Multiple sequence alignment - TraesCS3B01G400900

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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 TraesCS3B01G400900 chr3B 100.000 4549 0 0 943 5491 634237753 634233205 0.000000e+00 8401.0
1 TraesCS3B01G400900 chr3B 100.000 534 0 0 1 534 634238695 634238162 0.000000e+00 987.0
2 TraesCS3B01G400900 chr3D 95.014 1825 71 11 3672 5491 476198673 476200482 0.000000e+00 2848.0
3 TraesCS3B01G400900 chr3D 94.761 1737 76 10 943 2671 476195914 476197643 0.000000e+00 2689.0
4 TraesCS3B01G400900 chr3D 92.896 929 50 7 2662 3584 476197747 476198665 0.000000e+00 1336.0
5 TraesCS3B01G400900 chr3D 92.164 536 27 8 4 534 476195307 476195832 0.000000e+00 743.0
6 TraesCS3B01G400900 chr3D 89.038 520 52 4 1695 2214 445757418 445756904 1.670000e-179 640.0
7 TraesCS3B01G400900 chr3A 94.656 1703 71 11 975 2671 619646688 619648376 0.000000e+00 2623.0
8 TraesCS3B01G400900 chr3A 94.404 1501 65 8 3672 5161 619649310 619650802 0.000000e+00 2289.0
9 TraesCS3B01G400900 chr3A 92.888 703 42 4 2787 3485 619648560 619649258 0.000000e+00 1014.0
10 TraesCS3B01G400900 chr3A 93.519 540 23 9 1 534 619646055 619646588 0.000000e+00 793.0
11 TraesCS3B01G400900 chr3A 93.478 92 6 0 2662 2753 619648464 619648555 2.670000e-28 137.0
12 TraesCS3B01G400900 chr5B 89.251 521 52 3 1694 2214 599604478 599603962 0.000000e+00 649.0
13 TraesCS3B01G400900 chr1D 89.251 521 51 4 1694 2214 475274688 475274173 0.000000e+00 647.0
14 TraesCS3B01G400900 chr5A 88.469 503 55 2 1694 2196 55378564 55378065 6.080000e-169 604.0
15 TraesCS3B01G400900 chr5A 86.364 88 12 0 5245 5332 59700798 59700885 4.530000e-16 97.1
16 TraesCS3B01G400900 chr5A 83.673 98 14 2 5238 5334 427829070 427829166 2.110000e-14 91.6
17 TraesCS3B01G400900 chrUn 86.372 521 64 5 1694 2214 36554262 36554775 3.710000e-156 562.0
18 TraesCS3B01G400900 chr1A 89.535 86 9 0 5244 5329 251695786 251695701 5.820000e-20 110.0
19 TraesCS3B01G400900 chr1A 90.244 82 8 0 5245 5326 251695701 251695782 2.090000e-19 108.0
20 TraesCS3B01G400900 chr6B 92.000 75 6 0 5255 5329 40678303 40678229 7.520000e-19 106.0
21 TraesCS3B01G400900 chr6D 87.209 86 11 0 5245 5330 190909275 190909360 1.260000e-16 99.0
22 TraesCS3B01G400900 chr6A 84.694 98 10 2 5244 5336 22527538 22527635 5.860000e-15 93.5
23 TraesCS3B01G400900 chr4D 83.495 103 14 3 5244 5345 499391397 499391297 5.860000e-15 93.5


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 TraesCS3B01G400900 chr3B 634233205 634238695 5490 True 4694.0 8401 100.00000 1 5491 2 chr3B.!!$R1 5490
1 TraesCS3B01G400900 chr3D 476195307 476200482 5175 False 1904.0 2848 93.70875 4 5491 4 chr3D.!!$F1 5487
2 TraesCS3B01G400900 chr3D 445756904 445757418 514 True 640.0 640 89.03800 1695 2214 1 chr3D.!!$R1 519
3 TraesCS3B01G400900 chr3A 619646055 619650802 4747 False 1371.2 2623 93.78900 1 5161 5 chr3A.!!$F1 5160
4 TraesCS3B01G400900 chr5B 599603962 599604478 516 True 649.0 649 89.25100 1694 2214 1 chr5B.!!$R1 520
5 TraesCS3B01G400900 chr1D 475274173 475274688 515 True 647.0 647 89.25100 1694 2214 1 chr1D.!!$R1 520
6 TraesCS3B01G400900 chrUn 36554262 36554775 513 False 562.0 562 86.37200 1694 2214 1 chrUn.!!$F1 520

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
347 351 0.039035 CCCCAATTCCCTCCGAAACA 59.961 55.000 0.0 0.0 33.08 2.83 F
1440 1444 0.179045 GCGTTGGGCTGATGAGGTAT 60.179 55.000 0.0 0.0 39.11 2.73 F
1827 1838 1.340017 ACCTGCTTGCACGATAATGGT 60.340 47.619 0.0 0.0 0.00 3.55 F
2811 2939 0.034476 GGATGCTGATGCTCCGATGA 59.966 55.000 0.0 0.0 40.48 2.92 F
3330 3464 2.359900 GACTGCTTATGTCAGTTGGGG 58.640 52.381 0.0 0.0 44.09 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1714 0.039165 GCCACTTGCCTTTTTCCGAG 60.039 55.0 0.00 0.00 0.00 4.63 R
2791 2919 0.035036 CATCGGAGCATCAGCATCCT 59.965 55.0 0.00 0.00 45.49 3.24 R
3328 3462 0.899717 TCAAGCAGTCCAATTGGCCC 60.900 55.0 20.33 12.32 34.44 5.80 R
3643 3778 1.064003 TCATGGTGCAGGGTAGTTGT 58.936 50.0 0.00 0.00 0.00 3.32 R
4971 5116 1.360393 ACAGGGGAAAGCCACCTGAA 61.360 55.0 19.14 0.00 46.94 3.02 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
27 28 8.122472 AGTTTCTCAAAAGACCAAAAGAAGAA 57.878 30.769 0.00 0.00 0.00 2.52
48 49 8.934973 AAGAAGTAAAAACGATTTTGATCGAG 57.065 30.769 13.06 0.00 46.12 4.04
61 62 9.760660 CGATTTTGATCGAGAAAAAGAAGTAAT 57.239 29.630 12.06 0.00 46.12 1.89
105 106 6.546772 ACACGGTACCAATTTTCCTTCTAAAA 59.453 34.615 13.54 0.00 33.15 1.52
106 107 7.068470 ACACGGTACCAATTTTCCTTCTAAAAA 59.932 33.333 13.54 0.00 32.42 1.94
138 139 9.768215 ACCCTATATTTTTCCATTTCTGAAGAA 57.232 29.630 0.00 0.00 0.00 2.52
155 156 1.502163 GAATCATTGCCTCGCCTCCG 61.502 60.000 0.00 0.00 0.00 4.63
166 167 2.899044 CGCCTCCGTTCGCCAAAAA 61.899 57.895 0.00 0.00 0.00 1.94
174 175 3.564644 TCCGTTCGCCAAAAATAGAAACA 59.435 39.130 0.00 0.00 0.00 2.83
299 301 1.076438 CCCTTTTCTTCCCACCCTCT 58.924 55.000 0.00 0.00 0.00 3.69
307 311 2.692741 CCCACCCTCTTCCCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
334 338 2.983879 CGCCCAGTTCCTCCCCAAT 61.984 63.158 0.00 0.00 0.00 3.16
342 346 1.279025 TTCCTCCCCAATTCCCTCCG 61.279 60.000 0.00 0.00 0.00 4.63
345 349 0.623723 CTCCCCAATTCCCTCCGAAA 59.376 55.000 0.00 0.00 33.08 3.46
346 350 0.330267 TCCCCAATTCCCTCCGAAAC 59.670 55.000 0.00 0.00 33.08 2.78
347 351 0.039035 CCCCAATTCCCTCCGAAACA 59.961 55.000 0.00 0.00 33.08 2.83
352 356 0.551396 ATTCCCTCCGAAACATCCCC 59.449 55.000 0.00 0.00 33.08 4.81
973 977 4.604976 GGATCCGCTTCATTTCATTTCAG 58.395 43.478 0.00 0.00 0.00 3.02
974 978 4.096984 GGATCCGCTTCATTTCATTTCAGT 59.903 41.667 0.00 0.00 0.00 3.41
975 979 5.393461 GGATCCGCTTCATTTCATTTCAGTT 60.393 40.000 0.00 0.00 0.00 3.16
976 980 6.183360 GGATCCGCTTCATTTCATTTCAGTTA 60.183 38.462 0.00 0.00 0.00 2.24
977 981 6.567687 TCCGCTTCATTTCATTTCAGTTAA 57.432 33.333 0.00 0.00 0.00 2.01
1156 1160 3.027412 TCTAAGATCTCACTCCAGCCAC 58.973 50.000 0.00 0.00 0.00 5.01
1187 1191 1.237285 CCTTGTTTGGCTCTGACGGG 61.237 60.000 0.00 0.00 0.00 5.28
1440 1444 0.179045 GCGTTGGGCTGATGAGGTAT 60.179 55.000 0.00 0.00 39.11 2.73
1590 1598 7.069331 ACCTTGGAAACACATCTGACATTTTTA 59.931 33.333 0.00 0.00 42.67 1.52
1626 1635 8.259411 TCATTGTTGCTAAATTATTGGCTCAAT 58.741 29.630 5.84 5.84 42.94 2.57
1627 1636 8.545420 CATTGTTGCTAAATTATTGGCTCAATC 58.455 33.333 13.07 0.00 42.94 2.67
1628 1637 7.408756 TGTTGCTAAATTATTGGCTCAATCT 57.591 32.000 4.01 0.00 42.94 2.40
1629 1638 8.518430 TGTTGCTAAATTATTGGCTCAATCTA 57.482 30.769 4.01 0.00 42.94 1.98
1630 1639 8.965819 TGTTGCTAAATTATTGGCTCAATCTAA 58.034 29.630 4.01 0.00 42.94 2.10
1671 1681 7.627300 GCTGATCGATCATGCAGTACTAATAGA 60.627 40.741 29.12 7.24 36.02 1.98
1703 1713 7.707624 ATGCAGATACTTGAAAAATTCCAGA 57.292 32.000 0.00 0.00 0.00 3.86
1704 1714 6.913170 TGCAGATACTTGAAAAATTCCAGAC 58.087 36.000 0.00 0.00 0.00 3.51
1827 1838 1.340017 ACCTGCTTGCACGATAATGGT 60.340 47.619 0.00 0.00 0.00 3.55
1865 1876 8.599055 TTTGATCATGCTATCTGAACTGTATC 57.401 34.615 0.00 0.00 0.00 2.24
2007 2018 8.188799 TGATAGGTTAGTTTTCTGTGATACTCG 58.811 37.037 0.00 0.00 0.00 4.18
2034 2047 8.709646 CACCTACAATGTACACTTTTAACTCTC 58.290 37.037 0.00 0.00 0.00 3.20
2035 2048 8.648693 ACCTACAATGTACACTTTTAACTCTCT 58.351 33.333 0.00 0.00 0.00 3.10
2091 2104 7.305993 GCATTTTGTACTGTTTTGCTAACTGAC 60.306 37.037 13.23 8.94 0.00 3.51
2092 2105 5.398176 TTGTACTGTTTTGCTAACTGACG 57.602 39.130 13.23 0.00 0.00 4.35
2251 2264 6.625873 TGCTCATGTGTTTGTTGTTATGTA 57.374 33.333 0.00 0.00 0.00 2.29
2255 2268 6.082984 TCATGTGTTTGTTGTTATGTATGCG 58.917 36.000 0.00 0.00 0.00 4.73
2315 2328 4.010349 ACTAATTTACAGGCAAGCCACTC 58.990 43.478 14.40 0.00 38.92 3.51
2460 2474 7.328277 ACTGTTTTGCTGTATGTAACTTTGA 57.672 32.000 0.00 0.00 0.00 2.69
2461 2475 7.417612 ACTGTTTTGCTGTATGTAACTTTGAG 58.582 34.615 0.00 0.00 0.00 3.02
2551 2565 7.138054 AGGGTAAGTCCAGTTATCCTTAATG 57.862 40.000 0.60 0.00 40.11 1.90
2579 2593 7.308348 GGCAGTACTTTTTGTGAGCAAGTATAA 60.308 37.037 0.00 0.00 35.86 0.98
2625 2639 6.784969 AGACTATGGCTTAGAGTATCCACATT 59.215 38.462 13.76 0.00 33.66 2.71
2640 2654 5.196341 TCCACATTACTAGATGCTAACCG 57.804 43.478 0.00 0.00 0.00 4.44
2656 2670 4.322273 GCTAACCGAACACTAAAGGTAGGT 60.322 45.833 0.00 0.00 35.68 3.08
2748 2876 7.704727 TCTTAAATGGGGTTTAGGAAATCTGA 58.295 34.615 0.00 0.00 36.00 3.27
2786 2914 5.990668 CACCTAATTTAAGGGTGCTAGACT 58.009 41.667 0.00 0.00 42.91 3.24
2787 2915 5.817816 CACCTAATTTAAGGGTGCTAGACTG 59.182 44.000 0.00 0.00 42.91 3.51
2788 2916 4.816925 CCTAATTTAAGGGTGCTAGACTGC 59.183 45.833 0.00 0.00 32.55 4.40
2791 2919 5.693769 ATTTAAGGGTGCTAGACTGCTAA 57.306 39.130 0.00 0.00 0.00 3.09
2811 2939 0.034476 GGATGCTGATGCTCCGATGA 59.966 55.000 0.00 0.00 40.48 2.92
2916 3044 5.195001 TCTTGGTGTTTGCAGGTAATTTC 57.805 39.130 0.00 0.00 0.00 2.17
2922 3050 6.547880 TGGTGTTTGCAGGTAATTTCTTTCTA 59.452 34.615 0.00 0.00 0.00 2.10
2969 3099 7.275888 TGCAATCTGCCACCTTTATTATTAG 57.724 36.000 0.00 0.00 44.23 1.73
3023 3153 7.685481 TGTTGAAAGAGTTCTGGATATGGTTA 58.315 34.615 0.00 0.00 34.60 2.85
3038 3168 8.758829 TGGATATGGTTAGTGCTTATGTATAGG 58.241 37.037 0.00 0.00 0.00 2.57
3081 3211 5.066593 CCTTTTATCTATTCCAGGAGTGCC 58.933 45.833 0.00 0.00 0.00 5.01
3175 3305 6.523840 TCTCATGTTTATTTTTGCTTTGGCT 58.476 32.000 0.00 0.00 39.59 4.75
3190 3322 8.668510 TTGCTTTGGCTGAATGTTTAAATTTA 57.331 26.923 0.00 0.00 39.59 1.40
3222 3356 4.698780 GGTCTTTACACCAAACCATACCTC 59.301 45.833 0.00 0.00 36.32 3.85
3311 3445 7.757941 TCAGTTATGTTGAAATGAATGTGGA 57.242 32.000 0.00 0.00 30.96 4.02
3316 3450 3.890756 TGTTGAAATGAATGTGGACTGCT 59.109 39.130 0.00 0.00 0.00 4.24
3328 3462 2.744202 GTGGACTGCTTATGTCAGTTGG 59.256 50.000 0.00 0.00 44.09 3.77
3330 3464 2.359900 GACTGCTTATGTCAGTTGGGG 58.640 52.381 0.00 0.00 44.09 4.96
3355 3489 5.279106 CCAATTGGACTGCTTGAATCTTGAA 60.279 40.000 20.50 0.00 37.39 2.69
3408 3542 5.825532 TCCCAAATGACCAACTGATATTCA 58.174 37.500 0.00 0.00 0.00 2.57
3452 3586 8.233190 GGCTTGAATGTATCTTAACATGCTATC 58.767 37.037 0.00 0.00 39.98 2.08
3453 3587 8.777413 GCTTGAATGTATCTTAACATGCTATCA 58.223 33.333 0.00 0.00 39.98 2.15
3497 3631 7.719633 AGTGCACTAAATTACCTTTTTGAGAGA 59.280 33.333 20.16 0.00 0.00 3.10
3500 3634 9.346725 GCACTAAATTACCTTTTTGAGAGAATG 57.653 33.333 0.00 0.00 0.00 2.67
3513 3647 5.065704 TGAGAGAATGCTACAGAACAGAC 57.934 43.478 0.00 0.00 0.00 3.51
3522 3656 4.245660 GCTACAGAACAGACAACATGCTA 58.754 43.478 0.00 0.00 0.00 3.49
3524 3658 5.006165 GCTACAGAACAGACAACATGCTATC 59.994 44.000 0.00 0.00 0.00 2.08
3547 3681 4.201753 CGCTGTGTTCCTGTATCTGATTTG 60.202 45.833 0.00 0.00 0.00 2.32
3595 3730 9.018582 ACTTTCCTTTAAGAAGATCAAATCAGG 57.981 33.333 0.00 0.00 34.71 3.86
3596 3731 8.940397 TTTCCTTTAAGAAGATCAAATCAGGT 57.060 30.769 0.00 0.00 34.71 4.00
3598 3733 9.449719 TTCCTTTAAGAAGATCAAATCAGGTAC 57.550 33.333 0.00 0.00 34.71 3.34
3599 3734 8.602424 TCCTTTAAGAAGATCAAATCAGGTACA 58.398 33.333 0.00 0.00 34.71 2.90
3600 3735 8.887717 CCTTTAAGAAGATCAAATCAGGTACAG 58.112 37.037 0.00 0.00 34.71 2.74
3601 3736 8.792830 TTTAAGAAGATCAAATCAGGTACAGG 57.207 34.615 0.00 0.00 0.00 4.00
3602 3737 6.627087 AAGAAGATCAAATCAGGTACAGGA 57.373 37.500 0.00 0.00 0.00 3.86
3603 3738 6.627087 AGAAGATCAAATCAGGTACAGGAA 57.373 37.500 0.00 0.00 0.00 3.36
3604 3739 7.205515 AGAAGATCAAATCAGGTACAGGAAT 57.794 36.000 0.00 0.00 0.00 3.01
3605 3740 8.324191 AGAAGATCAAATCAGGTACAGGAATA 57.676 34.615 0.00 0.00 0.00 1.75
3606 3741 8.943085 AGAAGATCAAATCAGGTACAGGAATAT 58.057 33.333 0.00 0.00 0.00 1.28
3607 3742 8.915057 AAGATCAAATCAGGTACAGGAATATG 57.085 34.615 0.00 0.00 0.00 1.78
3608 3743 8.038862 AGATCAAATCAGGTACAGGAATATGT 57.961 34.615 0.00 0.00 37.19 2.29
3609 3744 8.153550 AGATCAAATCAGGTACAGGAATATGTC 58.846 37.037 0.00 0.00 34.56 3.06
3610 3745 7.194112 TCAAATCAGGTACAGGAATATGTCA 57.806 36.000 0.00 0.00 34.56 3.58
3611 3746 7.275183 TCAAATCAGGTACAGGAATATGTCAG 58.725 38.462 0.00 0.00 34.56 3.51
3612 3747 4.672587 TCAGGTACAGGAATATGTCAGC 57.327 45.455 0.00 0.00 34.56 4.26
3613 3748 4.290093 TCAGGTACAGGAATATGTCAGCT 58.710 43.478 0.00 0.00 34.56 4.24
3614 3749 4.100035 TCAGGTACAGGAATATGTCAGCTG 59.900 45.833 7.63 7.63 35.72 4.24
3615 3750 4.033709 AGGTACAGGAATATGTCAGCTGT 58.966 43.478 14.67 0.00 34.36 4.40
3616 3751 4.471386 AGGTACAGGAATATGTCAGCTGTT 59.529 41.667 14.67 0.00 32.77 3.16
3617 3752 5.661312 AGGTACAGGAATATGTCAGCTGTTA 59.339 40.000 14.67 4.26 32.77 2.41
3618 3753 5.753921 GGTACAGGAATATGTCAGCTGTTAC 59.246 44.000 14.67 6.07 32.77 2.50
3619 3754 5.683876 ACAGGAATATGTCAGCTGTTACT 57.316 39.130 14.67 3.02 27.71 2.24
3620 3755 6.054860 ACAGGAATATGTCAGCTGTTACTT 57.945 37.500 14.67 6.40 27.71 2.24
3621 3756 5.877012 ACAGGAATATGTCAGCTGTTACTTG 59.123 40.000 14.67 8.52 27.71 3.16
3622 3757 4.878397 AGGAATATGTCAGCTGTTACTTGC 59.122 41.667 14.67 7.73 0.00 4.01
3623 3758 4.635765 GGAATATGTCAGCTGTTACTTGCA 59.364 41.667 14.67 3.43 0.00 4.08
3624 3759 5.123820 GGAATATGTCAGCTGTTACTTGCAA 59.876 40.000 14.67 0.00 0.00 4.08
3625 3760 6.183360 GGAATATGTCAGCTGTTACTTGCAAT 60.183 38.462 14.67 0.00 0.00 3.56
3626 3761 4.691860 ATGTCAGCTGTTACTTGCAATC 57.308 40.909 14.67 0.00 0.00 2.67
3627 3762 3.743521 TGTCAGCTGTTACTTGCAATCT 58.256 40.909 14.67 0.00 0.00 2.40
3628 3763 4.893608 TGTCAGCTGTTACTTGCAATCTA 58.106 39.130 14.67 0.00 0.00 1.98
3629 3764 5.304778 TGTCAGCTGTTACTTGCAATCTAA 58.695 37.500 14.67 0.00 0.00 2.10
3630 3765 5.179368 TGTCAGCTGTTACTTGCAATCTAAC 59.821 40.000 14.67 15.52 0.00 2.34
3631 3766 5.179368 GTCAGCTGTTACTTGCAATCTAACA 59.821 40.000 20.52 20.52 0.00 2.41
3632 3767 5.939883 TCAGCTGTTACTTGCAATCTAACAT 59.060 36.000 21.40 11.27 31.59 2.71
3633 3768 7.064609 GTCAGCTGTTACTTGCAATCTAACATA 59.935 37.037 21.40 10.92 31.59 2.29
3634 3769 7.064609 TCAGCTGTTACTTGCAATCTAACATAC 59.935 37.037 21.40 17.81 31.59 2.39
3635 3770 7.065085 CAGCTGTTACTTGCAATCTAACATACT 59.935 37.037 21.40 19.04 31.59 2.12
3636 3771 7.065085 AGCTGTTACTTGCAATCTAACATACTG 59.935 37.037 21.40 14.60 31.59 2.74
3637 3772 7.064609 GCTGTTACTTGCAATCTAACATACTGA 59.935 37.037 21.40 6.46 31.59 3.41
3638 3773 9.102757 CTGTTACTTGCAATCTAACATACTGAT 57.897 33.333 21.40 0.00 31.59 2.90
3639 3774 9.098355 TGTTACTTGCAATCTAACATACTGATC 57.902 33.333 18.97 0.00 0.00 2.92
3640 3775 9.098355 GTTACTTGCAATCTAACATACTGATCA 57.902 33.333 16.73 0.00 0.00 2.92
3641 3776 9.665719 TTACTTGCAATCTAACATACTGATCAA 57.334 29.630 0.00 0.00 0.00 2.57
3642 3777 8.565896 ACTTGCAATCTAACATACTGATCAAA 57.434 30.769 0.00 0.00 0.00 2.69
3643 3778 9.013229 ACTTGCAATCTAACATACTGATCAAAA 57.987 29.630 0.00 0.00 0.00 2.44
3644 3779 9.282247 CTTGCAATCTAACATACTGATCAAAAC 57.718 33.333 0.00 0.00 0.00 2.43
3645 3780 8.334263 TGCAATCTAACATACTGATCAAAACA 57.666 30.769 0.00 0.00 0.00 2.83
3646 3781 8.791675 TGCAATCTAACATACTGATCAAAACAA 58.208 29.630 0.00 0.00 0.00 2.83
3647 3782 9.065871 GCAATCTAACATACTGATCAAAACAAC 57.934 33.333 0.00 0.00 0.00 3.32
3651 3786 9.431887 TCTAACATACTGATCAAAACAACTACC 57.568 33.333 0.00 0.00 0.00 3.18
3652 3787 7.448748 AACATACTGATCAAAACAACTACCC 57.551 36.000 0.00 0.00 0.00 3.69
3653 3788 6.779860 ACATACTGATCAAAACAACTACCCT 58.220 36.000 0.00 0.00 0.00 4.34
3654 3789 6.655003 ACATACTGATCAAAACAACTACCCTG 59.345 38.462 0.00 0.00 0.00 4.45
3655 3790 3.821033 ACTGATCAAAACAACTACCCTGC 59.179 43.478 0.00 0.00 0.00 4.85
3656 3791 3.820467 CTGATCAAAACAACTACCCTGCA 59.180 43.478 0.00 0.00 0.00 4.41
3657 3792 3.568007 TGATCAAAACAACTACCCTGCAC 59.432 43.478 0.00 0.00 0.00 4.57
3658 3793 2.303175 TCAAAACAACTACCCTGCACC 58.697 47.619 0.00 0.00 0.00 5.01
3659 3794 2.028130 CAAAACAACTACCCTGCACCA 58.972 47.619 0.00 0.00 0.00 4.17
3660 3795 2.627699 CAAAACAACTACCCTGCACCAT 59.372 45.455 0.00 0.00 0.00 3.55
3661 3796 1.909700 AACAACTACCCTGCACCATG 58.090 50.000 0.00 0.00 0.00 3.66
3662 3797 1.064003 ACAACTACCCTGCACCATGA 58.936 50.000 0.00 0.00 0.00 3.07
3663 3798 1.423541 ACAACTACCCTGCACCATGAA 59.576 47.619 0.00 0.00 0.00 2.57
3664 3799 2.158534 ACAACTACCCTGCACCATGAAA 60.159 45.455 0.00 0.00 0.00 2.69
3665 3800 2.489329 CAACTACCCTGCACCATGAAAG 59.511 50.000 0.00 0.00 0.00 2.62
3666 3801 1.985159 ACTACCCTGCACCATGAAAGA 59.015 47.619 0.00 0.00 0.00 2.52
3667 3802 2.375174 ACTACCCTGCACCATGAAAGAA 59.625 45.455 0.00 0.00 0.00 2.52
3668 3803 2.380064 ACCCTGCACCATGAAAGAAA 57.620 45.000 0.00 0.00 0.00 2.52
3669 3804 1.963515 ACCCTGCACCATGAAAGAAAC 59.036 47.619 0.00 0.00 0.00 2.78
3670 3805 1.962807 CCCTGCACCATGAAAGAAACA 59.037 47.619 0.00 0.00 0.00 2.83
3700 3835 3.519510 TCTTCTTAGACCCCACATTCCAG 59.480 47.826 0.00 0.00 0.00 3.86
3706 3841 2.039879 AGACCCCACATTCCAGTGTTAC 59.960 50.000 0.00 0.00 37.82 2.50
3707 3842 2.039879 GACCCCACATTCCAGTGTTACT 59.960 50.000 0.00 0.00 37.82 2.24
3768 3903 1.974265 TGGACATTGCCTTGTCGAAA 58.026 45.000 9.29 0.00 45.63 3.46
3900 4035 4.774660 AATCTCATTCTCACTCATGCCT 57.225 40.909 0.00 0.00 0.00 4.75
4073 4209 3.194116 AGTTGCCTATGAATGCCTTGTTG 59.806 43.478 0.00 0.00 0.00 3.33
4307 4446 5.451103 GGGCAATCCAAAGAAGATAAGCTTC 60.451 44.000 0.00 0.00 43.30 3.86
4377 4516 5.520748 AAGGTGTGGAAAGATGGTCTTAT 57.479 39.130 0.00 0.00 35.27 1.73
4379 4518 5.892348 AGGTGTGGAAAGATGGTCTTATTT 58.108 37.500 0.00 0.00 35.27 1.40
4406 4545 4.826274 ACTACACCAATATGTCAGCTGT 57.174 40.909 14.67 0.00 33.85 4.40
4466 4605 3.263425 AGGGTAGCCGATTCTTTGAGAAA 59.737 43.478 5.06 0.00 37.82 2.52
4601 4740 4.174704 TGCTATTCCTCCTGCATTCAAT 57.825 40.909 0.00 0.00 0.00 2.57
4675 4815 6.647334 TTATTTTGTTGAATCAGGTGCTCA 57.353 33.333 0.00 0.00 0.00 4.26
4716 4861 1.735920 CAGTCAGTCGTCTGCTGGC 60.736 63.158 18.68 9.59 39.61 4.85
4769 4914 2.543777 ACTGCCGAAAGTGTACATGT 57.456 45.000 2.69 2.69 0.00 3.21
4810 4955 7.685481 TGTCATACAGTTCCTCCAAAAGATAA 58.315 34.615 0.00 0.00 0.00 1.75
4917 5062 1.551883 TGAGCAGTAATGCAGAGCTGA 59.448 47.619 18.53 1.94 35.36 4.26
5044 5193 4.472691 TTCATCTTGTTTGTCTCAAGCG 57.527 40.909 0.00 0.00 41.13 4.68
5103 5252 7.095607 CCAATTCGGAGATTACTTAGTGCATAC 60.096 40.741 0.00 0.00 36.56 2.39
5174 5323 6.099341 GGCCAAAACATTATTTCTACACCAG 58.901 40.000 0.00 0.00 0.00 4.00
5180 5329 8.588290 AAACATTATTTCTACACCAGCCATAA 57.412 30.769 0.00 0.00 0.00 1.90
5181 5330 8.588290 AACATTATTTCTACACCAGCCATAAA 57.412 30.769 0.00 0.00 0.00 1.40
5213 5363 9.265901 CTGATTCAACTTTCTAGAGAAACTTGA 57.734 33.333 16.59 16.59 41.05 3.02
5302 5453 7.338196 TGTAGGCTATATTAGCTTGCAAAAACA 59.662 33.333 0.00 0.00 46.83 2.83
5326 5477 7.688534 ACATCTTATATTATGGGATGGAGGGAA 59.311 37.037 17.20 0.00 38.33 3.97
5357 5508 7.820648 AGAATTAATTGTGAAGACACCATCAC 58.179 34.615 5.17 0.00 45.40 3.06
5364 5515 3.428870 GTGAAGACACCATCACGTGTTAG 59.571 47.826 16.51 7.64 46.85 2.34
5397 5548 5.193679 GGTTGCAAAGTATCTCCCTACAAT 58.806 41.667 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 8.307921 AGTGGAGTCGTTATTACTTCTTTTTC 57.692 34.615 0.00 0.00 0.00 2.29
108 109 9.540538 TCAGAAATGGAAAAATATAGGGTTTCA 57.459 29.630 0.00 0.00 33.76 2.69
111 112 9.768215 TCTTCAGAAATGGAAAAATATAGGGTT 57.232 29.630 0.00 0.00 0.00 4.11
112 113 9.768215 TTCTTCAGAAATGGAAAAATATAGGGT 57.232 29.630 0.00 0.00 0.00 4.34
138 139 2.109799 CGGAGGCGAGGCAATGAT 59.890 61.111 0.00 0.00 0.00 2.45
155 156 4.147479 CGGTTGTTTCTATTTTTGGCGAAC 59.853 41.667 0.00 0.00 0.00 3.95
166 167 1.084289 GCGGCTTCGGTTGTTTCTAT 58.916 50.000 0.00 0.00 0.00 1.98
299 301 2.204244 GGGGTTGAGGGGAGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
307 311 3.920093 GAACTGGGCGGGGTTGAGG 62.920 68.421 0.00 0.00 0.00 3.86
334 338 1.568118 GGGGGATGTTTCGGAGGGAA 61.568 60.000 0.00 0.00 0.00 3.97
352 356 3.451894 GCTGGATTTGGCGGTGGG 61.452 66.667 0.00 0.00 0.00 4.61
973 977 6.688813 GTCAGGAGATGCGAAATGAAATTAAC 59.311 38.462 0.00 0.00 33.67 2.01
974 978 6.374053 TGTCAGGAGATGCGAAATGAAATTAA 59.626 34.615 0.00 0.00 33.67 1.40
975 979 5.879777 TGTCAGGAGATGCGAAATGAAATTA 59.120 36.000 0.00 0.00 33.67 1.40
976 980 4.701651 TGTCAGGAGATGCGAAATGAAATT 59.298 37.500 0.00 0.00 38.98 1.82
977 981 4.264253 TGTCAGGAGATGCGAAATGAAAT 58.736 39.130 0.00 0.00 0.00 2.17
983 987 2.743664 CACATTGTCAGGAGATGCGAAA 59.256 45.455 0.00 0.00 0.00 3.46
987 991 1.131883 GTGCACATTGTCAGGAGATGC 59.868 52.381 13.17 0.00 0.00 3.91
1077 1081 1.812922 GACGAGGTCGCCGTAGAGA 60.813 63.158 0.00 0.00 44.43 3.10
1208 1212 4.615815 ATCTGCGCCGGATCTGCC 62.616 66.667 5.05 0.00 0.00 4.85
1232 1236 3.939939 TGCAGCGCCTCCTTGACA 61.940 61.111 2.29 0.00 0.00 3.58
1263 1267 2.504274 AAACCAGACCGCACGAGGA 61.504 57.895 0.00 0.00 34.73 3.71
1274 1278 0.321564 CATCGTCCCTGCAAACCAGA 60.322 55.000 0.00 0.00 44.64 3.86
1308 1312 1.373497 ACGCCTTGCAGAACTCGAG 60.373 57.895 11.84 11.84 0.00 4.04
1424 1428 5.606749 ACTGTAATATACCTCATCAGCCCAA 59.393 40.000 0.00 0.00 0.00 4.12
1488 1495 5.835257 AGACAAATGACCACAATTTGACAG 58.165 37.500 14.06 0.00 38.32 3.51
1590 1598 3.146104 AGCAACAATGAGTACCTTGCT 57.854 42.857 1.40 1.40 42.11 3.91
1600 1608 7.167924 TGAGCCAATAATTTAGCAACAATGA 57.832 32.000 0.00 0.00 0.00 2.57
1626 1635 4.476846 TCAGCTTGGGGGTCAATAATTAGA 59.523 41.667 0.00 0.00 34.45 2.10
1627 1636 4.792068 TCAGCTTGGGGGTCAATAATTAG 58.208 43.478 0.00 0.00 34.45 1.73
1628 1637 4.871871 TCAGCTTGGGGGTCAATAATTA 57.128 40.909 0.00 0.00 34.45 1.40
1629 1638 3.756082 TCAGCTTGGGGGTCAATAATT 57.244 42.857 0.00 0.00 34.45 1.40
1630 1639 3.748668 CGATCAGCTTGGGGGTCAATAAT 60.749 47.826 0.00 0.00 34.45 1.28
1637 1647 0.982852 TGATCGATCAGCTTGGGGGT 60.983 55.000 23.99 0.00 32.11 4.95
1703 1713 1.318576 CCACTTGCCTTTTTCCGAGT 58.681 50.000 0.00 0.00 0.00 4.18
1704 1714 0.039165 GCCACTTGCCTTTTTCCGAG 60.039 55.000 0.00 0.00 0.00 4.63
1827 1838 5.998981 AGCATGATCAAAATGGCAAGAAAAA 59.001 32.000 0.00 0.00 0.00 1.94
1865 1876 0.674581 TCAATCTGGCAAGCGGTGAG 60.675 55.000 0.00 0.00 0.00 3.51
2007 2018 7.172703 AGAGTTAAAAGTGTACATTGTAGGTGC 59.827 37.037 0.00 0.00 0.00 5.01
2034 2047 8.722480 AAGATTGTTTTCCTTTTCTTTTCCAG 57.278 30.769 0.00 0.00 0.00 3.86
2035 2048 9.594478 GTAAGATTGTTTTCCTTTTCTTTTCCA 57.406 29.630 0.00 0.00 0.00 3.53
2091 2104 5.539582 TTCCTGAAAAACATAATCGACCG 57.460 39.130 0.00 0.00 0.00 4.79
2092 2105 6.253512 GCAATTCCTGAAAAACATAATCGACC 59.746 38.462 0.00 0.00 0.00 4.79
2251 2264 2.496899 AGTTCCCTTCATGTTCGCAT 57.503 45.000 0.00 0.00 38.60 4.73
2315 2328 5.404667 GGAATAGGCTCGGAAAGTTATAACG 59.595 44.000 9.91 0.00 0.00 3.18
2460 2474 9.787435 TCAAGAACCTGTATAATTAACAACACT 57.213 29.630 0.00 0.00 0.00 3.55
2551 2565 2.878406 TGCTCACAAAAAGTACTGCCTC 59.122 45.455 0.00 0.00 0.00 4.70
2602 2616 7.730784 AGTAATGTGGATACTCTAAGCCATAGT 59.269 37.037 0.00 0.00 33.08 2.12
2603 2617 8.128322 AGTAATGTGGATACTCTAAGCCATAG 57.872 38.462 0.00 0.00 32.26 2.23
2625 2639 7.395190 TTTAGTGTTCGGTTAGCATCTAGTA 57.605 36.000 0.00 0.00 0.00 1.82
2640 2654 8.037382 GGTAATTTCACCTACCTTTAGTGTTC 57.963 38.462 0.00 0.00 35.61 3.18
2656 2670 8.189119 ACTTCCAATTTTGCTAGGTAATTTCA 57.811 30.769 0.00 0.00 0.00 2.69
2675 2803 6.717289 ACACTTATAGGCACAAATACTTCCA 58.283 36.000 0.00 0.00 0.00 3.53
2748 2876 5.620738 ATTAGGTGCTGAGATGTACACAT 57.379 39.130 0.00 0.00 39.70 3.21
2781 2909 3.244009 GCATCAGCATCCTTAGCAGTCTA 60.244 47.826 0.00 0.00 41.58 2.59
2782 2910 2.485124 GCATCAGCATCCTTAGCAGTCT 60.485 50.000 0.00 0.00 41.58 3.24
2783 2911 1.872313 GCATCAGCATCCTTAGCAGTC 59.128 52.381 0.00 0.00 41.58 3.51
2784 2912 1.489649 AGCATCAGCATCCTTAGCAGT 59.510 47.619 0.00 0.00 45.49 4.40
2785 2913 2.144730 GAGCATCAGCATCCTTAGCAG 58.855 52.381 0.00 0.00 45.49 4.24
2786 2914 1.202734 GGAGCATCAGCATCCTTAGCA 60.203 52.381 0.00 0.00 45.49 3.49
2787 2915 1.521580 GGAGCATCAGCATCCTTAGC 58.478 55.000 0.00 0.00 45.49 3.09
2788 2916 1.342496 TCGGAGCATCAGCATCCTTAG 59.658 52.381 0.00 0.00 45.49 2.18
2791 2919 0.035036 CATCGGAGCATCAGCATCCT 59.965 55.000 0.00 0.00 45.49 3.24
2988 3118 9.605275 CCAGAACTCTTTCAACAATAGATATGA 57.395 33.333 0.00 0.00 33.72 2.15
3038 3168 7.713764 AAAGGACAAGCAACATTTCAATAAC 57.286 32.000 0.00 0.00 0.00 1.89
3081 3211 6.683974 AGTCCTGATTCAAATATTTCCACG 57.316 37.500 0.00 0.00 0.00 4.94
3190 3322 6.406512 GGTTTGGTGTAAAGACCACTTCATTT 60.407 38.462 0.00 0.00 46.03 2.32
3194 3326 3.949113 TGGTTTGGTGTAAAGACCACTTC 59.051 43.478 0.00 0.00 46.03 3.01
3204 3336 4.781087 AGCTAGAGGTATGGTTTGGTGTAA 59.219 41.667 0.00 0.00 0.00 2.41
3213 3345 4.221703 GTGCATATGAGCTAGAGGTATGGT 59.778 45.833 6.97 0.00 34.99 3.55
3222 3356 6.164176 TCAGATCATTGTGCATATGAGCTAG 58.836 40.000 23.50 18.86 44.44 3.42
3308 3442 2.290260 CCCAACTGACATAAGCAGTCCA 60.290 50.000 0.00 0.00 45.27 4.02
3316 3450 2.830923 CAATTGGCCCCAACTGACATAA 59.169 45.455 0.00 0.00 35.47 1.90
3328 3462 0.899717 TCAAGCAGTCCAATTGGCCC 60.900 55.000 20.33 12.32 34.44 5.80
3330 3464 2.494870 AGATTCAAGCAGTCCAATTGGC 59.505 45.455 20.33 14.47 34.44 4.52
3355 3489 5.999044 AGGATAGACAGAATGAAGCAACAT 58.001 37.500 0.00 0.00 39.69 2.71
3408 3542 4.910458 AGCCTAGTAGTGGATGTTGTTT 57.090 40.909 0.00 0.00 0.00 2.83
3452 3586 5.852738 CACTGAGGATTTAGAACACAGTG 57.147 43.478 0.00 0.00 44.27 3.66
3453 3587 4.202357 TGCACTGAGGATTTAGAACACAGT 60.202 41.667 0.00 0.00 37.56 3.55
3497 3631 4.083110 GCATGTTGTCTGTTCTGTAGCATT 60.083 41.667 0.00 0.00 0.00 3.56
3500 3634 3.070018 AGCATGTTGTCTGTTCTGTAGC 58.930 45.455 0.00 0.00 0.00 3.58
3522 3656 2.760650 TCAGATACAGGAACACAGCGAT 59.239 45.455 0.00 0.00 0.00 4.58
3524 3658 2.654749 TCAGATACAGGAACACAGCG 57.345 50.000 0.00 0.00 0.00 5.18
3579 3714 6.627087 TCCTGTACCTGATTTGATCTTCTT 57.373 37.500 0.00 0.00 0.00 2.52
3587 3722 6.017605 GCTGACATATTCCTGTACCTGATTTG 60.018 42.308 0.00 0.00 0.00 2.32
3588 3723 6.058183 GCTGACATATTCCTGTACCTGATTT 58.942 40.000 0.00 0.00 0.00 2.17
3590 3725 4.904251 AGCTGACATATTCCTGTACCTGAT 59.096 41.667 0.00 0.00 0.00 2.90
3591 3726 4.100035 CAGCTGACATATTCCTGTACCTGA 59.900 45.833 8.42 0.00 0.00 3.86
3592 3727 4.141846 ACAGCTGACATATTCCTGTACCTG 60.142 45.833 23.35 0.00 35.20 4.00
3593 3728 4.033709 ACAGCTGACATATTCCTGTACCT 58.966 43.478 23.35 0.00 35.20 3.08
3594 3729 4.408182 ACAGCTGACATATTCCTGTACC 57.592 45.455 23.35 0.00 35.20 3.34
3595 3730 6.574350 AGTAACAGCTGACATATTCCTGTAC 58.426 40.000 23.35 0.00 35.86 2.90
3596 3731 6.791867 AGTAACAGCTGACATATTCCTGTA 57.208 37.500 23.35 0.00 35.86 2.74
3597 3732 5.683876 AGTAACAGCTGACATATTCCTGT 57.316 39.130 23.35 0.00 38.30 4.00
3598 3733 5.220739 GCAAGTAACAGCTGACATATTCCTG 60.221 44.000 23.35 6.61 0.00 3.86
3599 3734 4.878397 GCAAGTAACAGCTGACATATTCCT 59.122 41.667 23.35 0.00 0.00 3.36
3600 3735 4.635765 TGCAAGTAACAGCTGACATATTCC 59.364 41.667 23.35 2.78 0.00 3.01
3601 3736 5.801350 TGCAAGTAACAGCTGACATATTC 57.199 39.130 23.35 5.05 0.00 1.75
3602 3737 6.600822 AGATTGCAAGTAACAGCTGACATATT 59.399 34.615 23.35 6.20 0.00 1.28
3603 3738 6.118170 AGATTGCAAGTAACAGCTGACATAT 58.882 36.000 23.35 0.00 0.00 1.78
3604 3739 5.491070 AGATTGCAAGTAACAGCTGACATA 58.509 37.500 23.35 7.63 0.00 2.29
3605 3740 4.330250 AGATTGCAAGTAACAGCTGACAT 58.670 39.130 23.35 8.69 0.00 3.06
3606 3741 3.743521 AGATTGCAAGTAACAGCTGACA 58.256 40.909 23.35 4.06 0.00 3.58
3607 3742 5.179368 TGTTAGATTGCAAGTAACAGCTGAC 59.821 40.000 23.35 9.33 32.90 3.51
3608 3743 5.304778 TGTTAGATTGCAAGTAACAGCTGA 58.695 37.500 23.35 0.00 32.90 4.26
3609 3744 5.611796 TGTTAGATTGCAAGTAACAGCTG 57.388 39.130 23.59 13.48 32.90 4.24
3610 3745 7.065085 CAGTATGTTAGATTGCAAGTAACAGCT 59.935 37.037 27.78 24.84 39.40 4.24
3611 3746 7.064609 TCAGTATGTTAGATTGCAAGTAACAGC 59.935 37.037 27.78 23.75 39.40 4.40
3612 3747 8.479313 TCAGTATGTTAGATTGCAAGTAACAG 57.521 34.615 27.78 19.61 39.40 3.16
3613 3748 9.098355 GATCAGTATGTTAGATTGCAAGTAACA 57.902 33.333 26.95 26.95 40.11 2.41
3614 3749 9.098355 TGATCAGTATGTTAGATTGCAAGTAAC 57.902 33.333 20.23 20.23 37.40 2.50
3615 3750 9.665719 TTGATCAGTATGTTAGATTGCAAGTAA 57.334 29.630 4.94 2.53 37.40 2.24
3616 3751 9.665719 TTTGATCAGTATGTTAGATTGCAAGTA 57.334 29.630 4.94 0.00 37.40 2.24
3617 3752 8.565896 TTTGATCAGTATGTTAGATTGCAAGT 57.434 30.769 4.94 0.00 37.40 3.16
3618 3753 9.282247 GTTTTGATCAGTATGTTAGATTGCAAG 57.718 33.333 4.94 0.00 37.40 4.01
3619 3754 8.791675 TGTTTTGATCAGTATGTTAGATTGCAA 58.208 29.630 0.00 0.00 37.40 4.08
3620 3755 8.334263 TGTTTTGATCAGTATGTTAGATTGCA 57.666 30.769 0.00 0.00 37.40 4.08
3621 3756 9.065871 GTTGTTTTGATCAGTATGTTAGATTGC 57.934 33.333 0.00 0.00 37.40 3.56
3625 3760 9.431887 GGTAGTTGTTTTGATCAGTATGTTAGA 57.568 33.333 0.00 0.00 37.40 2.10
3626 3761 8.665685 GGGTAGTTGTTTTGATCAGTATGTTAG 58.334 37.037 0.00 0.00 37.40 2.34
3627 3762 8.380099 AGGGTAGTTGTTTTGATCAGTATGTTA 58.620 33.333 0.00 0.00 37.40 2.41
3628 3763 7.174946 CAGGGTAGTTGTTTTGATCAGTATGTT 59.825 37.037 0.00 0.00 37.40 2.71
3629 3764 6.655003 CAGGGTAGTTGTTTTGATCAGTATGT 59.345 38.462 0.00 0.00 37.40 2.29
3630 3765 6.403636 GCAGGGTAGTTGTTTTGATCAGTATG 60.404 42.308 0.00 0.00 37.54 2.39
3631 3766 5.648092 GCAGGGTAGTTGTTTTGATCAGTAT 59.352 40.000 0.00 0.00 0.00 2.12
3632 3767 5.001232 GCAGGGTAGTTGTTTTGATCAGTA 58.999 41.667 0.00 0.00 0.00 2.74
3633 3768 3.821033 GCAGGGTAGTTGTTTTGATCAGT 59.179 43.478 0.00 0.00 0.00 3.41
3634 3769 3.820467 TGCAGGGTAGTTGTTTTGATCAG 59.180 43.478 0.00 0.00 0.00 2.90
3635 3770 3.568007 GTGCAGGGTAGTTGTTTTGATCA 59.432 43.478 0.00 0.00 0.00 2.92
3636 3771 3.057526 GGTGCAGGGTAGTTGTTTTGATC 60.058 47.826 0.00 0.00 0.00 2.92
3637 3772 2.890945 GGTGCAGGGTAGTTGTTTTGAT 59.109 45.455 0.00 0.00 0.00 2.57
3638 3773 2.303175 GGTGCAGGGTAGTTGTTTTGA 58.697 47.619 0.00 0.00 0.00 2.69
3639 3774 2.028130 TGGTGCAGGGTAGTTGTTTTG 58.972 47.619 0.00 0.00 0.00 2.44
3640 3775 2.445682 TGGTGCAGGGTAGTTGTTTT 57.554 45.000 0.00 0.00 0.00 2.43
3641 3776 2.158534 TCATGGTGCAGGGTAGTTGTTT 60.159 45.455 0.00 0.00 0.00 2.83
3642 3777 1.423541 TCATGGTGCAGGGTAGTTGTT 59.576 47.619 0.00 0.00 0.00 2.83
3643 3778 1.064003 TCATGGTGCAGGGTAGTTGT 58.936 50.000 0.00 0.00 0.00 3.32
3644 3779 2.198827 TTCATGGTGCAGGGTAGTTG 57.801 50.000 0.00 0.00 0.00 3.16
3645 3780 2.375174 TCTTTCATGGTGCAGGGTAGTT 59.625 45.455 0.00 0.00 0.00 2.24
3646 3781 1.985159 TCTTTCATGGTGCAGGGTAGT 59.015 47.619 0.00 0.00 0.00 2.73
3647 3782 2.787473 TCTTTCATGGTGCAGGGTAG 57.213 50.000 0.00 0.00 0.00 3.18
3648 3783 3.153919 GTTTCTTTCATGGTGCAGGGTA 58.846 45.455 0.00 0.00 0.00 3.69
3649 3784 1.963515 GTTTCTTTCATGGTGCAGGGT 59.036 47.619 0.00 0.00 0.00 4.34
3650 3785 1.962807 TGTTTCTTTCATGGTGCAGGG 59.037 47.619 0.00 0.00 0.00 4.45
3651 3786 3.006110 ACATGTTTCTTTCATGGTGCAGG 59.994 43.478 10.01 0.00 44.57 4.85
3652 3787 4.247267 ACATGTTTCTTTCATGGTGCAG 57.753 40.909 10.01 0.00 44.57 4.41
3653 3788 4.669206 AACATGTTTCTTTCATGGTGCA 57.331 36.364 4.92 0.00 44.57 4.57
3654 3789 6.624423 AGATAACATGTTTCTTTCATGGTGC 58.376 36.000 17.78 0.27 42.23 5.01
3655 3790 8.048534 AGAGATAACATGTTTCTTTCATGGTG 57.951 34.615 17.78 0.00 42.23 4.17
3656 3791 8.641498 AAGAGATAACATGTTTCTTTCATGGT 57.359 30.769 17.78 6.32 44.57 3.55
3657 3792 8.954350 AGAAGAGATAACATGTTTCTTTCATGG 58.046 33.333 17.78 0.00 44.57 3.66
3663 3798 9.660180 GGTCTAAGAAGAGATAACATGTTTCTT 57.340 33.333 17.78 18.67 38.18 2.52
3664 3799 8.261522 GGGTCTAAGAAGAGATAACATGTTTCT 58.738 37.037 17.78 17.67 30.45 2.52
3665 3800 7.496263 GGGGTCTAAGAAGAGATAACATGTTTC 59.504 40.741 17.78 13.46 30.45 2.78
3666 3801 7.037586 TGGGGTCTAAGAAGAGATAACATGTTT 60.038 37.037 17.78 4.68 30.45 2.83
3667 3802 6.443849 TGGGGTCTAAGAAGAGATAACATGTT 59.556 38.462 16.68 16.68 30.45 2.71
3668 3803 5.964477 TGGGGTCTAAGAAGAGATAACATGT 59.036 40.000 0.00 0.00 30.45 3.21
3669 3804 6.127054 TGTGGGGTCTAAGAAGAGATAACATG 60.127 42.308 0.00 0.00 30.45 3.21
3670 3805 5.964477 TGTGGGGTCTAAGAAGAGATAACAT 59.036 40.000 0.00 0.00 30.45 2.71
3706 3841 9.941664 CTGGTAGAATTTATGTTAGATTGCAAG 57.058 33.333 4.94 0.00 0.00 4.01
3707 3842 8.902806 CCTGGTAGAATTTATGTTAGATTGCAA 58.097 33.333 0.00 0.00 0.00 4.08
3768 3903 3.214696 ACTACTGCTGGCTTGAAAACT 57.785 42.857 0.00 0.00 0.00 2.66
3900 4035 2.862541 CACCATCTGTCCAACCAAGAA 58.137 47.619 0.00 0.00 0.00 2.52
4073 4209 6.609237 TCTATGTATGATTTGTTGAGCTGC 57.391 37.500 0.00 0.00 0.00 5.25
4233 4369 9.480053 CAACTCCATCAAACACTCAAAATATTT 57.520 29.630 0.00 0.00 0.00 1.40
4236 4372 6.040278 TGCAACTCCATCAAACACTCAAAATA 59.960 34.615 0.00 0.00 0.00 1.40
4307 4446 7.351414 TGTCAATCTGAAGTGTTATTCTTCG 57.649 36.000 0.00 0.00 42.68 3.79
4313 4452 8.853077 TCTGAAATGTCAATCTGAAGTGTTAT 57.147 30.769 0.00 0.00 31.88 1.89
4344 4483 6.045955 TCTTTCCACACCTTAAATGCAAAAC 58.954 36.000 0.00 0.00 0.00 2.43
4361 4500 8.383175 AGTTACAGAAATAAGACCATCTTTCCA 58.617 33.333 0.00 0.00 37.89 3.53
4377 4516 7.333423 GCTGACATATTGGTGTAGTTACAGAAA 59.667 37.037 0.00 0.00 36.78 2.52
4379 4518 6.154534 AGCTGACATATTGGTGTAGTTACAGA 59.845 38.462 0.00 0.00 36.78 3.41
4406 4545 7.690952 AACAGTAAGTACACCTGAAACAAAA 57.309 32.000 11.85 0.00 0.00 2.44
4509 4648 7.706179 TGTTTGCACTTCTTAAAGAAAATCCTG 59.294 33.333 0.00 0.00 33.19 3.86
4624 4763 9.561069 GGCTGAATTGTAAGGAATCTATAGAAA 57.439 33.333 6.52 0.00 0.00 2.52
4649 4789 6.458210 AGCACCTGATTCAACAAAATAAAGG 58.542 36.000 0.00 0.00 32.52 3.11
4675 4815 8.362639 ACTGAAAAAGCTTGATACAATGAATGT 58.637 29.630 0.00 0.00 46.36 2.71
4716 4861 4.412199 TCCTCCATAAATCAACCCTGGTAG 59.588 45.833 0.00 0.00 0.00 3.18
4971 5116 1.360393 ACAGGGGAAAGCCACCTGAA 61.360 55.000 19.14 0.00 46.94 3.02
5019 5168 6.268566 GCTTGAGACAAACAAGATGAAAAGT 58.731 36.000 11.08 0.00 44.92 2.66
5103 5252 7.094634 GGGTAGTATGCCATAAAGTTGATCATG 60.095 40.741 0.00 0.00 45.88 3.07
5139 5288 9.747293 AAATAATGTTTTGGCCAAAGAAATTTG 57.253 25.926 28.79 0.00 0.00 2.32
5180 5329 9.799106 TCTCTAGAAAGTTGAATCAGGATTTTT 57.201 29.630 0.00 0.00 0.00 1.94
5181 5330 9.799106 TTCTCTAGAAAGTTGAATCAGGATTTT 57.201 29.630 0.00 0.00 0.00 1.82
5302 5453 8.898751 ATTCCCTCCATCCCATAATATAAGAT 57.101 34.615 0.00 0.00 0.00 2.40
5357 5508 4.219033 GCAACCAGAAAATCACTAACACG 58.781 43.478 0.00 0.00 0.00 4.49
5364 5515 6.681777 AGATACTTTGCAACCAGAAAATCAC 58.318 36.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.