Multiple sequence alignment - TraesCS3B01G338700

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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 TraesCS3B01G338700 chr3B 100.000 2651 0 0 1 2651 545011902 545009252 0.000000e+00 4896.0
1 TraesCS3B01G338700 chr3B 87.997 1183 100 20 657 1808 770094470 770095641 0.000000e+00 1360.0
2 TraesCS3B01G338700 chr3B 87.574 1183 105 20 657 1808 770091060 770092231 0.000000e+00 1332.0
3 TraesCS3B01G338700 chr3B 83.571 700 86 17 656 1337 598031459 598032147 1.730000e-176 628.0
4 TraesCS3B01G338700 chr3B 87.194 531 66 2 2 531 598030901 598031430 1.050000e-168 603.0
5 TraesCS3B01G338700 chr3B 84.428 533 60 12 1 531 770093929 770094440 1.100000e-138 503.0
6 TraesCS3B01G338700 chr3B 84.240 533 61 12 1 531 770090519 770091030 5.100000e-137 497.0
7 TraesCS3B01G338700 chr3B 84.453 521 56 17 2135 2651 770095903 770096402 8.530000e-135 490.0
8 TraesCS3B01G338700 chr3B 87.133 443 39 9 1382 1808 598032151 598032591 1.100000e-133 486.0
9 TraesCS3B01G338700 chr3B 89.862 217 20 1 2113 2329 598032757 598032971 7.230000e-71 278.0
10 TraesCS3B01G338700 chr3B 95.556 135 6 0 528 662 572635999 572636133 1.600000e-52 217.0
11 TraesCS3B01G338700 chr3B 95.522 134 6 0 526 659 236361943 236362076 5.750000e-52 215.0
12 TraesCS3B01G338700 chr1A 87.380 1149 100 19 696 1808 50705044 50706183 0.000000e+00 1277.0
13 TraesCS3B01G338700 chr1A 88.646 229 20 2 1866 2094 50706209 50706431 9.350000e-70 274.0
14 TraesCS3B01G338700 chr1A 93.662 142 7 2 530 671 287275137 287274998 7.430000e-51 211.0
15 TraesCS3B01G338700 chr1A 91.391 151 11 2 530 680 2161889 2162037 3.460000e-49 206.0
16 TraesCS3B01G338700 chr7B 86.432 1194 113 20 656 1808 374424884 374423699 0.000000e+00 1262.0
17 TraesCS3B01G338700 chr7B 84.644 534 57 13 1 531 374425424 374424913 2.350000e-140 508.0
18 TraesCS3B01G338700 chr7B 89.474 228 24 0 1866 2093 374423673 374423446 3.340000e-74 289.0
19 TraesCS3B01G338700 chr7B 90.196 204 17 2 2133 2335 374423440 374423239 2.020000e-66 263.0
20 TraesCS3B01G338700 chr7B 87.037 216 19 8 2438 2651 374423179 374422971 4.410000e-58 235.0
21 TraesCS3B01G338700 chr7B 92.157 51 3 1 2602 2651 586263066 586263116 1.320000e-08 71.3
22 TraesCS3B01G338700 chr5B 85.690 1160 131 16 656 1784 509467778 509468933 0.000000e+00 1190.0
23 TraesCS3B01G338700 chr5B 88.511 470 52 2 1866 2335 509469064 509469531 3.830000e-158 568.0
24 TraesCS3B01G338700 chr5B 85.366 533 67 7 1 531 509467226 509467749 2.320000e-150 542.0
25 TraesCS3B01G338700 chr5B 84.267 375 43 9 1927 2294 675887246 675887611 4.200000e-93 351.0
26 TraesCS3B01G338700 chr5B 89.888 89 5 3 2429 2515 675888089 675888175 7.760000e-21 111.0
27 TraesCS3B01G338700 chr5D 86.047 1118 111 23 725 1808 127880903 127882009 0.000000e+00 1158.0
28 TraesCS3B01G338700 chr5D 80.473 676 84 38 1866 2515 127882035 127882688 8.590000e-130 473.0
29 TraesCS3B01G338700 chr5D 84.892 278 32 5 1927 2204 535134639 535134906 3.360000e-69 272.0
30 TraesCS3B01G338700 chr5D 95.588 136 6 0 530 665 382507970 382508105 4.440000e-53 219.0
31 TraesCS3B01G338700 chr5D 90.000 80 6 1 2438 2515 535135258 535135337 4.670000e-18 102.0
32 TraesCS3B01G338700 chr6B 85.162 1112 122 27 728 1808 683644918 683646017 0.000000e+00 1099.0
33 TraesCS3B01G338700 chr6B 83.747 886 104 19 941 1807 633848249 633847385 0.000000e+00 802.0
34 TraesCS3B01G338700 chr6B 80.267 674 91 31 1866 2515 683646043 683646698 1.110000e-128 470.0
35 TraesCS3B01G338700 chr6B 82.972 323 36 10 2176 2494 633847188 633846881 9.350000e-70 274.0
36 TraesCS3B01G338700 chr7A 87.340 940 93 18 656 1571 48911055 48911992 0.000000e+00 1053.0
37 TraesCS3B01G338700 chr7A 89.610 385 37 3 149 531 48910643 48911026 1.100000e-133 486.0
38 TraesCS3B01G338700 chr7A 93.805 113 6 1 2224 2335 48912087 48912199 4.540000e-38 169.0
39 TraesCS3B01G338700 chr2B 85.214 886 100 18 725 1589 1830797 1831672 0.000000e+00 881.0
40 TraesCS3B01G338700 chr2B 95.556 135 6 0 528 662 514512945 514512811 1.600000e-52 217.0
41 TraesCS3B01G338700 chr1B 84.716 844 95 13 982 1808 524272645 524273471 0.000000e+00 813.0
42 TraesCS3B01G338700 chr1B 90.244 82 7 1 451 531 524272564 524272645 3.610000e-19 106.0
43 TraesCS3B01G338700 chr6D 84.789 710 85 14 656 1346 121626868 121626163 0.000000e+00 691.0
44 TraesCS3B01G338700 chr6D 87.828 534 56 7 1 531 121627424 121626897 3.750000e-173 617.0
45 TraesCS3B01G338700 chr6D 87.770 417 35 6 1382 1784 121626168 121625754 8.590000e-130 473.0
46 TraesCS3B01G338700 chr6D 95.522 134 6 0 527 660 435990640 435990507 5.750000e-52 215.0
47 TraesCS3B01G338700 chr3A 88.931 533 55 4 1 531 713719518 713718988 0.000000e+00 654.0
48 TraesCS3B01G338700 chr3A 86.120 598 64 10 656 1236 713718959 713718364 6.230000e-176 627.0
49 TraesCS3B01G338700 chr4B 86.747 498 52 7 1324 1808 502993698 502994194 2.320000e-150 542.0
50 TraesCS3B01G338700 chr4B 82.297 418 44 17 2105 2515 502994479 502994873 4.230000e-88 335.0
51 TraesCS3B01G338700 chr3D 90.909 396 30 3 1414 1808 380384221 380383831 6.500000e-146 527.0
52 TraesCS3B01G338700 chr3D 88.140 430 47 3 1866 2295 380383805 380383380 2.350000e-140 508.0
53 TraesCS3B01G338700 chr3D 83.730 252 18 6 160 400 380441951 380441712 1.600000e-52 217.0
54 TraesCS3B01G338700 chr3D 93.007 143 9 1 525 666 496172751 496172893 9.620000e-50 207.0
55 TraesCS3B01G338700 chr3D 90.625 128 12 0 394 521 380385199 380385072 1.260000e-38 171.0
56 TraesCS3B01G338700 chr6A 86.253 371 36 7 2087 2455 564514623 564514980 3.200000e-104 388.0
57 TraesCS3B01G338700 chr6A 95.556 135 6 0 528 662 201188609 201188743 1.600000e-52 217.0
58 TraesCS3B01G338700 chr4A 86.471 340 33 7 1930 2268 636650959 636650632 6.980000e-96 361.0
59 TraesCS3B01G338700 chr4A 87.234 94 6 3 2438 2525 636648301 636648208 4.670000e-18 102.0
60 TraesCS3B01G338700 chr7D 88.554 166 13 5 526 687 397563330 397563167 2.080000e-46 196.0


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 TraesCS3B01G338700 chr3B 545009252 545011902 2650 True 4896.000000 4896 100.000000 1 2651 1 chr3B.!!$R1 2650
1 TraesCS3B01G338700 chr3B 770090519 770096402 5883 False 836.400000 1360 85.738400 1 2651 5 chr3B.!!$F4 2650
2 TraesCS3B01G338700 chr3B 598030901 598032971 2070 False 498.750000 628 86.940000 2 2329 4 chr3B.!!$F3 2327
3 TraesCS3B01G338700 chr1A 50705044 50706431 1387 False 775.500000 1277 88.013000 696 2094 2 chr1A.!!$F2 1398
4 TraesCS3B01G338700 chr7B 374422971 374425424 2453 True 511.400000 1262 87.556600 1 2651 5 chr7B.!!$R1 2650
5 TraesCS3B01G338700 chr5B 509467226 509469531 2305 False 766.666667 1190 86.522333 1 2335 3 chr5B.!!$F1 2334
6 TraesCS3B01G338700 chr5B 675887246 675888175 929 False 231.000000 351 87.077500 1927 2515 2 chr5B.!!$F2 588
7 TraesCS3B01G338700 chr5D 127880903 127882688 1785 False 815.500000 1158 83.260000 725 2515 2 chr5D.!!$F2 1790
8 TraesCS3B01G338700 chr6B 683644918 683646698 1780 False 784.500000 1099 82.714500 728 2515 2 chr6B.!!$F1 1787
9 TraesCS3B01G338700 chr6B 633846881 633848249 1368 True 538.000000 802 83.359500 941 2494 2 chr6B.!!$R1 1553
10 TraesCS3B01G338700 chr7A 48910643 48912199 1556 False 569.333333 1053 90.251667 149 2335 3 chr7A.!!$F1 2186
11 TraesCS3B01G338700 chr2B 1830797 1831672 875 False 881.000000 881 85.214000 725 1589 1 chr2B.!!$F1 864
12 TraesCS3B01G338700 chr1B 524272564 524273471 907 False 459.500000 813 87.480000 451 1808 2 chr1B.!!$F1 1357
13 TraesCS3B01G338700 chr6D 121625754 121627424 1670 True 593.666667 691 86.795667 1 1784 3 chr6D.!!$R2 1783
14 TraesCS3B01G338700 chr3A 713718364 713719518 1154 True 640.500000 654 87.525500 1 1236 2 chr3A.!!$R1 1235
15 TraesCS3B01G338700 chr4B 502993698 502994873 1175 False 438.500000 542 84.522000 1324 2515 2 chr4B.!!$F1 1191
16 TraesCS3B01G338700 chr3D 380383380 380385199 1819 True 402.000000 527 89.891333 394 2295 3 chr3D.!!$R2 1901
17 TraesCS3B01G338700 chr4A 636648208 636650959 2751 True 231.500000 361 86.852500 1930 2525 2 chr4A.!!$R1 595

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
68 69 0.321564 TGCTATTGTTGTGGAGCGCT 60.322 50.0 11.27 11.27 37.77 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 5479 0.179043 TCCTCCTCCGAGACTCATCG 60.179 60.0 2.82 0.0 38.52 3.84 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
26 27 3.324846 ACATTACAGCTCTGAACTCCACA 59.675 43.478 3.60 0.00 0.00 4.17
30 31 2.105477 ACAGCTCTGAACTCCACAACAT 59.895 45.455 3.60 0.00 0.00 2.71
68 69 0.321564 TGCTATTGTTGTGGAGCGCT 60.322 50.000 11.27 11.27 37.77 5.92
74 75 1.078848 GTTGTGGAGCGCTGAGGAT 60.079 57.895 18.48 0.00 0.00 3.24
78 79 2.894387 GGAGCGCTGAGGATGCAC 60.894 66.667 18.48 0.00 0.00 4.57
129 130 2.099062 CGCGAAATCTGCCACTGC 59.901 61.111 0.00 0.00 38.26 4.40
131 132 2.334946 GCGAAATCTGCCACTGCCA 61.335 57.895 0.00 0.00 36.33 4.92
132 133 1.798735 CGAAATCTGCCACTGCCAG 59.201 57.895 0.00 0.00 36.33 4.85
133 134 1.651240 CGAAATCTGCCACTGCCAGG 61.651 60.000 0.00 0.00 36.33 4.45
139 140 1.229177 TGCCACTGCCAGGTCTCTA 60.229 57.895 0.00 0.00 36.33 2.43
154 155 1.143305 CTCTATGTGCGCTGGTATGC 58.857 55.000 9.73 0.00 0.00 3.14
166 167 2.350772 GCTGGTATGCTTTGTGTGTGAC 60.351 50.000 0.00 0.00 0.00 3.67
169 170 4.709250 TGGTATGCTTTGTGTGTGACTTA 58.291 39.130 0.00 0.00 0.00 2.24
192 193 4.848000 TGGCAACTGGCATGATGT 57.152 50.000 1.18 0.00 46.12 3.06
255 256 6.181908 ACAGTTGGTTTGTTACTTTAGACCA 58.818 36.000 0.00 0.00 35.52 4.02
274 3685 1.800586 CAACGAGTGAATCCACAGGTG 59.199 52.381 0.00 0.00 45.54 4.00
294 3705 4.152223 GGTGATGTTTGCAGCAATAAAACC 59.848 41.667 9.12 9.80 43.08 3.27
307 3718 5.047660 AGCAATAAAACCGCAACCTTCATTA 60.048 36.000 0.00 0.00 0.00 1.90
319 3730 5.472137 GCAACCTTCATTACAGGACAAGTTA 59.528 40.000 0.00 0.00 35.14 2.24
426 3838 5.091431 CGTGAGATTTCTTTTCTGAATGCC 58.909 41.667 0.00 0.00 0.00 4.40
439 3851 2.352960 CTGAATGCCGAAGAAAGCTACC 59.647 50.000 0.00 0.00 0.00 3.18
440 3852 1.327764 GAATGCCGAAGAAAGCTACCG 59.672 52.381 0.00 0.00 0.00 4.02
464 3877 6.241207 AGCAAGTTCATGTATGTACAACAC 57.759 37.500 0.00 1.51 39.99 3.32
507 3920 0.393944 GCCCCAGTTGTAGGTAAGCC 60.394 60.000 0.00 0.00 0.00 4.35
531 3946 5.521735 CACACTGCCAATCTCATCTTACTAC 59.478 44.000 0.00 0.00 0.00 2.73
532 3947 5.423610 ACACTGCCAATCTCATCTTACTACT 59.576 40.000 0.00 0.00 0.00 2.57
535 3950 4.345257 TGCCAATCTCATCTTACTACTCCC 59.655 45.833 0.00 0.00 0.00 4.30
537 3952 5.279256 GCCAATCTCATCTTACTACTCCCTC 60.279 48.000 0.00 0.00 0.00 4.30
539 3954 4.088056 TCTCATCTTACTACTCCCTCCG 57.912 50.000 0.00 0.00 0.00 4.63
541 3956 3.816523 CTCATCTTACTACTCCCTCCGTC 59.183 52.174 0.00 0.00 0.00 4.79
542 3957 3.458857 TCATCTTACTACTCCCTCCGTCT 59.541 47.826 0.00 0.00 0.00 4.18
543 3958 3.557228 TCTTACTACTCCCTCCGTCTC 57.443 52.381 0.00 0.00 0.00 3.36
545 3960 3.265221 TCTTACTACTCCCTCCGTCTCAA 59.735 47.826 0.00 0.00 0.00 3.02
546 3961 2.599408 ACTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
547 3962 2.885616 ACTACTCCCTCCGTCTCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
552 3967 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
553 3968 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
555 3970 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
557 3972 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
558 3973 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
559 3974 6.091441 CCTCCGTCTCAAAATTCTTGTCTTAG 59.909 42.308 0.00 0.00 0.00 2.18
560 3975 6.755206 TCCGTCTCAAAATTCTTGTCTTAGA 58.245 36.000 0.00 0.00 0.00 2.10
561 3976 7.386851 TCCGTCTCAAAATTCTTGTCTTAGAT 58.613 34.615 0.00 0.00 0.00 1.98
562 3977 7.878127 TCCGTCTCAAAATTCTTGTCTTAGATT 59.122 33.333 0.00 0.00 0.00 2.40
563 3978 8.507249 CCGTCTCAAAATTCTTGTCTTAGATTT 58.493 33.333 0.00 0.00 0.00 2.17
564 3979 9.322776 CGTCTCAAAATTCTTGTCTTAGATTTG 57.677 33.333 0.00 0.00 30.65 2.32
575 3990 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
576 3991 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
577 3992 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
578 3993 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
579 3994 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
580 3995 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
596 4011 9.944376 ATACGGATGTATCTAATGCTAAAATGT 57.056 29.630 0.00 0.00 36.56 2.71
597 4012 8.087982 ACGGATGTATCTAATGCTAAAATGTG 57.912 34.615 0.00 0.00 0.00 3.21
598 4013 7.931407 ACGGATGTATCTAATGCTAAAATGTGA 59.069 33.333 0.00 0.00 0.00 3.58
599 4014 8.223769 CGGATGTATCTAATGCTAAAATGTGAC 58.776 37.037 0.00 0.00 0.00 3.67
600 4015 9.277783 GGATGTATCTAATGCTAAAATGTGACT 57.722 33.333 0.00 0.00 0.00 3.41
603 4018 9.665719 TGTATCTAATGCTAAAATGTGACTTGA 57.334 29.630 0.00 0.00 0.00 3.02
607 4022 9.665719 TCTAATGCTAAAATGTGACTTGATACA 57.334 29.630 0.00 0.00 0.00 2.29
610 4025 8.743085 ATGCTAAAATGTGACTTGATACATCT 57.257 30.769 0.00 0.00 36.56 2.90
611 4026 7.977904 TGCTAAAATGTGACTTGATACATCTG 58.022 34.615 0.00 0.00 36.56 2.90
612 4027 7.607607 TGCTAAAATGTGACTTGATACATCTGT 59.392 33.333 0.00 0.00 36.56 3.41
613 4028 9.098355 GCTAAAATGTGACTTGATACATCTGTA 57.902 33.333 0.00 0.00 36.56 2.74
643 4058 8.526147 AGACAAATCTAAGACATGAATTTTGGG 58.474 33.333 0.00 0.00 31.46 4.12
644 4059 8.421249 ACAAATCTAAGACATGAATTTTGGGA 57.579 30.769 0.00 0.00 0.00 4.37
645 4060 8.306761 ACAAATCTAAGACATGAATTTTGGGAC 58.693 33.333 0.00 0.00 0.00 4.46
646 4061 6.683974 ATCTAAGACATGAATTTTGGGACG 57.316 37.500 0.00 0.00 0.00 4.79
647 4062 4.941263 TCTAAGACATGAATTTTGGGACGG 59.059 41.667 0.00 0.00 0.00 4.79
648 4063 3.433306 AGACATGAATTTTGGGACGGA 57.567 42.857 0.00 0.00 0.00 4.69
649 4064 3.347216 AGACATGAATTTTGGGACGGAG 58.653 45.455 0.00 0.00 0.00 4.63
650 4065 2.423538 GACATGAATTTTGGGACGGAGG 59.576 50.000 0.00 0.00 0.00 4.30
651 4066 1.750778 CATGAATTTTGGGACGGAGGG 59.249 52.381 0.00 0.00 0.00 4.30
652 4067 1.068948 TGAATTTTGGGACGGAGGGA 58.931 50.000 0.00 0.00 0.00 4.20
653 4068 1.004277 TGAATTTTGGGACGGAGGGAG 59.996 52.381 0.00 0.00 0.00 4.30
654 4069 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
703 4118 7.669722 TCTTCTCCCTTGTTTTAGCAAATGTAT 59.330 33.333 0.00 0.00 0.00 2.29
716 4131 3.488047 GCAAATGTATTCAGCTGCGATGT 60.488 43.478 9.47 0.00 0.00 3.06
721 4136 2.293677 ATTCAGCTGCGATGTCGTTA 57.706 45.000 9.47 0.00 42.22 3.18
903 4347 6.388278 AGAGACTTTGTTAATCAGTACCGAC 58.612 40.000 0.00 0.00 0.00 4.79
930 4374 7.126726 GCATAACATCGATGCTAGAATCTTT 57.873 36.000 25.11 10.82 45.14 2.52
987 4451 7.603404 CAGGTCATAAATTGCTTGGAAAAATGA 59.397 33.333 0.00 0.00 0.00 2.57
1020 4488 4.517453 GCTAGAATCCTGACGAGACTATGT 59.483 45.833 0.00 0.00 0.00 2.29
1022 4490 4.527944 AGAATCCTGACGAGACTATGTCA 58.472 43.478 9.09 9.09 42.49 3.58
1111 4582 1.359848 GACATCGCCGTCTTCAACAT 58.640 50.000 0.00 0.00 32.92 2.71
1127 4598 6.388100 TCTTCAACATGGATAAGATCTCCCTT 59.612 38.462 0.00 0.00 31.32 3.95
1164 4635 2.837883 CGCACCTGCACTGCTGTTT 61.838 57.895 9.41 0.00 42.21 2.83
1182 4653 3.009473 TGTTTCCATTCCTTCTCCCTCTG 59.991 47.826 0.00 0.00 0.00 3.35
1259 4738 2.724273 GGGCGGGCGTAACCTCTTA 61.724 63.158 0.00 0.00 39.10 2.10
1315 4794 1.051008 CTGTCATGATCGGATGGGGA 58.949 55.000 0.00 0.00 0.00 4.81
1338 4824 2.040278 CCCAAGTTCAGTCCCATCTTCA 59.960 50.000 0.00 0.00 0.00 3.02
1349 4835 1.467920 CCATCTTCACTTTGCTCCCC 58.532 55.000 0.00 0.00 0.00 4.81
1351 4837 1.005215 CATCTTCACTTTGCTCCCCCT 59.995 52.381 0.00 0.00 0.00 4.79
1353 4839 0.401738 CTTCACTTTGCTCCCCCTCA 59.598 55.000 0.00 0.00 0.00 3.86
1354 4840 0.110486 TTCACTTTGCTCCCCCTCAC 59.890 55.000 0.00 0.00 0.00 3.51
1382 4873 6.039270 CAGTTTCTCTCCTATCTGTCGAGATT 59.961 42.308 0.00 0.00 39.76 2.40
1383 4874 6.605594 AGTTTCTCTCCTATCTGTCGAGATTT 59.394 38.462 0.00 0.00 39.76 2.17
1384 4875 7.776030 AGTTTCTCTCCTATCTGTCGAGATTTA 59.224 37.037 0.00 0.00 39.76 1.40
1385 4876 7.499321 TTCTCTCCTATCTGTCGAGATTTAC 57.501 40.000 0.00 0.00 39.76 2.01
1386 4877 6.833041 TCTCTCCTATCTGTCGAGATTTACT 58.167 40.000 0.00 0.00 39.76 2.24
1399 4904 7.985752 TGTCGAGATTTACTATGTCTCTCTACA 59.014 37.037 0.00 0.00 36.74 2.74
1412 4955 7.561021 TGTCTCTCTACAGCTATTCTACTTG 57.439 40.000 0.00 0.00 0.00 3.16
1453 4996 4.100808 TCAAAGGCAATTGCTTTACTGGTT 59.899 37.500 25.81 8.48 39.53 3.67
1469 5012 3.263425 ACTGGTTAACATGTGTAGGAGGG 59.737 47.826 8.10 0.00 0.00 4.30
1490 5033 5.947566 AGGGTTTGTGGTTTAGCGTTATTAT 59.052 36.000 0.00 0.00 0.00 1.28
1563 5107 1.758862 AGGCCATCAAAGCTAATTGCC 59.241 47.619 5.01 9.52 44.23 4.52
1566 5110 3.192466 GCCATCAAAGCTAATTGCCTTG 58.808 45.455 0.00 5.40 42.73 3.61
1572 5116 1.467920 AGCTAATTGCCTTGCTGGTC 58.532 50.000 0.00 0.00 44.23 4.02
1613 5184 4.943705 CCCTGTACATACATGTTTGCTCTT 59.056 41.667 15.22 0.03 41.97 2.85
1624 5195 9.793252 ATACATGTTTGCTCTTTGCTATAAAAG 57.207 29.630 2.30 0.00 43.37 2.27
1706 5282 5.755409 TTGGGTGAACTATAGAAGCTGAA 57.245 39.130 6.78 0.00 0.00 3.02
1808 5465 4.843220 ACAGAAAGAAAGCAGATTGTGG 57.157 40.909 0.00 0.00 0.00 4.17
1810 5467 4.276926 ACAGAAAGAAAGCAGATTGTGGTC 59.723 41.667 0.00 0.00 35.15 4.02
1811 5468 4.276678 CAGAAAGAAAGCAGATTGTGGTCA 59.723 41.667 0.00 0.00 35.15 4.02
1812 5469 4.889409 AGAAAGAAAGCAGATTGTGGTCAA 59.111 37.500 0.00 0.00 35.15 3.18
1813 5470 4.574599 AAGAAAGCAGATTGTGGTCAAC 57.425 40.909 0.00 0.00 35.15 3.18
1814 5471 3.825328 AGAAAGCAGATTGTGGTCAACT 58.175 40.909 0.00 0.00 35.15 3.16
1815 5472 3.567164 AGAAAGCAGATTGTGGTCAACTG 59.433 43.478 0.00 0.00 35.15 3.16
1816 5473 1.901591 AGCAGATTGTGGTCAACTGG 58.098 50.000 0.00 0.00 36.33 4.00
1817 5474 0.883833 GCAGATTGTGGTCAACTGGG 59.116 55.000 0.00 0.00 36.33 4.45
1819 5476 2.430465 CAGATTGTGGTCAACTGGGAG 58.570 52.381 0.00 0.00 36.33 4.30
1820 5477 2.038952 CAGATTGTGGTCAACTGGGAGA 59.961 50.000 0.00 0.00 36.33 3.71
1822 5479 2.341846 TTGTGGTCAACTGGGAGAAC 57.658 50.000 0.00 0.00 0.00 3.01
1824 5481 0.391597 GTGGTCAACTGGGAGAACGA 59.608 55.000 0.00 0.00 0.00 3.85
1829 5486 2.028930 GTCAACTGGGAGAACGATGAGT 60.029 50.000 0.00 0.00 0.00 3.41
1830 5487 2.231478 TCAACTGGGAGAACGATGAGTC 59.769 50.000 0.00 0.00 0.00 3.36
1831 5488 2.223803 ACTGGGAGAACGATGAGTCT 57.776 50.000 0.00 0.00 0.00 3.24
1832 5489 2.096248 ACTGGGAGAACGATGAGTCTC 58.904 52.381 0.00 0.00 0.00 3.36
1833 5490 1.064803 CTGGGAGAACGATGAGTCTCG 59.935 57.143 9.51 9.51 44.14 4.04
1834 5491 0.382515 GGGAGAACGATGAGTCTCGG 59.617 60.000 13.90 0.00 42.88 4.63
1835 5492 1.380524 GGAGAACGATGAGTCTCGGA 58.619 55.000 13.90 0.00 42.88 4.55
1836 5493 1.332375 GGAGAACGATGAGTCTCGGAG 59.668 57.143 13.90 0.00 42.88 4.63
1837 5494 1.332375 GAGAACGATGAGTCTCGGAGG 59.668 57.143 4.96 0.00 42.88 4.30
1838 5495 1.065345 AGAACGATGAGTCTCGGAGGA 60.065 52.381 4.96 0.00 42.88 3.71
1839 5496 1.332375 GAACGATGAGTCTCGGAGGAG 59.668 57.143 4.96 0.00 42.88 3.69
1840 5497 0.464735 ACGATGAGTCTCGGAGGAGG 60.465 60.000 4.96 0.00 42.88 4.30
1841 5498 0.179043 CGATGAGTCTCGGAGGAGGA 60.179 60.000 4.96 0.00 40.85 3.71
1842 5499 1.314730 GATGAGTCTCGGAGGAGGAC 58.685 60.000 4.96 0.00 40.85 3.85
1843 5500 0.626382 ATGAGTCTCGGAGGAGGACA 59.374 55.000 4.96 0.24 40.85 4.02
1844 5501 0.404426 TGAGTCTCGGAGGAGGACAA 59.596 55.000 4.96 0.00 40.85 3.18
1845 5502 1.099689 GAGTCTCGGAGGAGGACAAG 58.900 60.000 4.96 0.00 40.85 3.16
1846 5503 0.406361 AGTCTCGGAGGAGGACAAGT 59.594 55.000 4.96 0.00 40.85 3.16
1847 5504 0.528470 GTCTCGGAGGAGGACAAGTG 59.472 60.000 4.96 0.00 40.85 3.16
1848 5505 0.612174 TCTCGGAGGAGGACAAGTGG 60.612 60.000 4.96 0.00 40.85 4.00
1849 5506 0.900647 CTCGGAGGAGGACAAGTGGT 60.901 60.000 0.00 0.00 36.61 4.16
1850 5507 1.185618 TCGGAGGAGGACAAGTGGTG 61.186 60.000 0.00 0.00 0.00 4.17
1851 5508 1.679898 GGAGGAGGACAAGTGGTGG 59.320 63.158 0.00 0.00 0.00 4.61
1852 5509 1.679898 GAGGAGGACAAGTGGTGGG 59.320 63.158 0.00 0.00 0.00 4.61
1853 5510 2.034221 GGAGGACAAGTGGTGGGC 59.966 66.667 0.00 0.00 0.00 5.36
1854 5511 2.358737 GAGGACAAGTGGTGGGCG 60.359 66.667 0.00 0.00 0.00 6.13
1855 5512 3.168528 AGGACAAGTGGTGGGCGT 61.169 61.111 0.00 0.00 0.00 5.68
1856 5513 1.823169 GAGGACAAGTGGTGGGCGTA 61.823 60.000 0.00 0.00 0.00 4.42
1857 5514 1.375523 GGACAAGTGGTGGGCGTAG 60.376 63.158 0.00 0.00 0.00 3.51
1949 5609 6.945938 TTGTGTTTCTTTTCGGAGGATAAA 57.054 33.333 0.00 0.00 0.00 1.40
1967 5627 5.163733 GGATAAATTTTGCCAGCAATTGTGG 60.164 40.000 17.67 17.67 35.70 4.17
1991 5651 4.766969 CTTGCAAGCAGAAAACTTGTTC 57.233 40.909 14.65 0.00 45.09 3.18
2000 5660 7.992180 AGCAGAAAACTTGTTCATTTAGTTG 57.008 32.000 0.00 0.00 32.76 3.16
2026 5686 4.467438 TCACCACTGATTCTGCTGAAGATA 59.533 41.667 11.86 0.46 35.44 1.98
2075 5735 6.876155 TGTGCCAATCCTAACGTTAGTATAA 58.124 36.000 28.60 14.61 0.00 0.98
2204 5894 2.386661 TCTTCTGCTTTCCGTCCATC 57.613 50.000 0.00 0.00 0.00 3.51
2218 5915 1.394917 GTCCATCGAGACATGCAACAC 59.605 52.381 0.00 0.00 36.73 3.32
2251 5948 3.944015 AGAAACTAGGTGCAATCTGATGC 59.056 43.478 0.00 0.00 46.58 3.91
2320 7921 3.003793 GCTTTCCACTCTCTTTTGGTGAC 59.996 47.826 0.00 0.00 34.19 3.67
2325 7926 5.794894 TCCACTCTCTTTTGGTGACTATTC 58.205 41.667 0.00 0.00 34.19 1.75
2335 7936 7.939039 TCTTTTGGTGACTATTCTGTGATTCTT 59.061 33.333 0.00 0.00 0.00 2.52
2337 7938 5.734720 TGGTGACTATTCTGTGATTCTTCC 58.265 41.667 0.00 0.00 0.00 3.46
2338 7939 5.485353 TGGTGACTATTCTGTGATTCTTCCT 59.515 40.000 0.00 0.00 0.00 3.36
2340 7941 6.314896 GGTGACTATTCTGTGATTCTTCCTTG 59.685 42.308 0.00 0.00 0.00 3.61
2341 7942 6.314896 GTGACTATTCTGTGATTCTTCCTTGG 59.685 42.308 0.00 0.00 0.00 3.61
2342 7943 6.013379 TGACTATTCTGTGATTCTTCCTTGGT 60.013 38.462 0.00 0.00 0.00 3.67
2344 7945 7.918076 ACTATTCTGTGATTCTTCCTTGGTAA 58.082 34.615 0.00 0.00 0.00 2.85
2345 7946 8.383175 ACTATTCTGTGATTCTTCCTTGGTAAA 58.617 33.333 0.00 0.00 0.00 2.01
2346 7947 9.231297 CTATTCTGTGATTCTTCCTTGGTAAAA 57.769 33.333 0.00 0.00 0.00 1.52
2347 7948 8.655935 ATTCTGTGATTCTTCCTTGGTAAAAT 57.344 30.769 0.00 0.00 0.00 1.82
2349 7950 8.792830 TCTGTGATTCTTCCTTGGTAAAATAG 57.207 34.615 0.00 0.00 0.00 1.73
2350 7951 8.383175 TCTGTGATTCTTCCTTGGTAAAATAGT 58.617 33.333 0.00 0.00 0.00 2.12
2351 7952 9.667107 CTGTGATTCTTCCTTGGTAAAATAGTA 57.333 33.333 0.00 0.00 0.00 1.82
2352 7953 9.444600 TGTGATTCTTCCTTGGTAAAATAGTAC 57.555 33.333 0.00 0.00 0.00 2.73
2353 7954 8.890718 GTGATTCTTCCTTGGTAAAATAGTACC 58.109 37.037 0.00 0.00 43.45 3.34
2354 7955 8.050930 TGATTCTTCCTTGGTAAAATAGTACCC 58.949 37.037 0.00 0.00 42.63 3.69
2355 7956 6.956102 TCTTCCTTGGTAAAATAGTACCCA 57.044 37.500 0.00 0.00 42.63 4.51
2356 7957 6.714278 TCTTCCTTGGTAAAATAGTACCCAC 58.286 40.000 0.00 0.00 42.63 4.61
2357 7958 6.502863 TCTTCCTTGGTAAAATAGTACCCACT 59.497 38.462 0.00 0.00 42.63 4.00
2364 7965 8.168790 TGGTAAAATAGTACCCACTTTGAAAC 57.831 34.615 0.00 0.00 42.63 2.78
2366 7967 7.449395 GGTAAAATAGTACCCACTTTGAAACCT 59.551 37.037 0.00 0.00 38.08 3.50
2367 7968 7.907841 AAAATAGTACCCACTTTGAAACCTT 57.092 32.000 0.00 0.00 36.14 3.50
2370 7971 8.999905 AATAGTACCCACTTTGAAACCTTTTA 57.000 30.769 0.00 0.00 36.14 1.52
2436 8347 7.041576 TCAGCTTGTGATATATCTTGCATGTTC 60.042 37.037 13.79 2.80 0.00 3.18
2442 8353 7.495606 TGTGATATATCTTGCATGTTCGAAACT 59.504 33.333 13.79 0.00 0.00 2.66
2495 8406 3.771577 AGGTAGAGTTGGAGTTGGTTG 57.228 47.619 0.00 0.00 0.00 3.77
2506 8419 5.037383 TGGAGTTGGTTGTGTTGTACATA 57.963 39.130 0.00 0.00 39.48 2.29
2515 8428 5.938125 GGTTGTGTTGTACATATCTGGTCTT 59.062 40.000 0.00 0.00 39.48 3.01
2516 8429 6.128282 GGTTGTGTTGTACATATCTGGTCTTG 60.128 42.308 0.00 0.00 39.48 3.02
2518 8431 7.234661 TGTGTTGTACATATCTGGTCTTGTA 57.765 36.000 0.00 0.00 33.42 2.41
2519 8432 7.320399 TGTGTTGTACATATCTGGTCTTGTAG 58.680 38.462 0.00 0.00 33.42 2.74
2520 8433 7.039293 TGTGTTGTACATATCTGGTCTTGTAGT 60.039 37.037 0.00 0.00 33.42 2.73
2522 8435 8.372459 TGTTGTACATATCTGGTCTTGTAGTTT 58.628 33.333 0.00 0.00 0.00 2.66
2523 8436 8.656849 GTTGTACATATCTGGTCTTGTAGTTTG 58.343 37.037 0.00 0.00 0.00 2.93
2524 8437 8.129496 TGTACATATCTGGTCTTGTAGTTTGA 57.871 34.615 0.00 0.00 0.00 2.69
2525 8438 8.251026 TGTACATATCTGGTCTTGTAGTTTGAG 58.749 37.037 0.00 0.00 0.00 3.02
2526 8439 7.246171 ACATATCTGGTCTTGTAGTTTGAGT 57.754 36.000 0.00 0.00 0.00 3.41
2533 8446 6.119536 TGGTCTTGTAGTTTGAGTGTTTGAT 58.880 36.000 0.00 0.00 0.00 2.57
2547 8460 7.051623 TGAGTGTTTGATTAAGGTACTGTTGT 58.948 34.615 0.00 0.00 40.86 3.32
2561 8474 7.878036 AGGTACTGTTGTATTAATGCGTTTTT 58.122 30.769 0.00 0.00 37.18 1.94
2584 8497 7.447374 TTGTTAATTCTGTATGGTTGTCTGG 57.553 36.000 0.00 0.00 0.00 3.86
2587 8500 8.158132 TGTTAATTCTGTATGGTTGTCTGGTTA 58.842 33.333 0.00 0.00 0.00 2.85
2616 8529 4.119136 CCACTATGTGCATGTTCGATACA 58.881 43.478 0.00 3.49 35.04 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.133901 TGTTGTGGAGTTCAGAGCTGTAA 59.866 43.478 0.00 0.00 0.00 2.41
26 27 6.624423 GCAACAGAATGAGAGCAATGTATGTT 60.624 38.462 0.00 0.00 39.69 2.71
30 31 4.582869 AGCAACAGAATGAGAGCAATGTA 58.417 39.130 0.00 0.00 39.69 2.29
88 89 0.036952 CTGACTGGAAGACACGGCAT 60.037 55.000 0.00 0.00 32.69 4.40
89 90 1.367471 CTGACTGGAAGACACGGCA 59.633 57.895 0.00 0.00 32.69 5.69
94 95 1.248486 CGTCTCCTGACTGGAAGACA 58.752 55.000 20.38 0.00 45.63 3.41
95 96 0.109039 GCGTCTCCTGACTGGAAGAC 60.109 60.000 15.08 15.08 45.63 3.01
109 110 1.016130 CAGTGGCAGATTTCGCGTCT 61.016 55.000 5.77 0.00 0.00 4.18
129 130 0.529337 CAGCGCACATAGAGACCTGG 60.529 60.000 11.47 0.00 0.00 4.45
131 132 0.972983 ACCAGCGCACATAGAGACCT 60.973 55.000 11.47 0.00 0.00 3.85
132 133 0.744874 TACCAGCGCACATAGAGACC 59.255 55.000 11.47 0.00 0.00 3.85
133 134 2.398498 CATACCAGCGCACATAGAGAC 58.602 52.381 11.47 0.00 0.00 3.36
139 140 0.452987 CAAAGCATACCAGCGCACAT 59.547 50.000 11.47 0.00 40.15 3.21
154 155 5.288472 GCCAAACTTTAAGTCACACACAAAG 59.712 40.000 0.00 0.00 31.54 2.77
166 167 3.451141 TGCCAGTTGCCAAACTTTAAG 57.549 42.857 0.00 0.00 44.47 1.85
169 170 1.761784 TCATGCCAGTTGCCAAACTTT 59.238 42.857 0.00 0.00 44.47 2.66
215 216 2.786777 ACTGTCAGCAATTGATGAGCA 58.213 42.857 25.81 22.36 41.51 4.26
216 217 3.499048 CAACTGTCAGCAATTGATGAGC 58.501 45.455 25.81 19.46 41.51 4.26
218 219 3.489355 ACCAACTGTCAGCAATTGATGA 58.511 40.909 21.91 21.91 38.29 2.92
255 256 1.691976 TCACCTGTGGATTCACTCGTT 59.308 47.619 5.55 0.00 43.94 3.85
274 3685 3.181531 GCGGTTTTATTGCTGCAAACATC 60.182 43.478 20.06 8.89 37.00 3.06
294 3705 2.422597 TGTCCTGTAATGAAGGTTGCG 58.577 47.619 0.00 0.00 36.14 4.85
307 3718 5.568620 AGATTCAGGTTAACTTGTCCTGT 57.431 39.130 16.37 0.43 46.04 4.00
319 3730 7.890127 TGAAGACAAATCCATTAGATTCAGGTT 59.110 33.333 0.00 0.00 44.75 3.50
330 3742 9.028284 AGAACATTATGTGAAGACAAATCCATT 57.972 29.630 0.00 0.00 35.11 3.16
397 3809 7.912056 TCAGAAAAGAAATCTCACGATGATT 57.088 32.000 0.00 0.00 35.88 2.57
439 3851 5.120053 TGTTGTACATACATGAACTTGCTCG 59.880 40.000 0.00 0.00 35.89 5.03
440 3852 6.147821 AGTGTTGTACATACATGAACTTGCTC 59.852 38.462 0.00 0.01 35.89 4.26
507 3920 4.511527 AGTAAGATGAGATTGGCAGTGTG 58.488 43.478 0.00 0.00 0.00 3.82
531 3946 3.618690 AGAATTTTGAGACGGAGGGAG 57.381 47.619 0.00 0.00 0.00 4.30
532 3947 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
535 3950 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
537 3952 7.602517 ATCTAAGACAAGAATTTTGAGACGG 57.397 36.000 7.18 0.00 0.00 4.79
552 3967 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
553 3968 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
570 3985 9.944376 ACATTTTAGCATTAGATACATCCGTAT 57.056 29.630 0.00 0.00 41.16 3.06
571 3986 9.203421 CACATTTTAGCATTAGATACATCCGTA 57.797 33.333 0.00 0.00 0.00 4.02
572 3987 7.931407 TCACATTTTAGCATTAGATACATCCGT 59.069 33.333 0.00 0.00 0.00 4.69
573 3988 8.223769 GTCACATTTTAGCATTAGATACATCCG 58.776 37.037 0.00 0.00 0.00 4.18
574 3989 9.277783 AGTCACATTTTAGCATTAGATACATCC 57.722 33.333 0.00 0.00 0.00 3.51
577 3992 9.665719 TCAAGTCACATTTTAGCATTAGATACA 57.334 29.630 0.00 0.00 0.00 2.29
581 3996 9.665719 TGTATCAAGTCACATTTTAGCATTAGA 57.334 29.630 0.00 0.00 0.00 2.10
584 3999 9.182214 AGATGTATCAAGTCACATTTTAGCATT 57.818 29.630 0.00 0.00 35.55 3.56
585 4000 8.618677 CAGATGTATCAAGTCACATTTTAGCAT 58.381 33.333 0.00 0.00 35.55 3.79
586 4001 7.607607 ACAGATGTATCAAGTCACATTTTAGCA 59.392 33.333 0.00 0.00 35.55 3.49
587 4002 7.978982 ACAGATGTATCAAGTCACATTTTAGC 58.021 34.615 0.00 0.00 35.55 3.09
590 4005 9.453572 ACATACAGATGTATCAAGTCACATTTT 57.546 29.630 2.47 0.00 44.77 1.82
592 4007 9.755804 CTACATACAGATGTATCAAGTCACATT 57.244 33.333 2.47 0.00 45.42 2.71
593 4008 9.136323 TCTACATACAGATGTATCAAGTCACAT 57.864 33.333 2.47 0.00 45.42 3.21
594 4009 8.406297 GTCTACATACAGATGTATCAAGTCACA 58.594 37.037 2.47 0.00 45.42 3.58
595 4010 8.406297 TGTCTACATACAGATGTATCAAGTCAC 58.594 37.037 2.47 1.59 45.42 3.67
596 4011 8.519799 TGTCTACATACAGATGTATCAAGTCA 57.480 34.615 2.47 5.20 45.42 3.41
597 4012 9.803315 TTTGTCTACATACAGATGTATCAAGTC 57.197 33.333 2.47 3.09 45.42 3.01
617 4032 8.526147 CCCAAAATTCATGTCTTAGATTTGTCT 58.474 33.333 0.00 0.00 0.00 3.41
618 4033 8.522830 TCCCAAAATTCATGTCTTAGATTTGTC 58.477 33.333 0.00 0.00 0.00 3.18
619 4034 8.306761 GTCCCAAAATTCATGTCTTAGATTTGT 58.693 33.333 0.00 0.00 0.00 2.83
620 4035 7.485913 CGTCCCAAAATTCATGTCTTAGATTTG 59.514 37.037 0.00 0.00 0.00 2.32
621 4036 7.362920 CCGTCCCAAAATTCATGTCTTAGATTT 60.363 37.037 0.00 0.00 0.00 2.17
622 4037 6.095440 CCGTCCCAAAATTCATGTCTTAGATT 59.905 38.462 0.00 0.00 0.00 2.40
623 4038 5.590259 CCGTCCCAAAATTCATGTCTTAGAT 59.410 40.000 0.00 0.00 0.00 1.98
624 4039 4.941263 CCGTCCCAAAATTCATGTCTTAGA 59.059 41.667 0.00 0.00 0.00 2.10
625 4040 4.941263 TCCGTCCCAAAATTCATGTCTTAG 59.059 41.667 0.00 0.00 0.00 2.18
626 4041 4.912586 TCCGTCCCAAAATTCATGTCTTA 58.087 39.130 0.00 0.00 0.00 2.10
627 4042 3.758554 CTCCGTCCCAAAATTCATGTCTT 59.241 43.478 0.00 0.00 0.00 3.01
628 4043 3.347216 CTCCGTCCCAAAATTCATGTCT 58.653 45.455 0.00 0.00 0.00 3.41
629 4044 2.423538 CCTCCGTCCCAAAATTCATGTC 59.576 50.000 0.00 0.00 0.00 3.06
630 4045 2.446435 CCTCCGTCCCAAAATTCATGT 58.554 47.619 0.00 0.00 0.00 3.21
631 4046 1.750778 CCCTCCGTCCCAAAATTCATG 59.249 52.381 0.00 0.00 0.00 3.07
632 4047 1.638589 TCCCTCCGTCCCAAAATTCAT 59.361 47.619 0.00 0.00 0.00 2.57
633 4048 1.004277 CTCCCTCCGTCCCAAAATTCA 59.996 52.381 0.00 0.00 0.00 2.57
634 4049 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
635 4050 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
636 4051 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
637 4052 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
638 4053 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
639 4054 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
640 4055 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
641 4056 3.735720 ATATAGTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
642 4057 7.118060 AGAAATATATAGTACTCCCTCCGTCC 58.882 42.308 0.00 0.00 0.00 4.79
643 4058 9.850198 ATAGAAATATATAGTACTCCCTCCGTC 57.150 37.037 0.00 0.00 0.00 4.79
683 4098 6.311200 GCTGAATACATTTGCTAAAACAAGGG 59.689 38.462 0.00 0.00 0.00 3.95
688 4103 5.003778 CGCAGCTGAATACATTTGCTAAAAC 59.996 40.000 20.43 0.00 34.99 2.43
703 4118 1.336424 TGTAACGACATCGCAGCTGAA 60.336 47.619 20.43 4.53 44.43 3.02
716 4131 6.854496 AAAACATAAAGAGCTGTGTAACGA 57.146 33.333 0.00 0.00 42.39 3.85
721 4136 8.451908 AAGACTAAAAACATAAAGAGCTGTGT 57.548 30.769 0.00 0.00 0.00 3.72
793 4208 6.058183 GGGCATAATAGTCTCACAGTTCATT 58.942 40.000 0.00 0.00 0.00 2.57
797 4212 4.716784 TCTGGGCATAATAGTCTCACAGTT 59.283 41.667 0.00 0.00 0.00 3.16
987 4451 5.053145 GTCAGGATTCTAGCATCGATGTTT 58.947 41.667 25.47 16.61 0.00 2.83
1020 4488 5.133322 AGCCAAAATAATCTCCCTCATCTGA 59.867 40.000 0.00 0.00 0.00 3.27
1022 4490 5.133322 TCAGCCAAAATAATCTCCCTCATCT 59.867 40.000 0.00 0.00 0.00 2.90
1028 4496 4.038402 CACCATCAGCCAAAATAATCTCCC 59.962 45.833 0.00 0.00 0.00 4.30
1111 4582 1.694150 CGGCAAGGGAGATCTTATCCA 59.306 52.381 0.00 0.00 38.70 3.41
1164 4635 1.207791 GCAGAGGGAGAAGGAATGGA 58.792 55.000 0.00 0.00 0.00 3.41
1182 4653 2.097825 ACATCAGAAGCCAATTCCTGC 58.902 47.619 0.00 0.00 38.84 4.85
1218 4697 3.801638 GCCACCATATACTGCAGAGACAG 60.802 52.174 23.35 6.98 43.59 3.51
1221 4700 1.341209 CGCCACCATATACTGCAGAGA 59.659 52.381 23.35 8.26 0.00 3.10
1250 4729 2.185387 GGGAGCAGTGGTAAGAGGTTA 58.815 52.381 0.00 0.00 0.00 2.85
1315 4794 2.566746 AGATGGGACTGAACTTGGGAT 58.433 47.619 0.00 0.00 0.00 3.85
1321 4800 4.392940 CAAAGTGAAGATGGGACTGAACT 58.607 43.478 0.00 0.00 0.00 3.01
1338 4824 1.763770 CAGTGAGGGGGAGCAAAGT 59.236 57.895 0.00 0.00 0.00 2.66
1349 4835 1.622811 AGGAGAGAAACTGCAGTGAGG 59.377 52.381 22.49 0.00 39.46 3.86
1351 4837 4.159321 CAGATAGGAGAGAAACTGCAGTGA 59.841 45.833 22.49 0.00 39.46 3.41
1353 4839 4.093011 ACAGATAGGAGAGAAACTGCAGT 58.907 43.478 15.25 15.25 39.46 4.40
1354 4840 4.681744 GACAGATAGGAGAGAAACTGCAG 58.318 47.826 13.48 13.48 39.46 4.41
1383 4874 9.932207 GTAGAATAGCTGTAGAGAGACATAGTA 57.068 37.037 0.00 0.00 0.00 1.82
1384 4875 8.656806 AGTAGAATAGCTGTAGAGAGACATAGT 58.343 37.037 0.00 0.00 0.00 2.12
1385 4876 9.502091 AAGTAGAATAGCTGTAGAGAGACATAG 57.498 37.037 0.00 0.00 0.00 2.23
1386 4877 9.278978 CAAGTAGAATAGCTGTAGAGAGACATA 57.721 37.037 0.00 0.00 0.00 2.29
1399 4904 9.553064 CCAAGAACAATATCAAGTAGAATAGCT 57.447 33.333 0.00 0.00 0.00 3.32
1412 4955 6.501781 CCTTTGATGCTCCAAGAACAATATC 58.498 40.000 0.00 0.00 0.00 1.63
1453 4996 4.505918 CCACAAACCCTCCTACACATGTTA 60.506 45.833 0.00 0.00 0.00 2.41
1469 5012 7.977904 AGGTATAATAACGCTAAACCACAAAC 58.022 34.615 0.00 0.00 0.00 2.93
1490 5033 9.529823 CCTCCTATACATGTATTTACAGAGGTA 57.470 37.037 22.90 11.13 39.92 3.08
1563 5107 5.295292 CCTCTTATACATGTTGACCAGCAAG 59.705 44.000 2.30 0.00 37.12 4.01
1566 5110 4.811557 GTCCTCTTATACATGTTGACCAGC 59.188 45.833 2.30 0.00 0.00 4.85
1572 5116 4.164221 ACAGGGGTCCTCTTATACATGTTG 59.836 45.833 2.30 0.00 0.00 3.33
1734 5390 5.624159 TCTCAATCCTGCAAGAAAGAAAGA 58.376 37.500 0.00 0.00 34.07 2.52
1808 5465 2.028930 ACTCATCGTTCTCCCAGTTGAC 60.029 50.000 0.00 0.00 0.00 3.18
1810 5467 2.232452 AGACTCATCGTTCTCCCAGTTG 59.768 50.000 0.00 0.00 0.00 3.16
1811 5468 2.494073 GAGACTCATCGTTCTCCCAGTT 59.506 50.000 0.00 0.00 0.00 3.16
1812 5469 2.096248 GAGACTCATCGTTCTCCCAGT 58.904 52.381 0.00 0.00 0.00 4.00
1813 5470 1.064803 CGAGACTCATCGTTCTCCCAG 59.935 57.143 2.82 0.00 37.91 4.45
1814 5471 1.095600 CGAGACTCATCGTTCTCCCA 58.904 55.000 2.82 0.00 37.91 4.37
1815 5472 0.382515 CCGAGACTCATCGTTCTCCC 59.617 60.000 2.82 0.00 41.12 4.30
1816 5473 1.332375 CTCCGAGACTCATCGTTCTCC 59.668 57.143 2.82 0.00 41.12 3.71
1817 5474 1.332375 CCTCCGAGACTCATCGTTCTC 59.668 57.143 2.82 0.00 41.12 2.87
1819 5476 1.332375 CTCCTCCGAGACTCATCGTTC 59.668 57.143 2.82 0.00 41.12 3.95
1820 5477 1.384525 CTCCTCCGAGACTCATCGTT 58.615 55.000 2.82 0.00 41.12 3.85
1822 5479 0.179043 TCCTCCTCCGAGACTCATCG 60.179 60.000 2.82 0.00 38.52 3.84
1824 5481 0.626382 TGTCCTCCTCCGAGACTCAT 59.374 55.000 2.82 0.00 38.52 2.90
1829 5486 0.612174 CCACTTGTCCTCCTCCGAGA 60.612 60.000 0.00 0.00 38.52 4.04
1830 5487 0.900647 ACCACTTGTCCTCCTCCGAG 60.901 60.000 0.00 0.00 35.72 4.63
1831 5488 1.155390 ACCACTTGTCCTCCTCCGA 59.845 57.895 0.00 0.00 0.00 4.55
1832 5489 1.293498 CACCACTTGTCCTCCTCCG 59.707 63.158 0.00 0.00 0.00 4.63
1833 5490 1.679898 CCACCACTTGTCCTCCTCC 59.320 63.158 0.00 0.00 0.00 4.30
1834 5491 1.679898 CCCACCACTTGTCCTCCTC 59.320 63.158 0.00 0.00 0.00 3.71
1835 5492 2.529744 GCCCACCACTTGTCCTCCT 61.530 63.158 0.00 0.00 0.00 3.69
1836 5493 2.034221 GCCCACCACTTGTCCTCC 59.966 66.667 0.00 0.00 0.00 4.30
1837 5494 1.823169 TACGCCCACCACTTGTCCTC 61.823 60.000 0.00 0.00 0.00 3.71
1838 5495 1.827399 CTACGCCCACCACTTGTCCT 61.827 60.000 0.00 0.00 0.00 3.85
1839 5496 1.375523 CTACGCCCACCACTTGTCC 60.376 63.158 0.00 0.00 0.00 4.02
1840 5497 2.033194 GCTACGCCCACCACTTGTC 61.033 63.158 0.00 0.00 0.00 3.18
1841 5498 2.032071 GCTACGCCCACCACTTGT 59.968 61.111 0.00 0.00 0.00 3.16
1842 5499 2.034879 CAGCTACGCCCACCACTTG 61.035 63.158 0.00 0.00 0.00 3.16
1843 5500 2.347490 CAGCTACGCCCACCACTT 59.653 61.111 0.00 0.00 0.00 3.16
1844 5501 3.706373 CCAGCTACGCCCACCACT 61.706 66.667 0.00 0.00 0.00 4.00
1845 5502 4.016706 ACCAGCTACGCCCACCAC 62.017 66.667 0.00 0.00 0.00 4.16
1846 5503 4.015406 CACCAGCTACGCCCACCA 62.015 66.667 0.00 0.00 0.00 4.17
1847 5504 4.778143 CCACCAGCTACGCCCACC 62.778 72.222 0.00 0.00 0.00 4.61
1848 5505 3.952628 GACCACCAGCTACGCCCAC 62.953 68.421 0.00 0.00 0.00 4.61
1849 5506 3.702048 GACCACCAGCTACGCCCA 61.702 66.667 0.00 0.00 0.00 5.36
1850 5507 2.741486 TTTGACCACCAGCTACGCCC 62.741 60.000 0.00 0.00 0.00 6.13
1851 5508 0.676782 ATTTGACCACCAGCTACGCC 60.677 55.000 0.00 0.00 0.00 5.68
1852 5509 1.165270 AATTTGACCACCAGCTACGC 58.835 50.000 0.00 0.00 0.00 4.42
1853 5510 4.201910 CCATAAATTTGACCACCAGCTACG 60.202 45.833 0.00 0.00 0.00 3.51
1854 5511 4.705023 ACCATAAATTTGACCACCAGCTAC 59.295 41.667 0.00 0.00 0.00 3.58
1855 5512 4.929479 ACCATAAATTTGACCACCAGCTA 58.071 39.130 0.00 0.00 0.00 3.32
1856 5513 3.778265 ACCATAAATTTGACCACCAGCT 58.222 40.909 0.00 0.00 0.00 4.24
1857 5514 5.451798 CCATACCATAAATTTGACCACCAGC 60.452 44.000 0.00 0.00 0.00 4.85
1858 5515 5.068987 CCCATACCATAAATTTGACCACCAG 59.931 44.000 0.00 0.00 0.00 4.00
1859 5516 4.959210 CCCATACCATAAATTTGACCACCA 59.041 41.667 0.00 0.00 0.00 4.17
1860 5517 4.343814 CCCCATACCATAAATTTGACCACC 59.656 45.833 0.00 0.00 0.00 4.61
1861 5518 5.205056 TCCCCATACCATAAATTTGACCAC 58.795 41.667 0.00 0.00 0.00 4.16
1862 5519 5.194740 TCTCCCCATACCATAAATTTGACCA 59.805 40.000 0.00 0.00 0.00 4.02
1863 5520 5.701224 TCTCCCCATACCATAAATTTGACC 58.299 41.667 0.00 0.00 0.00 4.02
1864 5521 6.263168 CACTCTCCCCATACCATAAATTTGAC 59.737 42.308 0.00 0.00 0.00 3.18
1924 5583 4.829064 TCCTCCGAAAAGAAACACAATG 57.171 40.909 0.00 0.00 0.00 2.82
1940 5599 4.470334 TTGCTGGCAAAATTTATCCTCC 57.530 40.909 5.47 0.53 32.44 4.30
1949 5609 2.496111 CACCACAATTGCTGGCAAAAT 58.504 42.857 20.36 2.02 39.55 1.82
1983 5643 6.601613 TGGTGAGACAACTAAATGAACAAGTT 59.398 34.615 0.00 0.00 33.82 2.66
1988 5648 5.758296 TCAGTGGTGAGACAACTAAATGAAC 59.242 40.000 0.00 0.00 0.00 3.18
1991 5651 6.652481 AGAATCAGTGGTGAGACAACTAAATG 59.348 38.462 0.00 0.00 35.66 2.32
2000 5660 2.028658 TCAGCAGAATCAGTGGTGAGAC 60.029 50.000 1.01 0.00 45.15 3.36
2055 5715 7.042254 GGTTGCTTATACTAACGTTAGGATTGG 60.042 40.741 32.46 25.02 35.88 3.16
2075 5735 6.017109 CAGTAAACTCAACATGTTAGGTTGCT 60.017 38.462 21.16 20.62 44.02 3.91
2197 5887 0.647410 GTTGCATGTCTCGATGGACG 59.353 55.000 0.00 0.00 44.09 4.79
2218 5915 4.256920 CACCTAGTTTCTGGTTCTCCATG 58.743 47.826 0.00 0.00 43.43 3.66
2251 5948 1.280457 AGCAGGTTCTACCAAGGGAG 58.720 55.000 0.00 0.00 41.95 4.30
2320 7921 8.792830 TTTACCAAGGAAGAATCACAGAATAG 57.207 34.615 0.00 0.00 0.00 1.73
2325 7926 8.567285 ACTATTTTACCAAGGAAGAATCACAG 57.433 34.615 0.00 0.00 0.00 3.66
2335 7936 6.707273 AAGTGGGTACTATTTTACCAAGGA 57.293 37.500 1.90 0.00 43.15 3.36
2337 7938 7.989416 TCAAAGTGGGTACTATTTTACCAAG 57.011 36.000 1.90 0.00 43.15 3.61
2338 7939 8.631797 GTTTCAAAGTGGGTACTATTTTACCAA 58.368 33.333 1.90 0.00 43.15 3.67
2340 7941 7.449395 AGGTTTCAAAGTGGGTACTATTTTACC 59.551 37.037 0.00 0.00 40.94 2.85
2341 7942 8.400184 AGGTTTCAAAGTGGGTACTATTTTAC 57.600 34.615 0.00 0.00 35.69 2.01
2342 7943 8.999905 AAGGTTTCAAAGTGGGTACTATTTTA 57.000 30.769 0.00 0.00 35.69 1.52
2344 7945 7.907841 AAAGGTTTCAAAGTGGGTACTATTT 57.092 32.000 0.00 0.00 35.69 1.40
2345 7946 7.907841 AAAAGGTTTCAAAGTGGGTACTATT 57.092 32.000 0.00 0.00 35.69 1.73
2346 7947 8.442374 TCTAAAAGGTTTCAAAGTGGGTACTAT 58.558 33.333 0.00 0.00 35.69 2.12
2347 7948 7.804147 TCTAAAAGGTTTCAAAGTGGGTACTA 58.196 34.615 0.00 0.00 35.69 1.82
2349 7950 6.947644 TCTAAAAGGTTTCAAAGTGGGTAC 57.052 37.500 0.00 0.00 0.00 3.34
2350 7951 6.717997 GGATCTAAAAGGTTTCAAAGTGGGTA 59.282 38.462 0.00 0.00 0.00 3.69
2351 7952 5.538813 GGATCTAAAAGGTTTCAAAGTGGGT 59.461 40.000 0.00 0.00 0.00 4.51
2352 7953 5.047306 GGGATCTAAAAGGTTTCAAAGTGGG 60.047 44.000 0.00 0.00 0.00 4.61
2353 7954 5.047306 GGGGATCTAAAAGGTTTCAAAGTGG 60.047 44.000 0.00 0.00 0.00 4.00
2354 7955 5.047306 GGGGGATCTAAAAGGTTTCAAAGTG 60.047 44.000 0.00 0.00 0.00 3.16
2355 7956 5.084519 GGGGGATCTAAAAGGTTTCAAAGT 58.915 41.667 0.00 0.00 0.00 2.66
2356 7957 5.661056 GGGGGATCTAAAAGGTTTCAAAG 57.339 43.478 0.00 0.00 0.00 2.77
2495 8406 7.321153 ACTACAAGACCAGATATGTACAACAC 58.679 38.462 0.00 0.00 0.00 3.32
2506 8419 5.552870 ACACTCAAACTACAAGACCAGAT 57.447 39.130 0.00 0.00 0.00 2.90
2515 8428 9.048446 GTACCTTAATCAAACACTCAAACTACA 57.952 33.333 0.00 0.00 0.00 2.74
2516 8429 9.269453 AGTACCTTAATCAAACACTCAAACTAC 57.731 33.333 0.00 0.00 0.00 2.73
2518 8431 7.773690 ACAGTACCTTAATCAAACACTCAAACT 59.226 33.333 0.00 0.00 0.00 2.66
2519 8432 7.927048 ACAGTACCTTAATCAAACACTCAAAC 58.073 34.615 0.00 0.00 0.00 2.93
2520 8433 8.402472 CAACAGTACCTTAATCAAACACTCAAA 58.598 33.333 0.00 0.00 0.00 2.69
2522 8435 7.051623 ACAACAGTACCTTAATCAAACACTCA 58.948 34.615 0.00 0.00 0.00 3.41
2523 8436 7.492352 ACAACAGTACCTTAATCAAACACTC 57.508 36.000 0.00 0.00 0.00 3.51
2524 8437 9.569122 AATACAACAGTACCTTAATCAAACACT 57.431 29.630 0.00 0.00 0.00 3.55
2533 8446 8.550710 AACGCATTAATACAACAGTACCTTAA 57.449 30.769 0.00 0.00 0.00 1.85
2555 8468 8.568732 ACAACCATACAGAATTAACAAAAACG 57.431 30.769 0.00 0.00 0.00 3.60
2561 8474 6.539173 ACCAGACAACCATACAGAATTAACA 58.461 36.000 0.00 0.00 0.00 2.41
2584 8497 5.643777 ACATGCACATAGTGGACTTCTTAAC 59.356 40.000 0.00 0.00 36.59 2.01
2587 8500 4.292186 ACATGCACATAGTGGACTTCTT 57.708 40.909 0.00 0.00 36.59 2.52


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

AutoCloner maintained by Alex Coulton.