0.00 0.00 2.90
2605 3198 4.100189 CCACTACCTAGCAGCTAACAAGAT 59.900 45.833 3.09 0.00 0.00 2.40
2606 3199 3.447586 CCACTACCTAGCAGCTAACAAGA 59.552 47.826 3.09 0.00 0.00 3.02
2632 3225 2.527624 AGTGGGAGCTCAGGTGCA 60.528 61.111 17.19 0.00 34.99 4.57
2636 3229 1.134280 CCATAACAGTGGGAGCTCAGG 60.134 57.143 17.19 1.96 35.55 3.86
2639 3232 0.543749 AGCCATAACAGTGGGAGCTC 59.456 55.000 4.71 4.71 39.73 4.09
2642 3235 3.627395 TGTTAGCCATAACAGTGGGAG 57.373 47.619 0.00 0.00 44.94 4.30
2672 3265 9.286946 CAGTCAGATCAAGCAAATTATTTCTTC 57.713 33.333 0.00 0.00 0.00 2.87
2673 3266 9.017509 TCAGTCAGATCAAGCAAATTATTTCTT 57.982 29.630 0.00 0.00 0.00 2.52
2692 3285 1.000955 AGTTAACGCACCCTCAGTCAG 59.999 52.381 0.00 0.00 0.00 3.51
2705 3298 8.156553 GCATAATTCATCGACTCATAGTTAACG 58.843 37.037 0.00 0.00 0.00 3.18
2711 3304 7.544915 AGTGATGCATAATTCATCGACTCATAG 59.455 37.037 0.00 0.00 42.32 2.23
2723 3316 7.670009 AGCTATCTGAAGTGATGCATAATTC 57.330 36.000 0.00 5.14 0.00 2.17
2724 3317 8.997323 GTTAGCTATCTGAAGTGATGCATAATT 58.003 33.333 0.00 0.00 0.00 1.40
2725 3318 7.605691 GGTTAGCTATCTGAAGTGATGCATAAT 59.394 37.037 0.00 0.00 0.00 1.28
2727 3320 6.268617 AGGTTAGCTATCTGAAGTGATGCATA 59.731 38.462 0.00 0.00 0.00 3.14
2729 3322 4.406972 AGGTTAGCTATCTGAAGTGATGCA 59.593 41.667 0.00 0.00 0.00 3.96
2730 3323 4.954875 AGGTTAGCTATCTGAAGTGATGC 58.045 43.478 0.00 0.00 0.00 3.91
2731 3324 6.344500 ACAAGGTTAGCTATCTGAAGTGATG 58.656 40.000 0.00 0.00 0.00 3.07
2732 3325 6.552445 ACAAGGTTAGCTATCTGAAGTGAT 57.448 37.500 0.00 0.00 0.00 3.06
2733 3326 6.360370 AACAAGGTTAGCTATCTGAAGTGA 57.640 37.500 0.00 0.00 0.00 3.41
2734 3327 5.582665 GGAACAAGGTTAGCTATCTGAAGTG 59.417 44.000 0.00 0.00 0.00 3.16
2735 3328 5.338463 GGGAACAAGGTTAGCTATCTGAAGT 60.338 44.000 0.00 0.00 0.00 3.01
2736 3329 5.104735 AGGGAACAAGGTTAGCTATCTGAAG 60.105 44.000 0.00 0.00 0.00 3.02
2771 3364 1.684450 TGTCTCTCTGTGCCGTTTACA 59.316 47.619 0.00 0.00 0.00 2.41
2777 3370 1.735920 GCAGTGTCTCTCTGTGCCG 60.736 63.158 0.00 0.00 35.60 5.69
2779 3372 1.735920 CGGCAGTGTCTCTCTGTGC 60.736 63.158 0.00 0.00 35.60 4.57
2796 3389 0.895530 TGTTCTTGGTAGAGAGCCCG 59.104 55.000 0.00 0.00 0.00 6.13
2809 3402 2.481952 GCATCTTCAGTTCGCTGTTCTT 59.518 45.455 0.00 0.00 45.19 2.52
2838 3431 1.135915 TGGATTTGTTGCTGCACGTTT 59.864 42.857 0.00 0.00 0.00 3.60
2845 3438 5.437289 TCTTGTAAGTGGATTTGTTGCTG 57.563 39.130 0.00 0.00 0.00 4.41
2878 3471 7.596749 AAGACAATGAGTAACTGGAATTACG 57.403 36.000 0.00 0.00 39.58 3.18
2895 3488 6.681368 GCAGAACAAAGAAGGTGAAAGACAAT 60.681 38.462 0.00 0.00 0.00 2.71
2913 3506 4.937620 GTCTCTTACATTCATGGCAGAACA 59.062 41.667 0.00 0.00 0.00 3.18
2953 3548 2.456840 CCTTCCCCCAGTCTCCCT 59.543 66.667 0.00 0.00 0.00 4.20
2960 3555 4.249638 TCAATTAATCACCTTCCCCCAG 57.750 45.455 0.00 0.00 0.00 4.45
2961 3556 4.683766 TTCAATTAATCACCTTCCCCCA 57.316 40.909 0.00 0.00 0.00 4.96
2963 3558 5.023452 ACCTTTCAATTAATCACCTTCCCC 58.977 41.667 0.00 0.00 0.00 4.81
2965 3560 7.939784 AGTACCTTTCAATTAATCACCTTCC 57.060 36.000 0.00 0.00 0.00 3.46
2976 3571 9.793259 TCAAGAAGTTCATAGTACCTTTCAATT 57.207 29.630 5.50 0.00 0.00 2.32
2980 3575 9.606631 ATGATCAAGAAGTTCATAGTACCTTTC 57.393 33.333 5.50 0.00 35.44 2.62
2987 3582 7.495279 GCTCAAGATGATCAAGAAGTTCATAGT 59.505 37.037 5.50 0.00 36.92 2.12
2990 3585 5.293814 CGCTCAAGATGATCAAGAAGTTCAT 59.706 40.000 5.50 0.00 38.93 2.57
3006 3601 2.507102 GTGCTAGCGCGCTCAAGA 60.507 61.111 40.23 20.05 43.21 3.02
3016 3614 3.886123 TCCCCTTCTTTTATGTGCTAGC 58.114 45.455 8.10 8.10 0.00 3.42
3027 3625 7.498900 GTCATGAAAAATTGTTTCCCCTTCTTT 59.501 33.333 0.00 0.00 0.00 2.52
3035 3633 7.861872 CCAAAATGGTCATGAAAAATTGTTTCC 59.138 33.333 0.00 0.00 31.35 3.13
3036 3634 7.861872 CCCAAAATGGTCATGAAAAATTGTTTC 59.138 33.333 0.00 0.00 35.17 2.78
3038 3636 6.264970 CCCCAAAATGGTCATGAAAAATTGTT 59.735 34.615 0.00 0.00 35.17 2.83
3040 3638 5.769162 ACCCCAAAATGGTCATGAAAAATTG 59.231 36.000 0.00 0.00 35.17 2.32
3046 3644 5.372373 GAAAAACCCCAAAATGGTCATGAA 58.628 37.500 0.00 0.00 35.17 2.57
3217 3815 0.251787 ATTGGCTGGTTCCCTCCAAC 60.252 55.000 11.89 0.00 38.70 3.77
3219 3817 1.383799 CATTGGCTGGTTCCCTCCA 59.616 57.895 0.00 0.00 36.00 3.86
3503 4104 0.242555 CCGGTGGGGATTTTCGTTTG 59.757 55.000 0.00 0.00 38.47 2.93
3670 4274 6.092259 CCCCATAAGAACGTAACTCTTTCTTG 59.908 42.308 6.31 3.53 42.12 3.02
3677 4281 4.732672 AGACCCCATAAGAACGTAACTC 57.267 45.455 0.00 0.00 0.00 3.01
3682 4286 2.764572 CCTGTAGACCCCATAAGAACGT 59.235 50.000 0.00 0.00 0.00 3.99
3683 4287 2.764572 ACCTGTAGACCCCATAAGAACG 59.235 50.000 0.00 0.00 0.00 3.95
3707 4311 7.926018 GGTAACATTTTCCTTCAACAAACATCT 59.074 33.333 0.00 0.00 0.00 2.90
3740 4344 4.091424 GTTTTGAATCCGAAGAATCTGCG 58.909 43.478 3.09 3.09 31.28 5.18
3757 4361 3.181443 ACCTGTAGACCCCAGAAGTTTTG 60.181 47.826 0.00 0.00 31.38 2.44
3788 4393 5.659079 AGTTGGTACCATTTTCCTTCAACAA 59.341 36.000 17.17 0.00 36.63 2.83
3804 4409 4.033358 CGAAGAATCTGCATGAGTTGGTAC 59.967 45.833 0.00 0.00 0.00 3.34
3902 4507 1.137404 CATACAAAGGCCAGCGCAC 59.863 57.895 11.47 0.00 36.38 5.34
3998 4603 2.663826 AGAACGCAGAGAGGACATTC 57.336 50.000 0.00 0.00 0.00 2.67
4069 4674 8.970691 ATTGTAAATTACACTTGACAGATTGC 57.029 30.769 5.19 0.00 38.63 3.56
4091 4696 7.973388 TGGTGAGTCTTTTGAAAAACACTATTG 59.027 33.333 12.64 0.00 29.16 1.90
4093 4698 7.639113 TGGTGAGTCTTTTGAAAAACACTAT 57.361 32.000 12.64 0.00 29.16 2.12
4104 4709 5.694910 ACGTACTGTATTGGTGAGTCTTTTG 59.305 40.000 0.00 0.00 0.00 2.44
4121 4726 7.906527 GCAATTAACCCAACTATTAACGTACTG 59.093 37.037 0.00 0.00 0.00 2.74
4236 4845 8.617290 AGTCTTTCAATAAATACACGGTTCTT 57.383 30.769 0.00 0.00 0.00 2.52
4336 4947 3.562141 CGTGGAGATTTGGTGTGTGTTAA 59.438 43.478 0.00 0.00 0.00 2.01
4337 4948 3.135225 CGTGGAGATTTGGTGTGTGTTA 58.865 45.455 0.00 0.00 0.00 2.41
4421 5032 3.716601 CAACCTTGGTTGTGAATGGAAC 58.283 45.455 20.87 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.