Multiple sequence alignment - TraesCS6D01G283700

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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 TraesCS6D01G283700 chr6D 100.000 4468 0 0 1 4468 390832482 390836949 0.000000e+00 8251.0
1 TraesCS6D01G283700 chr6D 96.859 191 6 0 3258 3448 390835640 390835830 2.010000e-83 320.0
2 TraesCS6D01G283700 chr6D 96.859 191 6 0 3159 3349 390835739 390835929 2.010000e-83 320.0
3 TraesCS6D01G283700 chr6D 96.739 92 3 0 3357 3448 390835640 390835731 2.150000e-33 154.0
4 TraesCS6D01G283700 chr6D 96.739 92 3 0 3159 3250 390835838 390835929 2.150000e-33 154.0
5 TraesCS6D01G283700 chr6D 83.735 166 12 10 2028 2192 390834363 390834514 4.660000e-30 143.0
6 TraesCS6D01G283700 chr6D 83.735 166 12 10 1882 2033 390834509 390834673 4.660000e-30 143.0
7 TraesCS6D01G283700 chr6B 93.948 2710 108 17 573 3250 583629443 583626758 0.000000e+00 4045.0
8 TraesCS6D01G283700 chr6B 86.364 572 56 8 4 567 583631413 583630856 4.940000e-169 604.0
9 TraesCS6D01G283700 chr6B 94.286 350 16 3 3357 3702 583626849 583626500 2.370000e-147 532.0
10 TraesCS6D01G283700 chr6B 84.008 494 35 14 3706 4187 583626421 583625960 6.860000e-118 435.0
11 TraesCS6D01G283700 chr6B 89.928 278 15 3 4178 4451 583625921 583625653 3.310000e-91 346.0
12 TraesCS6D01G283700 chr6B 96.739 92 3 0 3258 3349 583626849 583626758 2.150000e-33 154.0
13 TraesCS6D01G283700 chr6B 83.735 166 12 10 2028 2192 583628126 583627975 4.660000e-30 143.0
14 TraesCS6D01G283700 chr6A 88.979 2087 141 31 5 2026 537312206 537314268 0.000000e+00 2497.0
15 TraesCS6D01G283700 chr6A 96.740 1227 36 2 2028 3250 537314110 537315336 0.000000e+00 2041.0
16 TraesCS6D01G283700 chr6A 89.346 1117 60 15 3354 4442 537315242 537316327 0.000000e+00 1349.0
17 TraesCS6D01G283700 chr6A 95.833 96 4 0 3254 3349 537315241 537315336 5.980000e-34 156.0
18 TraesCS6D01G283700 chr1A 75.342 438 69 20 1567 2001 33219428 33219829 1.650000e-39 174.0
19 TraesCS6D01G283700 chr7A 100.000 28 0 0 355 382 719507713 719507686 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G283700 chr6D 390832482 390836949 4467 False 1355.000000 8251 93.523714 1 4468 7 chr6D.!!$F1 4467
1 TraesCS6D01G283700 chr6B 583625653 583631413 5760 True 894.142857 4045 89.858286 4 4451 7 chr6B.!!$R1 4447
2 TraesCS6D01G283700 chr6A 537312206 537316327 4121 False 1510.750000 2497 92.724500 5 4442 4 chr6A.!!$F1 4437

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
78 79 0.249238 GGCGACTGGAGTATCAGCTG 60.249 60.0 7.63 7.63 38.26 4.24 F
569 588 1.118838 CTGCCCAAAGTCACCCAAAA 58.881 50.0 0.00 0.00 0.00 2.44 F
1600 3052 0.405585 AGGTTTCTGTGGTGGATGGG 59.594 55.0 0.00 0.00 0.00 4.00 F
3252 4723 0.033504 GGCAGTTCTCCTTCGTGACA 59.966 55.0 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 3049 0.042731 ATCCGGACTTCTCCTTCCCA 59.957 55.0 6.12 0.00 33.79 4.37 R
2377 3841 0.940126 AAACACAGCTGCTCAGTTCG 59.060 50.0 15.27 0.00 0.00 3.95 R
3233 4704 0.033504 TGTCACGAAGGAGAACTGCC 59.966 55.0 0.00 0.00 0.00 4.85 R
4374 5995 1.264295 TTGCATGCAGGGCAATACAA 58.736 45.0 21.50 3.91 45.57 2.41 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
37 38 5.560375 GCTCATCCAACGATCATGAAATCAG 60.560 44.000 0.00 0.00 0.00 2.90
38 39 4.274214 TCATCCAACGATCATGAAATCAGC 59.726 41.667 0.00 0.00 0.00 4.26
47 48 2.040145 TCATGAAATCAGCTGGGTGTGA 59.960 45.455 15.13 8.41 0.00 3.58
49 50 2.229792 TGAAATCAGCTGGGTGTGAAC 58.770 47.619 15.13 0.00 0.00 3.18
76 77 2.119886 AGGCGACTGGAGTATCAGC 58.880 57.895 0.00 0.00 41.13 4.26
77 78 0.396417 AGGCGACTGGAGTATCAGCT 60.396 55.000 0.00 0.00 41.13 4.24
78 79 0.249238 GGCGACTGGAGTATCAGCTG 60.249 60.000 7.63 7.63 38.26 4.24
79 80 0.249238 GCGACTGGAGTATCAGCTGG 60.249 60.000 15.13 0.00 38.26 4.85
89 90 4.444022 GGAGTATCAGCTGGATTGTGACAT 60.444 45.833 15.13 0.00 37.44 3.06
108 109 9.898152 TGTGACATGTTTGTATAATCAATAGGA 57.102 29.630 0.00 0.00 35.79 2.94
141 142 2.680577 ACTCATTTACGACCGTCCAAC 58.319 47.619 0.00 0.00 0.00 3.77
191 192 7.355332 GTGTGAAACGGTAAGATAAAGCTAA 57.645 36.000 0.00 0.00 42.39 3.09
213 214 2.225727 AGGTCAAAGAAATTTCGACGGC 59.774 45.455 12.42 6.24 0.00 5.68
250 251 7.148656 CGAAGATTTTGCCAAAATTAATCGGTT 60.149 33.333 23.51 10.26 40.97 4.44
265 266 8.725405 ATTAATCGGTTCATAACATACACACA 57.275 30.769 0.00 0.00 0.00 3.72
308 309 6.641723 TCAATAGTGAGACGTAGATCTACTCG 59.358 42.308 26.32 18.38 34.04 4.18
370 379 7.307989 CGAAACATCAAGATGAAACTAGTGGTT 60.308 37.037 16.39 0.00 41.20 3.67
445 454 2.042831 AGTTGCATTGCTCGAGCCC 61.043 57.895 33.23 18.99 41.18 5.19
481 490 3.000674 CGATCGATTCTGTTGTTCCTTCG 60.001 47.826 10.26 0.00 0.00 3.79
496 505 2.438614 TCGGAGCCAGACTCGGAG 60.439 66.667 2.83 2.83 46.48 4.63
530 539 1.676916 CGTGCCATCCAGACTCAACAT 60.677 52.381 0.00 0.00 0.00 2.71
569 588 1.118838 CTGCCCAAAGTCACCCAAAA 58.881 50.000 0.00 0.00 0.00 2.44
570 589 1.484240 CTGCCCAAAGTCACCCAAAAA 59.516 47.619 0.00 0.00 0.00 1.94
575 595 3.392882 CCAAAGTCACCCAAAAAGCATC 58.607 45.455 0.00 0.00 0.00 3.91
585 2011 3.091545 CCAAAAAGCATCCTCAAGGCTA 58.908 45.455 0.00 0.00 36.76 3.93
596 2022 3.330701 TCCTCAAGGCTAGTTGGACAATT 59.669 43.478 0.00 0.00 34.44 2.32
632 2058 2.584236 GCCTACTTCGGTGATAGAGGA 58.416 52.381 0.00 0.00 0.00 3.71
705 2131 9.878667 TCGTCAAGTGGTCTATGAATTTATTTA 57.121 29.630 0.00 0.00 0.00 1.40
897 2326 1.944024 TGCGTACACCTTTCCTGTTTG 59.056 47.619 0.00 0.00 0.00 2.93
1442 2894 2.854522 CCATGAAGGTCGGTGGTTC 58.145 57.895 0.00 0.00 0.00 3.62
1539 2991 6.705381 TGGTGTTAATTTGAAATCTTTGCAGG 59.295 34.615 0.00 0.00 0.00 4.85
1591 3043 3.326297 AGGAGAAGGAGAAGGTTTCTGTG 59.674 47.826 0.00 0.00 40.87 3.66
1597 3049 2.040412 GGAGAAGGTTTCTGTGGTGGAT 59.960 50.000 0.00 0.00 40.87 3.41
1600 3052 0.405585 AGGTTTCTGTGGTGGATGGG 59.594 55.000 0.00 0.00 0.00 4.00
1736 3188 6.414732 TCGATATCCTTGGTTTCATGTCTTT 58.585 36.000 0.00 0.00 0.00 2.52
1744 3196 4.630111 TGGTTTCATGTCTTTTCATTGCC 58.370 39.130 0.00 0.00 0.00 4.52
1790 3242 9.013229 AGAGTATGATTAGTGTTTGATTTTGCA 57.987 29.630 0.00 0.00 0.00 4.08
1872 3324 4.092771 TGCACGCTACTACTGTCTAAAG 57.907 45.455 0.00 0.00 0.00 1.85
2213 3675 6.364165 TGTTTCTGGTTACTTTACGAGATTCG 59.636 38.462 0.00 0.00 46.93 3.34
2377 3841 6.318648 TGAACAGCCATGAGTTTTGGTATATC 59.681 38.462 0.00 0.00 36.57 1.63
2420 3884 4.342092 ACTTCACTTAGTGCTTTGCCAATT 59.658 37.500 7.61 0.00 32.98 2.32
2717 4182 4.934001 AGATCTTGCACTATCAACACAGTG 59.066 41.667 0.00 0.00 44.07 3.66
2819 4284 2.346803 GACGATGTGAAGCAAAGCCTA 58.653 47.619 0.00 0.00 0.00 3.93
3140 4611 1.277273 CAGCAGGAGGAGTTCATGACA 59.723 52.381 0.00 0.00 39.95 3.58
3218 4689 2.692041 AGCAAATTTGAGAGCTATGGCC 59.308 45.455 22.31 0.00 39.73 5.36
3219 4690 2.692041 GCAAATTTGAGAGCTATGGCCT 59.308 45.455 22.31 0.00 39.73 5.19
3220 4691 3.243334 GCAAATTTGAGAGCTATGGCCTC 60.243 47.826 22.31 11.07 39.73 4.70
3221 4692 4.205587 CAAATTTGAGAGCTATGGCCTCT 58.794 43.478 13.08 10.60 39.73 3.69
3222 4693 3.767902 ATTTGAGAGCTATGGCCTCTC 57.232 47.619 17.57 17.57 40.13 3.20
3223 4694 1.035923 TTGAGAGCTATGGCCTCTCG 58.964 55.000 18.49 0.00 41.31 4.04
3224 4695 0.183731 TGAGAGCTATGGCCTCTCGA 59.816 55.000 18.49 10.04 41.31 4.04
3225 4696 0.881118 GAGAGCTATGGCCTCTCGAG 59.119 60.000 5.93 5.93 39.73 4.04
3226 4697 1.178534 AGAGCTATGGCCTCTCGAGC 61.179 60.000 7.81 5.55 39.73 5.03
3244 4715 4.026300 CGAGAGGGCAGTTCTCCT 57.974 61.111 7.15 0.00 38.24 3.69
3245 4716 2.281830 CGAGAGGGCAGTTCTCCTT 58.718 57.895 7.15 0.00 38.24 3.36
3246 4717 0.174617 CGAGAGGGCAGTTCTCCTTC 59.825 60.000 7.15 0.00 38.24 3.46
3247 4718 0.174617 GAGAGGGCAGTTCTCCTTCG 59.825 60.000 2.55 0.00 36.01 3.79
3248 4719 0.543174 AGAGGGCAGTTCTCCTTCGT 60.543 55.000 0.00 0.00 35.16 3.85
3249 4720 0.390472 GAGGGCAGTTCTCCTTCGTG 60.390 60.000 0.00 0.00 32.74 4.35
3250 4721 0.832135 AGGGCAGTTCTCCTTCGTGA 60.832 55.000 0.00 0.00 0.00 4.35
3251 4722 0.670854 GGGCAGTTCTCCTTCGTGAC 60.671 60.000 0.00 0.00 0.00 3.67
3252 4723 0.033504 GGCAGTTCTCCTTCGTGACA 59.966 55.000 0.00 0.00 0.00 3.58
3253 4724 1.540363 GGCAGTTCTCCTTCGTGACAA 60.540 52.381 0.00 0.00 0.00 3.18
3254 4725 2.417719 GCAGTTCTCCTTCGTGACAAT 58.582 47.619 0.00 0.00 0.00 2.71
3255 4726 2.158449 GCAGTTCTCCTTCGTGACAATG 59.842 50.000 0.00 0.00 0.00 2.82
3256 4727 3.653344 CAGTTCTCCTTCGTGACAATGA 58.347 45.455 0.00 0.00 0.00 2.57
3257 4728 3.677121 CAGTTCTCCTTCGTGACAATGAG 59.323 47.826 0.00 0.00 0.00 2.90
3258 4729 2.996621 GTTCTCCTTCGTGACAATGAGG 59.003 50.000 0.00 0.00 0.00 3.86
3259 4730 1.550524 TCTCCTTCGTGACAATGAGGG 59.449 52.381 1.75 1.75 39.42 4.30
3260 4731 1.550524 CTCCTTCGTGACAATGAGGGA 59.449 52.381 8.84 8.84 43.42 4.20
3261 4732 1.550524 TCCTTCGTGACAATGAGGGAG 59.449 52.381 5.88 0.00 41.41 4.30
3262 4733 1.550524 CCTTCGTGACAATGAGGGAGA 59.449 52.381 1.93 0.00 40.28 3.71
3263 4734 2.417924 CCTTCGTGACAATGAGGGAGAG 60.418 54.545 1.93 0.00 40.28 3.20
3264 4735 2.215942 TCGTGACAATGAGGGAGAGA 57.784 50.000 0.00 0.00 0.00 3.10
3265 4736 2.095461 TCGTGACAATGAGGGAGAGAG 58.905 52.381 0.00 0.00 0.00 3.20
3266 4737 1.135915 CGTGACAATGAGGGAGAGAGG 59.864 57.143 0.00 0.00 0.00 3.69
3267 4738 1.134551 GTGACAATGAGGGAGAGAGGC 60.135 57.143 0.00 0.00 0.00 4.70
3268 4739 1.198713 GACAATGAGGGAGAGAGGCA 58.801 55.000 0.00 0.00 0.00 4.75
3269 4740 1.138661 GACAATGAGGGAGAGAGGCAG 59.861 57.143 0.00 0.00 0.00 4.85
3270 4741 0.179051 CAATGAGGGAGAGAGGCAGC 60.179 60.000 0.00 0.00 0.00 5.25
3271 4742 1.344191 AATGAGGGAGAGAGGCAGCC 61.344 60.000 1.84 1.84 0.00 4.85
3272 4743 2.364842 GAGGGAGAGAGGCAGCCA 60.365 66.667 15.80 0.00 0.00 4.75
3273 4744 2.686835 AGGGAGAGAGGCAGCCAC 60.687 66.667 15.80 7.68 0.00 5.01
3274 4745 3.005539 GGGAGAGAGGCAGCCACA 61.006 66.667 15.80 0.00 0.00 4.17
3275 4746 2.583520 GGAGAGAGGCAGCCACAG 59.416 66.667 15.80 0.00 0.00 3.66
3276 4747 2.583520 GAGAGAGGCAGCCACAGG 59.416 66.667 15.80 0.00 0.00 4.00
3277 4748 1.986757 GAGAGAGGCAGCCACAGGA 60.987 63.158 15.80 0.00 0.00 3.86
3278 4749 2.237534 GAGAGAGGCAGCCACAGGAC 62.238 65.000 15.80 0.91 0.00 3.85
3279 4750 2.527624 AGAGGCAGCCACAGGACA 60.528 61.111 15.80 0.00 0.00 4.02
3280 4751 2.359230 GAGGCAGCCACAGGACAC 60.359 66.667 15.80 0.00 0.00 3.67
3281 4752 3.909086 GAGGCAGCCACAGGACACC 62.909 68.421 15.80 0.00 0.00 4.16
3282 4753 4.269523 GGCAGCCACAGGACACCA 62.270 66.667 6.55 0.00 0.00 4.17
3283 4754 2.034687 GCAGCCACAGGACACCAT 59.965 61.111 0.00 0.00 0.00 3.55
3284 4755 1.299648 GCAGCCACAGGACACCATA 59.700 57.895 0.00 0.00 0.00 2.74
3285 4756 0.107017 GCAGCCACAGGACACCATAT 60.107 55.000 0.00 0.00 0.00 1.78
3286 4757 1.959042 CAGCCACAGGACACCATATC 58.041 55.000 0.00 0.00 0.00 1.63
3287 4758 1.487976 CAGCCACAGGACACCATATCT 59.512 52.381 0.00 0.00 0.00 1.98
3288 4759 2.700371 CAGCCACAGGACACCATATCTA 59.300 50.000 0.00 0.00 0.00 1.98
3289 4760 2.700897 AGCCACAGGACACCATATCTAC 59.299 50.000 0.00 0.00 0.00 2.59
3290 4761 2.700897 GCCACAGGACACCATATCTACT 59.299 50.000 0.00 0.00 0.00 2.57
3291 4762 3.493350 GCCACAGGACACCATATCTACTG 60.493 52.174 0.00 0.00 0.00 2.74
3292 4763 3.493350 CCACAGGACACCATATCTACTGC 60.493 52.174 0.00 0.00 0.00 4.40
3293 4764 2.700897 ACAGGACACCATATCTACTGCC 59.299 50.000 0.00 0.00 0.00 4.85
3294 4765 2.037772 CAGGACACCATATCTACTGCCC 59.962 54.545 0.00 0.00 0.00 5.36
3295 4766 1.000955 GGACACCATATCTACTGCCCG 59.999 57.143 0.00 0.00 0.00 6.13
3296 4767 1.961394 GACACCATATCTACTGCCCGA 59.039 52.381 0.00 0.00 0.00 5.14
3297 4768 1.964223 ACACCATATCTACTGCCCGAG 59.036 52.381 0.00 0.00 0.00 4.63
3298 4769 0.969894 ACCATATCTACTGCCCGAGC 59.030 55.000 0.00 0.00 40.48 5.03
3310 4781 0.179153 GCCCGAGCAAATTTGAGAGC 60.179 55.000 22.31 11.89 39.53 4.09
3311 4782 1.457346 CCCGAGCAAATTTGAGAGCT 58.543 50.000 22.31 11.30 40.60 4.09
3312 4783 2.632377 CCCGAGCAAATTTGAGAGCTA 58.368 47.619 22.31 0.00 37.48 3.32
3313 4784 3.209410 CCCGAGCAAATTTGAGAGCTAT 58.791 45.455 22.31 0.00 37.48 2.97
3314 4785 3.003068 CCCGAGCAAATTTGAGAGCTATG 59.997 47.826 22.31 7.49 37.48 2.23
3315 4786 3.003068 CCGAGCAAATTTGAGAGCTATGG 59.997 47.826 22.31 12.15 37.48 2.74
3316 4787 3.547613 CGAGCAAATTTGAGAGCTATGGC 60.548 47.826 22.31 2.08 37.48 4.40
3317 4788 2.692041 AGCAAATTTGAGAGCTATGGCC 59.308 45.455 22.31 0.00 39.73 5.36
3318 4789 2.692041 GCAAATTTGAGAGCTATGGCCT 59.308 45.455 22.31 0.00 39.73 5.19
3319 4790 3.243334 GCAAATTTGAGAGCTATGGCCTC 60.243 47.826 22.31 11.07 39.73 4.70
3320 4791 4.205587 CAAATTTGAGAGCTATGGCCTCT 58.794 43.478 13.08 10.60 39.73 3.69
3321 4792 3.767902 ATTTGAGAGCTATGGCCTCTC 57.232 47.619 17.57 17.57 40.13 3.20
3322 4793 1.035923 TTGAGAGCTATGGCCTCTCG 58.964 55.000 18.49 0.00 41.31 4.04
3323 4794 0.825425 TGAGAGCTATGGCCTCTCGG 60.825 60.000 18.49 0.00 41.31 4.63
3324 4795 1.531739 GAGAGCTATGGCCTCTCGGG 61.532 65.000 3.32 0.00 39.73 5.14
3343 4814 4.026300 CGAGAGGGCAGTTCTCCT 57.974 61.111 7.15 0.00 38.24 3.69
3344 4815 2.281830 CGAGAGGGCAGTTCTCCTT 58.718 57.895 7.15 0.00 38.24 3.36
3345 4816 0.174617 CGAGAGGGCAGTTCTCCTTC 59.825 60.000 7.15 0.00 38.24 3.46
3346 4817 0.174617 GAGAGGGCAGTTCTCCTTCG 59.825 60.000 2.55 0.00 36.01 3.79
3347 4818 0.543174 AGAGGGCAGTTCTCCTTCGT 60.543 55.000 0.00 0.00 35.16 3.85
3348 4819 0.390472 GAGGGCAGTTCTCCTTCGTG 60.390 60.000 0.00 0.00 32.74 4.35
3349 4820 0.832135 AGGGCAGTTCTCCTTCGTGA 60.832 55.000 0.00 0.00 0.00 4.35
3350 4821 0.670854 GGGCAGTTCTCCTTCGTGAC 60.671 60.000 0.00 0.00 0.00 3.67
3351 4822 0.033504 GGCAGTTCTCCTTCGTGACA 59.966 55.000 0.00 0.00 0.00 3.58
3352 4823 1.423395 GCAGTTCTCCTTCGTGACAG 58.577 55.000 0.00 0.00 0.00 3.51
3353 4824 1.269831 GCAGTTCTCCTTCGTGACAGT 60.270 52.381 0.00 0.00 0.00 3.55
3354 4825 2.398498 CAGTTCTCCTTCGTGACAGTG 58.602 52.381 0.00 0.00 0.00 3.66
3355 4826 2.034685 CAGTTCTCCTTCGTGACAGTGA 59.965 50.000 0.00 0.00 0.00 3.41
3356 4827 2.294791 AGTTCTCCTTCGTGACAGTGAG 59.705 50.000 0.00 0.00 0.00 3.51
3357 4828 1.248486 TCTCCTTCGTGACAGTGAGG 58.752 55.000 0.00 0.00 0.00 3.86
3358 4829 0.244994 CTCCTTCGTGACAGTGAGGG 59.755 60.000 0.00 0.55 32.93 4.30
3359 4830 0.178973 TCCTTCGTGACAGTGAGGGA 60.179 55.000 0.00 4.79 37.96 4.20
3360 4831 0.244994 CCTTCGTGACAGTGAGGGAG 59.755 60.000 0.00 0.00 33.43 4.30
3361 4832 1.248486 CTTCGTGACAGTGAGGGAGA 58.752 55.000 0.00 0.00 0.00 3.71
3362 4833 1.201181 CTTCGTGACAGTGAGGGAGAG 59.799 57.143 0.00 0.00 0.00 3.20
3363 4834 0.400594 TCGTGACAGTGAGGGAGAGA 59.599 55.000 0.00 0.00 0.00 3.10
3364 4835 0.808125 CGTGACAGTGAGGGAGAGAG 59.192 60.000 0.00 0.00 0.00 3.20
3365 4836 1.181786 GTGACAGTGAGGGAGAGAGG 58.818 60.000 0.00 0.00 0.00 3.69
3366 4837 0.613292 TGACAGTGAGGGAGAGAGGC 60.613 60.000 0.00 0.00 0.00 4.70
3367 4838 0.613292 GACAGTGAGGGAGAGAGGCA 60.613 60.000 0.00 0.00 0.00 4.75
3368 4839 0.614415 ACAGTGAGGGAGAGAGGCAG 60.614 60.000 0.00 0.00 0.00 4.85
3369 4840 1.685421 AGTGAGGGAGAGAGGCAGC 60.685 63.158 0.00 0.00 0.00 5.25
3370 4841 2.364842 TGAGGGAGAGAGGCAGCC 60.365 66.667 1.84 1.84 0.00 4.85
3371 4842 2.364842 GAGGGAGAGAGGCAGCCA 60.365 66.667 15.80 0.00 0.00 4.75
3372 4843 2.686835 AGGGAGAGAGGCAGCCAC 60.687 66.667 15.80 7.68 0.00 5.01
3373 4844 3.005539 GGGAGAGAGGCAGCCACA 61.006 66.667 15.80 0.00 0.00 4.17
3374 4845 2.583520 GGAGAGAGGCAGCCACAG 59.416 66.667 15.80 0.00 0.00 3.66
3375 4846 1.986757 GGAGAGAGGCAGCCACAGA 60.987 63.158 15.80 0.00 0.00 3.41
3376 4847 1.548357 GGAGAGAGGCAGCCACAGAA 61.548 60.000 15.80 0.00 0.00 3.02
3377 4848 0.390998 GAGAGAGGCAGCCACAGAAC 60.391 60.000 15.80 0.91 0.00 3.01
3378 4849 1.123861 AGAGAGGCAGCCACAGAACA 61.124 55.000 15.80 0.00 0.00 3.18
3379 4850 0.952984 GAGAGGCAGCCACAGAACAC 60.953 60.000 15.80 0.00 0.00 3.32
3380 4851 1.968540 GAGGCAGCCACAGAACACC 60.969 63.158 15.80 0.00 0.00 4.16
3381 4852 2.203337 GGCAGCCACAGAACACCA 60.203 61.111 6.55 0.00 0.00 4.17
3382 4853 1.604593 GGCAGCCACAGAACACCAT 60.605 57.895 6.55 0.00 0.00 3.55
3383 4854 0.322456 GGCAGCCACAGAACACCATA 60.322 55.000 6.55 0.00 0.00 2.74
3384 4855 1.683011 GGCAGCCACAGAACACCATAT 60.683 52.381 6.55 0.00 0.00 1.78
3385 4856 1.672881 GCAGCCACAGAACACCATATC 59.327 52.381 0.00 0.00 0.00 1.63
3386 4857 2.681976 GCAGCCACAGAACACCATATCT 60.682 50.000 0.00 0.00 0.00 1.98
3387 4858 3.432186 GCAGCCACAGAACACCATATCTA 60.432 47.826 0.00 0.00 0.00 1.98
3388 4859 4.122776 CAGCCACAGAACACCATATCTAC 58.877 47.826 0.00 0.00 0.00 2.59
3389 4860 4.033709 AGCCACAGAACACCATATCTACT 58.966 43.478 0.00 0.00 0.00 2.57
3390 4861 4.122776 GCCACAGAACACCATATCTACTG 58.877 47.826 0.00 0.00 0.00 2.74
3391 4862 4.122776 CCACAGAACACCATATCTACTGC 58.877 47.826 0.00 0.00 0.00 4.40
3392 4863 4.122776 CACAGAACACCATATCTACTGCC 58.877 47.826 0.00 0.00 0.00 4.85
3393 4864 3.134804 ACAGAACACCATATCTACTGCCC 59.865 47.826 0.00 0.00 0.00 5.36
3394 4865 2.365617 AGAACACCATATCTACTGCCCG 59.634 50.000 0.00 0.00 0.00 6.13
3395 4866 2.082140 ACACCATATCTACTGCCCGA 57.918 50.000 0.00 0.00 0.00 5.14
3396 4867 1.964223 ACACCATATCTACTGCCCGAG 59.036 52.381 0.00 0.00 0.00 4.63
3397 4868 0.969894 ACCATATCTACTGCCCGAGC 59.030 55.000 0.00 0.00 40.48 5.03
3409 4880 1.453155 GCCCGAGCAAATTTGAGAGA 58.547 50.000 22.31 0.00 39.53 3.10
3410 4881 2.019984 GCCCGAGCAAATTTGAGAGAT 58.980 47.619 22.31 1.47 39.53 2.75
3411 4882 3.206150 GCCCGAGCAAATTTGAGAGATA 58.794 45.455 22.31 0.00 39.53 1.98
3412 4883 3.817647 GCCCGAGCAAATTTGAGAGATAT 59.182 43.478 22.31 0.00 39.53 1.63
3413 4884 4.320057 GCCCGAGCAAATTTGAGAGATATG 60.320 45.833 22.31 3.20 39.53 1.78
3414 4885 4.214971 CCCGAGCAAATTTGAGAGATATGG 59.785 45.833 22.31 10.14 0.00 2.74
3415 4886 4.320057 CCGAGCAAATTTGAGAGATATGGC 60.320 45.833 22.31 2.08 0.00 4.40
3416 4887 4.320057 CGAGCAAATTTGAGAGATATGGCC 60.320 45.833 22.31 0.00 0.00 5.36
3419 4890 4.826183 GCAAATTTGAGAGATATGGCCTCT 59.174 41.667 22.31 0.00 43.16 3.69
3471 4942 0.804989 CGGCTGGCCTCTTTAGTTTG 59.195 55.000 3.32 0.00 0.00 2.93
3531 5002 7.561722 TCTCTGGAAGAATGTAGCATAAGTACT 59.438 37.037 0.00 0.00 46.34 2.73
3581 5052 3.866910 TGAAAGTAAAACGACGACAAGCT 59.133 39.130 0.00 0.00 0.00 3.74
3586 5061 7.823149 AAGTAAAACGACGACAAGCTATATT 57.177 32.000 0.00 0.00 0.00 1.28
3619 5094 9.838975 CTGTAATACACACAAATTTAGATTGCA 57.161 29.630 0.00 0.00 32.33 4.08
3678 5153 7.566879 TCTCTAGCTGGATTAAGGATTTTCTCT 59.433 37.037 0.00 0.00 0.00 3.10
3685 5160 5.220873 GGATTAAGGATTTTCTCTGTTCGGC 60.221 44.000 0.00 0.00 0.00 5.54
3702 5177 2.552315 TCGGCAGTTTGATCAAAGAACC 59.448 45.455 21.05 18.91 0.00 3.62
3704 5179 2.627699 GGCAGTTTGATCAAAGAACCCA 59.372 45.455 21.05 0.00 0.00 4.51
3709 5259 6.928492 GCAGTTTGATCAAAGAACCCATTTAA 59.072 34.615 21.05 0.00 0.00 1.52
3761 5312 4.658901 TCTGGAAGTTTACCTTGTCTCCTT 59.341 41.667 0.00 0.00 32.03 3.36
3845 5399 3.574826 GACTATATGTGTCCTGGGTCTCC 59.425 52.174 0.00 0.00 0.00 3.71
3846 5400 2.568546 ATATGTGTCCTGGGTCTCCA 57.431 50.000 0.00 0.00 41.58 3.86
3872 5426 4.877378 ACTCCGTTTCACTGTATACCAA 57.123 40.909 0.00 0.00 0.00 3.67
3873 5427 4.817517 ACTCCGTTTCACTGTATACCAAG 58.182 43.478 0.00 0.00 0.00 3.61
3874 5428 4.181578 CTCCGTTTCACTGTATACCAAGG 58.818 47.826 0.00 0.00 0.00 3.61
3875 5429 3.833650 TCCGTTTCACTGTATACCAAGGA 59.166 43.478 0.00 0.00 0.00 3.36
3880 5442 8.145767 CCGTTTCACTGTATACCAAGGATATTA 58.854 37.037 0.00 0.00 0.00 0.98
3915 5477 4.322080 TCCGCTCTATACCAATGTTCAG 57.678 45.455 0.00 0.00 0.00 3.02
3916 5478 3.704566 TCCGCTCTATACCAATGTTCAGT 59.295 43.478 0.00 0.00 0.00 3.41
3920 5482 4.878397 GCTCTATACCAATGTTCAGTGCTT 59.122 41.667 0.00 0.00 0.00 3.91
3921 5483 5.355350 GCTCTATACCAATGTTCAGTGCTTT 59.645 40.000 0.00 0.00 0.00 3.51
3922 5484 6.676456 GCTCTATACCAATGTTCAGTGCTTTG 60.676 42.308 0.00 0.00 0.00 2.77
3923 5485 6.472016 TCTATACCAATGTTCAGTGCTTTGA 58.528 36.000 0.00 0.00 0.00 2.69
3924 5486 6.939730 TCTATACCAATGTTCAGTGCTTTGAA 59.060 34.615 0.20 0.20 34.83 2.69
3925 5487 4.734398 ACCAATGTTCAGTGCTTTGAAA 57.266 36.364 5.26 0.00 38.69 2.69
3926 5488 5.083533 ACCAATGTTCAGTGCTTTGAAAA 57.916 34.783 5.26 1.41 38.69 2.29
3927 5489 5.486526 ACCAATGTTCAGTGCTTTGAAAAA 58.513 33.333 5.26 0.00 38.69 1.94
3928 5490 5.581874 ACCAATGTTCAGTGCTTTGAAAAAG 59.418 36.000 5.26 0.00 38.69 2.27
3929 5491 5.495502 CAATGTTCAGTGCTTTGAAAAAGC 58.504 37.500 15.99 15.99 38.69 3.51
3930 5492 3.520569 TGTTCAGTGCTTTGAAAAAGCC 58.479 40.909 19.10 11.86 42.36 4.35
3977 5539 5.677319 TCTAATTGACGGACATTTCTCCT 57.323 39.130 0.00 0.00 0.00 3.69
4058 5620 6.540914 TGAACCAAAACTTCGAGAAATACAGT 59.459 34.615 0.00 0.00 0.00 3.55
4059 5621 6.937436 ACCAAAACTTCGAGAAATACAGTT 57.063 33.333 0.00 0.00 0.00 3.16
4060 5622 8.441312 AACCAAAACTTCGAGAAATACAGTTA 57.559 30.769 0.00 0.00 0.00 2.24
4061 5623 8.617290 ACCAAAACTTCGAGAAATACAGTTAT 57.383 30.769 0.00 0.00 0.00 1.89
4062 5624 8.718734 ACCAAAACTTCGAGAAATACAGTTATC 58.281 33.333 0.00 0.00 0.00 1.75
4063 5625 8.936864 CCAAAACTTCGAGAAATACAGTTATCT 58.063 33.333 0.00 0.00 0.00 1.98
4066 5628 9.490379 AAACTTCGAGAAATACAGTTATCTTGT 57.510 29.630 0.00 0.00 0.00 3.16
4067 5629 8.690680 ACTTCGAGAAATACAGTTATCTTGTC 57.309 34.615 0.00 0.00 0.00 3.18
4068 5630 8.304596 ACTTCGAGAAATACAGTTATCTTGTCA 58.695 33.333 0.00 0.00 0.00 3.58
4069 5631 9.307121 CTTCGAGAAATACAGTTATCTTGTCAT 57.693 33.333 0.00 0.00 0.00 3.06
4205 5826 6.258287 ACACGTTATACAAACAACAAGCAGTA 59.742 34.615 0.00 0.00 0.00 2.74
4213 5834 1.942657 ACAACAAGCAGTAGCACACAG 59.057 47.619 0.00 0.00 45.49 3.66
4288 5909 8.539770 TTGAAAATAAAACAACAACAAGCTCA 57.460 26.923 0.00 0.00 0.00 4.26
4296 5917 6.799926 AACAACAACAAGCTCAACAATTTT 57.200 29.167 0.00 0.00 0.00 1.82
4298 5919 7.524294 ACAACAACAAGCTCAACAATTTTAG 57.476 32.000 0.00 0.00 0.00 1.85
4347 5968 4.825085 TCCAGACAAATTTAGACCGCTTTT 59.175 37.500 0.00 0.00 0.00 2.27
4374 5995 2.572556 TGACGGTAATGGGTGTAATGGT 59.427 45.455 0.00 0.00 0.00 3.55
4432 6054 7.571080 TGAAATATTAGCTTCATGCACATCA 57.429 32.000 0.00 0.00 45.94 3.07
4442 6064 5.813672 GCTTCATGCACATCAATAAACCATT 59.186 36.000 0.00 0.00 42.31 3.16
4445 6067 7.114866 TCATGCACATCAATAAACCATTCAT 57.885 32.000 0.00 0.00 0.00 2.57
4451 6073 8.885722 GCACATCAATAAACCATTCATTGATTT 58.114 29.630 6.34 0.00 43.48 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.137872 GGATGAGCATTCGAGGACTGT 59.862 52.381 0.00 0.00 0.00 3.55
1 2 1.137675 TGGATGAGCATTCGAGGACTG 59.862 52.381 0.00 0.00 0.00 3.51
2 3 1.489481 TGGATGAGCATTCGAGGACT 58.511 50.000 0.00 0.00 0.00 3.85
37 38 0.458260 AAAAACGGTTCACACCCAGC 59.542 50.000 0.00 0.00 40.52 4.85
38 39 1.746220 TGAAAAACGGTTCACACCCAG 59.254 47.619 0.00 0.00 40.52 4.45
47 48 0.661020 CAGTCGCCTGAAAAACGGTT 59.339 50.000 0.00 0.00 41.50 4.44
49 50 0.882927 TCCAGTCGCCTGAAAAACGG 60.883 55.000 0.00 0.00 41.50 4.44
67 68 4.128925 TGTCACAATCCAGCTGATACTC 57.871 45.455 17.39 0.00 31.83 2.59
68 69 4.080695 ACATGTCACAATCCAGCTGATACT 60.081 41.667 17.39 0.00 31.83 2.12
70 71 4.492494 ACATGTCACAATCCAGCTGATA 57.508 40.909 17.39 2.75 31.83 2.15
71 72 3.361281 ACATGTCACAATCCAGCTGAT 57.639 42.857 17.39 3.92 34.22 2.90
72 73 2.865119 ACATGTCACAATCCAGCTGA 57.135 45.000 17.39 1.21 0.00 4.26
73 74 3.005050 ACAAACATGTCACAATCCAGCTG 59.995 43.478 6.78 6.78 0.00 4.24
74 75 3.225104 ACAAACATGTCACAATCCAGCT 58.775 40.909 0.00 0.00 0.00 4.24
75 76 3.648339 ACAAACATGTCACAATCCAGC 57.352 42.857 0.00 0.00 0.00 4.85
76 77 8.676401 TGATTATACAAACATGTCACAATCCAG 58.324 33.333 0.00 0.00 0.00 3.86
77 78 8.572855 TGATTATACAAACATGTCACAATCCA 57.427 30.769 0.00 0.00 0.00 3.41
106 107 8.784994 TCGTAAATGAGTAGATCTATGTCTTCC 58.215 37.037 5.57 0.00 0.00 3.46
108 109 8.569641 GGTCGTAAATGAGTAGATCTATGTCTT 58.430 37.037 5.57 2.22 0.00 3.01
125 126 1.619827 TCTGGTTGGACGGTCGTAAAT 59.380 47.619 1.43 0.00 0.00 1.40
184 185 7.648112 GTCGAAATTTCTTTGACCTTTAGCTTT 59.352 33.333 15.92 0.00 0.00 3.51
191 192 3.304458 GCCGTCGAAATTTCTTTGACCTT 60.304 43.478 15.92 0.00 0.00 3.50
213 214 1.176527 AAATCTTCGCACATGGTGGG 58.823 50.000 7.05 7.05 45.77 4.61
250 251 6.401955 CACGTTCATGTGTGTATGTTATGA 57.598 37.500 0.00 0.00 35.12 2.15
265 266 7.009815 CACTATTGACCGTATAAACACGTTCAT 59.990 37.037 0.00 0.00 41.92 2.57
279 280 3.603532 TCTACGTCTCACTATTGACCGT 58.396 45.455 0.00 7.77 37.73 4.83
280 281 4.512198 AGATCTACGTCTCACTATTGACCG 59.488 45.833 0.00 0.00 0.00 4.79
281 282 6.707161 AGTAGATCTACGTCTCACTATTGACC 59.293 42.308 23.82 0.00 40.80 4.02
282 283 7.358600 CGAGTAGATCTACGTCTCACTATTGAC 60.359 44.444 23.82 0.56 40.80 3.18
283 284 6.641723 CGAGTAGATCTACGTCTCACTATTGA 59.358 42.308 23.82 0.00 40.80 2.57
284 285 6.421501 ACGAGTAGATCTACGTCTCACTATTG 59.578 42.308 23.82 11.54 40.80 1.90
285 286 6.514947 ACGAGTAGATCTACGTCTCACTATT 58.485 40.000 23.82 5.57 40.80 1.73
286 287 6.088016 ACGAGTAGATCTACGTCTCACTAT 57.912 41.667 23.82 6.26 40.80 2.12
308 309 5.684184 TGTTGTGCATTATACGATCGTAGAC 59.316 40.000 29.63 16.01 42.51 2.59
318 319 6.462995 CGATTTTCGTGTTGTGCATTATAC 57.537 37.500 0.00 0.00 34.72 1.47
344 353 6.147821 ACCACTAGTTTCATCTTGATGTTTCG 59.852 38.462 10.01 0.00 0.00 3.46
351 360 9.621629 TTTCTTTAACCACTAGTTTCATCTTGA 57.378 29.630 0.00 0.00 40.05 3.02
370 379 7.681939 AGCGTATGAGGTGAAATTTTCTTTA 57.318 32.000 10.33 0.00 0.00 1.85
423 432 1.069022 GCTCGAGCAATGCAACTGAAA 60.069 47.619 31.91 0.00 41.59 2.69
426 435 1.136147 GGCTCGAGCAATGCAACTG 59.864 57.895 36.27 0.00 44.36 3.16
445 454 0.291989 CGATCGTTTCAAGCGAGTCG 59.708 55.000 8.54 8.54 41.83 4.18
481 490 2.363147 ACCTCCGAGTCTGGCTCC 60.363 66.667 3.28 0.00 41.10 4.70
496 505 0.727398 GGCACGATACTTGAAGCACC 59.273 55.000 0.00 0.00 0.00 5.01
530 539 4.331168 GCAGTTTGGTTTGTGTGCAAATAA 59.669 37.500 0.00 0.00 45.11 1.40
569 588 2.356535 CCAACTAGCCTTGAGGATGCTT 60.357 50.000 0.06 0.00 36.57 3.91
570 589 1.211457 CCAACTAGCCTTGAGGATGCT 59.789 52.381 0.06 0.00 39.10 3.79
575 595 2.859165 TTGTCCAACTAGCCTTGAGG 57.141 50.000 0.00 0.00 38.53 3.86
585 2011 4.202524 TGGTAGCCTACAAATTGTCCAACT 60.203 41.667 0.22 0.00 0.00 3.16
840 2266 1.586564 CTTCGTCGCCAGGATCGTC 60.587 63.158 0.00 0.00 0.00 4.20
878 2307 1.265905 CCAAACAGGAAAGGTGTACGC 59.734 52.381 0.00 0.00 41.22 4.42
897 2326 1.700042 ATTGGCAGATCCCGTCCTCC 61.700 60.000 0.00 0.00 0.00 4.30
902 2331 4.695455 CGAAATTATATTGGCAGATCCCGT 59.305 41.667 0.00 0.00 0.00 5.28
1328 2780 2.186384 CTCCGCTTCCTGCAGGAG 59.814 66.667 33.16 26.41 46.89 3.69
1539 2991 1.813178 GCTTTACCTCCTTCTTGCCAC 59.187 52.381 0.00 0.00 0.00 5.01
1591 3043 1.210722 GACTTCTCCTTCCCATCCACC 59.789 57.143 0.00 0.00 0.00 4.61
1597 3049 0.042731 ATCCGGACTTCTCCTTCCCA 59.957 55.000 6.12 0.00 33.79 4.37
1600 3052 1.202475 GCAGATCCGGACTTCTCCTTC 60.202 57.143 6.12 0.00 33.79 3.46
1619 3071 1.311651 GCTGCTTCTCCTTCCTTGGC 61.312 60.000 0.00 0.00 0.00 4.52
1672 3124 1.323271 CGCAAGACAGCTCCTCCCTA 61.323 60.000 0.00 0.00 43.02 3.53
1706 3158 3.409026 AACCAAGGATATCGATCTGCC 57.591 47.619 0.00 1.73 32.15 4.85
1736 3188 6.005823 CAGGGATAATCACATAGGCAATGAA 58.994 40.000 5.38 0.00 39.07 2.57
1744 3196 9.693739 ATACTCTACTCAGGGATAATCACATAG 57.306 37.037 0.00 0.00 0.00 2.23
1790 3242 4.789807 AGCAGATATCCAAGCAAATCTGT 58.210 39.130 13.00 0.00 44.62 3.41
2118 3580 3.765511 ACATCACACATTGAATCTTGGGG 59.234 43.478 0.00 0.00 37.92 4.96
2213 3675 5.048364 TGCCACAAGTGATTAACAACATACC 60.048 40.000 0.94 0.00 0.00 2.73
2377 3841 0.940126 AAACACAGCTGCTCAGTTCG 59.060 50.000 15.27 0.00 0.00 3.95
2677 4142 7.553760 TGCAAGATCTTGAATTACTGCAGAATA 59.446 33.333 34.43 5.11 42.93 1.75
2717 4182 1.168714 GTTGGATGGTGTTCCAGAGC 58.831 55.000 0.00 0.00 46.22 4.09
2819 4284 5.373222 TGTGTATAGTTGTTGCTTCTTGGT 58.627 37.500 0.00 0.00 0.00 3.67
2850 4315 1.202770 ACTGCCACTGGTGTTCCTAAC 60.203 52.381 0.00 0.00 34.23 2.34
2989 4460 0.247736 GCTCCTACCCTGTGTGTCAG 59.752 60.000 0.00 0.00 43.27 3.51
3140 4611 2.938956 CCCCCTCATTATCGAAAGCT 57.061 50.000 0.00 0.00 0.00 3.74
3226 4697 1.261238 AAGGAGAACTGCCCTCTCGG 61.261 60.000 0.00 0.00 40.29 4.63
3227 4698 0.174617 GAAGGAGAACTGCCCTCTCG 59.825 60.000 0.00 0.00 40.29 4.04
3228 4699 0.174617 CGAAGGAGAACTGCCCTCTC 59.825 60.000 0.00 0.00 38.92 3.20
3229 4700 0.543174 ACGAAGGAGAACTGCCCTCT 60.543 55.000 0.00 0.00 31.17 3.69
3230 4701 0.390472 CACGAAGGAGAACTGCCCTC 60.390 60.000 0.00 0.00 31.17 4.30
3231 4702 0.832135 TCACGAAGGAGAACTGCCCT 60.832 55.000 0.00 0.00 0.00 5.19
3232 4703 0.670854 GTCACGAAGGAGAACTGCCC 60.671 60.000 0.00 0.00 0.00 5.36
3233 4704 0.033504 TGTCACGAAGGAGAACTGCC 59.966 55.000 0.00 0.00 0.00 4.85
3234 4705 1.865865 TTGTCACGAAGGAGAACTGC 58.134 50.000 0.00 0.00 0.00 4.40
3235 4706 3.653344 TCATTGTCACGAAGGAGAACTG 58.347 45.455 0.00 0.00 0.00 3.16
3236 4707 3.306364 CCTCATTGTCACGAAGGAGAACT 60.306 47.826 0.00 0.00 36.12 3.01
3237 4708 2.996621 CCTCATTGTCACGAAGGAGAAC 59.003 50.000 0.00 0.00 36.12 3.01
3238 4709 2.028112 CCCTCATTGTCACGAAGGAGAA 60.028 50.000 0.00 0.00 36.12 2.87
3239 4710 1.550524 CCCTCATTGTCACGAAGGAGA 59.449 52.381 0.00 0.00 36.12 3.71
3240 4711 1.550524 TCCCTCATTGTCACGAAGGAG 59.449 52.381 0.00 0.00 34.28 3.69
3241 4712 1.550524 CTCCCTCATTGTCACGAAGGA 59.449 52.381 0.00 0.00 0.00 3.36
3242 4713 1.550524 TCTCCCTCATTGTCACGAAGG 59.449 52.381 0.00 0.00 0.00 3.46
3243 4714 2.493675 TCTCTCCCTCATTGTCACGAAG 59.506 50.000 0.00 0.00 0.00 3.79
3244 4715 2.493675 CTCTCTCCCTCATTGTCACGAA 59.506 50.000 0.00 0.00 0.00 3.85
3245 4716 2.095461 CTCTCTCCCTCATTGTCACGA 58.905 52.381 0.00 0.00 0.00 4.35
3246 4717 1.135915 CCTCTCTCCCTCATTGTCACG 59.864 57.143 0.00 0.00 0.00 4.35
3247 4718 1.134551 GCCTCTCTCCCTCATTGTCAC 60.135 57.143 0.00 0.00 0.00 3.67
3248 4719 1.198713 GCCTCTCTCCCTCATTGTCA 58.801 55.000 0.00 0.00 0.00 3.58
3249 4720 1.138661 CTGCCTCTCTCCCTCATTGTC 59.861 57.143 0.00 0.00 0.00 3.18
3250 4721 1.202330 CTGCCTCTCTCCCTCATTGT 58.798 55.000 0.00 0.00 0.00 2.71
3251 4722 0.179051 GCTGCCTCTCTCCCTCATTG 60.179 60.000 0.00 0.00 0.00 2.82
3252 4723 1.344191 GGCTGCCTCTCTCCCTCATT 61.344 60.000 12.43 0.00 0.00 2.57
3253 4724 1.765657 GGCTGCCTCTCTCCCTCAT 60.766 63.158 12.43 0.00 0.00 2.90
3254 4725 2.364842 GGCTGCCTCTCTCCCTCA 60.365 66.667 12.43 0.00 0.00 3.86
3255 4726 2.364842 TGGCTGCCTCTCTCCCTC 60.365 66.667 21.03 0.00 0.00 4.30
3256 4727 2.686835 GTGGCTGCCTCTCTCCCT 60.687 66.667 21.03 0.00 0.00 4.20
3257 4728 3.005539 TGTGGCTGCCTCTCTCCC 61.006 66.667 21.03 0.00 0.00 4.30
3258 4729 2.583520 CTGTGGCTGCCTCTCTCC 59.416 66.667 21.03 1.53 0.00 3.71
3259 4730 1.986757 TCCTGTGGCTGCCTCTCTC 60.987 63.158 21.03 5.92 0.00 3.20
3260 4731 2.121385 TCCTGTGGCTGCCTCTCT 59.879 61.111 21.03 0.00 0.00 3.10
3261 4732 2.267324 GTCCTGTGGCTGCCTCTC 59.733 66.667 21.03 10.76 0.00 3.20
3262 4733 2.527624 TGTCCTGTGGCTGCCTCT 60.528 61.111 21.03 0.00 0.00 3.69
3263 4734 2.359230 GTGTCCTGTGGCTGCCTC 60.359 66.667 21.03 17.16 0.00 4.70
3264 4735 3.958860 GGTGTCCTGTGGCTGCCT 61.959 66.667 21.03 0.00 0.00 4.75
3265 4736 2.196997 TATGGTGTCCTGTGGCTGCC 62.197 60.000 12.87 12.87 0.00 4.85
3266 4737 0.107017 ATATGGTGTCCTGTGGCTGC 60.107 55.000 0.00 0.00 0.00 5.25
3267 4738 1.487976 AGATATGGTGTCCTGTGGCTG 59.512 52.381 0.00 0.00 0.00 4.85
3268 4739 1.885049 AGATATGGTGTCCTGTGGCT 58.115 50.000 0.00 0.00 0.00 4.75
3269 4740 2.700897 AGTAGATATGGTGTCCTGTGGC 59.299 50.000 0.00 0.00 0.00 5.01
3270 4741 3.493350 GCAGTAGATATGGTGTCCTGTGG 60.493 52.174 0.00 0.00 0.00 4.17
3271 4742 3.493350 GGCAGTAGATATGGTGTCCTGTG 60.493 52.174 0.00 0.00 0.00 3.66
3272 4743 2.700897 GGCAGTAGATATGGTGTCCTGT 59.299 50.000 0.00 0.00 0.00 4.00
3273 4744 2.037772 GGGCAGTAGATATGGTGTCCTG 59.962 54.545 0.00 0.00 31.59 3.86
3274 4745 2.330216 GGGCAGTAGATATGGTGTCCT 58.670 52.381 0.00 0.00 31.59 3.85
3275 4746 1.000955 CGGGCAGTAGATATGGTGTCC 59.999 57.143 0.00 0.00 0.00 4.02
3276 4747 1.961394 TCGGGCAGTAGATATGGTGTC 59.039 52.381 0.00 0.00 0.00 3.67
3277 4748 1.964223 CTCGGGCAGTAGATATGGTGT 59.036 52.381 0.00 0.00 0.00 4.16
3278 4749 1.337260 GCTCGGGCAGTAGATATGGTG 60.337 57.143 0.00 0.00 38.54 4.17
3279 4750 0.969894 GCTCGGGCAGTAGATATGGT 59.030 55.000 0.00 0.00 38.54 3.55
3280 4751 0.969149 TGCTCGGGCAGTAGATATGG 59.031 55.000 5.44 0.00 44.28 2.74
3291 4762 0.179153 GCTCTCAAATTTGCTCGGGC 60.179 55.000 13.54 0.00 39.26 6.13
3292 4763 1.457346 AGCTCTCAAATTTGCTCGGG 58.543 50.000 13.54 5.52 0.00 5.14
3293 4764 3.003068 CCATAGCTCTCAAATTTGCTCGG 59.997 47.826 13.54 7.56 37.02 4.63
3294 4765 3.547613 GCCATAGCTCTCAAATTTGCTCG 60.548 47.826 13.54 4.69 37.02 5.03
3295 4766 3.243334 GGCCATAGCTCTCAAATTTGCTC 60.243 47.826 13.54 2.56 39.73 4.26
3296 4767 2.692041 GGCCATAGCTCTCAAATTTGCT 59.308 45.455 13.54 9.41 39.73 3.91
3297 4768 2.692041 AGGCCATAGCTCTCAAATTTGC 59.308 45.455 13.54 1.59 39.73 3.68
3298 4769 4.205587 AGAGGCCATAGCTCTCAAATTTG 58.794 43.478 12.15 12.15 38.22 2.32
3299 4770 4.459330 GAGAGGCCATAGCTCTCAAATTT 58.541 43.478 5.01 0.00 40.29 1.82
3300 4771 3.494048 CGAGAGGCCATAGCTCTCAAATT 60.494 47.826 16.67 0.00 40.44 1.82
3301 4772 2.036992 CGAGAGGCCATAGCTCTCAAAT 59.963 50.000 16.67 0.00 40.44 2.32
3302 4773 1.410517 CGAGAGGCCATAGCTCTCAAA 59.589 52.381 16.67 0.00 40.44 2.69
3303 4774 1.035923 CGAGAGGCCATAGCTCTCAA 58.964 55.000 16.67 0.00 40.44 3.02
3304 4775 2.725811 CGAGAGGCCATAGCTCTCA 58.274 57.895 16.67 0.00 40.44 3.27
3325 4796 1.261238 AAGGAGAACTGCCCTCTCGG 61.261 60.000 0.00 0.00 40.29 4.63
3326 4797 0.174617 GAAGGAGAACTGCCCTCTCG 59.825 60.000 0.00 0.00 40.29 4.04
3327 4798 0.174617 CGAAGGAGAACTGCCCTCTC 59.825 60.000 0.00 0.00 38.92 3.20
3328 4799 0.543174 ACGAAGGAGAACTGCCCTCT 60.543 55.000 0.00 0.00 31.17 3.69
3329 4800 0.390472 CACGAAGGAGAACTGCCCTC 60.390 60.000 0.00 0.00 31.17 4.30
3330 4801 0.832135 TCACGAAGGAGAACTGCCCT 60.832 55.000 0.00 0.00 0.00 5.19
3331 4802 0.670854 GTCACGAAGGAGAACTGCCC 60.671 60.000 0.00 0.00 0.00 5.36
3332 4803 0.033504 TGTCACGAAGGAGAACTGCC 59.966 55.000 0.00 0.00 0.00 4.85
3333 4804 1.269831 ACTGTCACGAAGGAGAACTGC 60.270 52.381 0.00 0.00 0.00 4.40
3334 4805 2.034685 TCACTGTCACGAAGGAGAACTG 59.965 50.000 0.00 0.00 0.00 3.16
3335 4806 2.294791 CTCACTGTCACGAAGGAGAACT 59.705 50.000 0.00 0.00 0.00 3.01
3336 4807 2.608261 CCTCACTGTCACGAAGGAGAAC 60.608 54.545 0.00 0.00 0.00 3.01
3337 4808 1.613925 CCTCACTGTCACGAAGGAGAA 59.386 52.381 0.00 0.00 0.00 2.87
3338 4809 1.248486 CCTCACTGTCACGAAGGAGA 58.752 55.000 0.00 0.00 0.00 3.71
3339 4810 0.244994 CCCTCACTGTCACGAAGGAG 59.755 60.000 0.00 0.00 0.00 3.69
3340 4811 0.178973 TCCCTCACTGTCACGAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
3341 4812 0.244994 CTCCCTCACTGTCACGAAGG 59.755 60.000 0.00 0.00 0.00 3.46
3342 4813 1.201181 CTCTCCCTCACTGTCACGAAG 59.799 57.143 0.00 0.00 0.00 3.79
3343 4814 1.202891 TCTCTCCCTCACTGTCACGAA 60.203 52.381 0.00 0.00 0.00 3.85
3344 4815 0.400594 TCTCTCCCTCACTGTCACGA 59.599 55.000 0.00 0.00 0.00 4.35
3345 4816 0.808125 CTCTCTCCCTCACTGTCACG 59.192 60.000 0.00 0.00 0.00 4.35
3346 4817 1.181786 CCTCTCTCCCTCACTGTCAC 58.818 60.000 0.00 0.00 0.00 3.67
3347 4818 0.613292 GCCTCTCTCCCTCACTGTCA 60.613 60.000 0.00 0.00 0.00 3.58
3348 4819 0.613292 TGCCTCTCTCCCTCACTGTC 60.613 60.000 0.00 0.00 0.00 3.51
3349 4820 0.614415 CTGCCTCTCTCCCTCACTGT 60.614 60.000 0.00 0.00 0.00 3.55
3350 4821 1.958902 GCTGCCTCTCTCCCTCACTG 61.959 65.000 0.00 0.00 0.00 3.66
3351 4822 1.685421 GCTGCCTCTCTCCCTCACT 60.685 63.158 0.00 0.00 0.00 3.41
3352 4823 2.730524 GGCTGCCTCTCTCCCTCAC 61.731 68.421 12.43 0.00 0.00 3.51
3353 4824 2.364842 GGCTGCCTCTCTCCCTCA 60.365 66.667 12.43 0.00 0.00 3.86
3354 4825 2.364842 TGGCTGCCTCTCTCCCTC 60.365 66.667 21.03 0.00 0.00 4.30
3355 4826 2.686835 GTGGCTGCCTCTCTCCCT 60.687 66.667 21.03 0.00 0.00 4.20
3356 4827 3.005539 TGTGGCTGCCTCTCTCCC 61.006 66.667 21.03 0.00 0.00 4.30
3357 4828 1.548357 TTCTGTGGCTGCCTCTCTCC 61.548 60.000 21.03 1.53 0.00 3.71
3358 4829 0.390998 GTTCTGTGGCTGCCTCTCTC 60.391 60.000 21.03 5.92 0.00 3.20
3359 4830 1.123861 TGTTCTGTGGCTGCCTCTCT 61.124 55.000 21.03 0.00 0.00 3.10
3360 4831 0.952984 GTGTTCTGTGGCTGCCTCTC 60.953 60.000 21.03 10.76 0.00 3.20
3361 4832 1.072159 GTGTTCTGTGGCTGCCTCT 59.928 57.895 21.03 0.00 0.00 3.69
3362 4833 1.968540 GGTGTTCTGTGGCTGCCTC 60.969 63.158 21.03 17.16 0.00 4.70
3363 4834 2.072874 ATGGTGTTCTGTGGCTGCCT 62.073 55.000 21.03 0.00 0.00 4.75
3364 4835 0.322456 TATGGTGTTCTGTGGCTGCC 60.322 55.000 12.87 12.87 0.00 4.85
3365 4836 1.672881 GATATGGTGTTCTGTGGCTGC 59.327 52.381 0.00 0.00 0.00 5.25
3366 4837 3.272574 AGATATGGTGTTCTGTGGCTG 57.727 47.619 0.00 0.00 0.00 4.85
3367 4838 4.033709 AGTAGATATGGTGTTCTGTGGCT 58.966 43.478 0.00 0.00 0.00 4.75
3368 4839 4.122776 CAGTAGATATGGTGTTCTGTGGC 58.877 47.826 0.00 0.00 0.00 5.01
3369 4840 4.122776 GCAGTAGATATGGTGTTCTGTGG 58.877 47.826 0.00 0.00 0.00 4.17
3370 4841 4.122776 GGCAGTAGATATGGTGTTCTGTG 58.877 47.826 0.00 0.00 0.00 3.66
3371 4842 3.134804 GGGCAGTAGATATGGTGTTCTGT 59.865 47.826 0.00 0.00 0.00 3.41
3372 4843 3.733337 GGGCAGTAGATATGGTGTTCTG 58.267 50.000 0.00 0.00 0.00 3.02
3373 4844 2.365617 CGGGCAGTAGATATGGTGTTCT 59.634 50.000 0.00 0.00 0.00 3.01
3374 4845 2.364324 TCGGGCAGTAGATATGGTGTTC 59.636 50.000 0.00 0.00 0.00 3.18
3375 4846 2.365617 CTCGGGCAGTAGATATGGTGTT 59.634 50.000 0.00 0.00 0.00 3.32
3376 4847 1.964223 CTCGGGCAGTAGATATGGTGT 59.036 52.381 0.00 0.00 0.00 4.16
3377 4848 1.337260 GCTCGGGCAGTAGATATGGTG 60.337 57.143 0.00 0.00 38.54 4.17
3378 4849 0.969894 GCTCGGGCAGTAGATATGGT 59.030 55.000 0.00 0.00 38.54 3.55
3379 4850 0.969149 TGCTCGGGCAGTAGATATGG 59.031 55.000 5.44 0.00 44.28 2.74
3390 4861 1.453155 TCTCTCAAATTTGCTCGGGC 58.547 50.000 13.54 0.00 39.26 6.13
3391 4862 4.214971 CCATATCTCTCAAATTTGCTCGGG 59.785 45.833 13.54 4.62 0.00 5.14
3392 4863 4.320057 GCCATATCTCTCAAATTTGCTCGG 60.320 45.833 13.54 6.17 0.00 4.63
3393 4864 4.320057 GGCCATATCTCTCAAATTTGCTCG 60.320 45.833 13.54 4.69 0.00 5.03
3394 4865 4.826183 AGGCCATATCTCTCAAATTTGCTC 59.174 41.667 13.54 0.00 0.00 4.26
3395 4866 4.801164 AGGCCATATCTCTCAAATTTGCT 58.199 39.130 13.54 0.00 0.00 3.91
3396 4867 4.826183 AGAGGCCATATCTCTCAAATTTGC 59.174 41.667 13.54 0.00 36.99 3.68
3436 4907 2.578178 CGCGAGCACGAAGGAGAG 60.578 66.667 8.01 0.00 42.66 3.20
3619 5094 8.060075 AGGGCTATACGACCATTATCTAGTAAT 58.940 37.037 0.00 0.00 46.64 1.89
3678 5153 3.210227 TCTTTGATCAAACTGCCGAACA 58.790 40.909 16.91 0.00 0.00 3.18
3685 5160 8.885494 TTTAAATGGGTTCTTTGATCAAACTG 57.115 30.769 16.91 8.77 0.00 3.16
3739 5289 4.625607 AGGAGACAAGGTAAACTTCCAG 57.374 45.455 0.00 0.00 37.29 3.86
3761 5312 3.091545 GCTGATGGAAAATGAGTTGGGA 58.908 45.455 0.00 0.00 0.00 4.37
3812 5363 6.547880 AGGACACATATAGTCTGTAAGGAGTG 59.452 42.308 7.25 0.00 36.29 3.51
3872 5426 8.299570 GCGGATTTTTGTTGATGATAATATCCT 58.700 33.333 0.00 0.00 0.00 3.24
3873 5427 8.299570 AGCGGATTTTTGTTGATGATAATATCC 58.700 33.333 0.00 0.00 0.00 2.59
3874 5428 9.334693 GAGCGGATTTTTGTTGATGATAATATC 57.665 33.333 0.00 0.00 0.00 1.63
3875 5429 9.071276 AGAGCGGATTTTTGTTGATGATAATAT 57.929 29.630 0.00 0.00 0.00 1.28
3880 5442 6.949352 ATAGAGCGGATTTTTGTTGATGAT 57.051 33.333 0.00 0.00 0.00 2.45
3893 5455 4.345257 ACTGAACATTGGTATAGAGCGGAT 59.655 41.667 0.00 0.00 0.00 4.18
3897 5459 4.446371 AGCACTGAACATTGGTATAGAGC 58.554 43.478 0.00 1.35 31.56 4.09
3915 5477 2.892374 ACAGTGGCTTTTTCAAAGCAC 58.108 42.857 19.99 15.62 44.71 4.40
3916 5478 4.935352 ATACAGTGGCTTTTTCAAAGCA 57.065 36.364 19.99 6.45 44.71 3.91
3920 5482 7.777095 ACAACTTTATACAGTGGCTTTTTCAA 58.223 30.769 0.00 0.00 0.00 2.69
3921 5483 7.067615 TGACAACTTTATACAGTGGCTTTTTCA 59.932 33.333 0.00 0.00 0.00 2.69
3922 5484 7.422399 TGACAACTTTATACAGTGGCTTTTTC 58.578 34.615 0.00 0.00 0.00 2.29
3923 5485 7.341445 TGACAACTTTATACAGTGGCTTTTT 57.659 32.000 0.00 0.00 0.00 1.94
3924 5486 6.952773 TGACAACTTTATACAGTGGCTTTT 57.047 33.333 0.00 0.00 0.00 2.27
3925 5487 6.490040 ACATGACAACTTTATACAGTGGCTTT 59.510 34.615 0.00 0.00 0.00 3.51
3926 5488 6.003950 ACATGACAACTTTATACAGTGGCTT 58.996 36.000 0.00 0.00 0.00 4.35
3927 5489 5.412594 CACATGACAACTTTATACAGTGGCT 59.587 40.000 0.00 0.00 0.00 4.75
3928 5490 5.631026 CACATGACAACTTTATACAGTGGC 58.369 41.667 0.00 0.00 0.00 5.01
3929 5491 5.391950 GGCACATGACAACTTTATACAGTGG 60.392 44.000 0.00 0.00 0.00 4.00
3930 5492 5.181056 TGGCACATGACAACTTTATACAGTG 59.819 40.000 0.00 0.00 0.00 3.66
4012 5574 7.749126 GGTTCAATTTACGGAACAGATAACAAG 59.251 37.037 8.22 0.00 43.96 3.16
4058 5620 5.534278 TGTTCAAAGGCACATGACAAGATAA 59.466 36.000 0.00 0.00 0.00 1.75
4059 5621 5.069318 TGTTCAAAGGCACATGACAAGATA 58.931 37.500 0.00 0.00 0.00 1.98
4060 5622 3.890756 TGTTCAAAGGCACATGACAAGAT 59.109 39.130 0.00 0.00 0.00 2.40
4061 5623 3.286353 TGTTCAAAGGCACATGACAAGA 58.714 40.909 0.00 0.00 0.00 3.02
4062 5624 3.713858 TGTTCAAAGGCACATGACAAG 57.286 42.857 0.00 0.00 0.00 3.16
4063 5625 4.431809 CTTTGTTCAAAGGCACATGACAA 58.568 39.130 15.08 0.00 0.00 3.18
4064 5626 3.737663 GCTTTGTTCAAAGGCACATGACA 60.738 43.478 21.56 0.00 0.00 3.58
4065 5627 2.796593 GCTTTGTTCAAAGGCACATGAC 59.203 45.455 21.56 4.27 0.00 3.06
4066 5628 2.429971 TGCTTTGTTCAAAGGCACATGA 59.570 40.909 21.56 0.00 0.00 3.07
4067 5629 2.823984 TGCTTTGTTCAAAGGCACATG 58.176 42.857 21.56 0.00 0.00 3.21
4068 5630 3.756933 ATGCTTTGTTCAAAGGCACAT 57.243 38.095 21.56 15.09 0.00 3.21
4069 5631 3.540314 AATGCTTTGTTCAAAGGCACA 57.460 38.095 21.56 13.85 0.00 4.57
4183 5753 5.788531 GCTACTGCTTGTTGTTTGTATAACG 59.211 40.000 0.00 0.00 36.03 3.18
4187 5757 4.578516 TGTGCTACTGCTTGTTGTTTGTAT 59.421 37.500 0.00 0.00 40.48 2.29
4188 5758 3.942115 TGTGCTACTGCTTGTTGTTTGTA 59.058 39.130 0.00 0.00 40.48 2.41
4190 5760 3.108144 GTGTGCTACTGCTTGTTGTTTG 58.892 45.455 0.00 0.00 40.48 2.93
4191 5761 2.752354 TGTGTGCTACTGCTTGTTGTTT 59.248 40.909 0.00 0.00 40.48 2.83
4192 5762 2.355756 CTGTGTGCTACTGCTTGTTGTT 59.644 45.455 0.00 0.00 40.48 2.83
4193 5763 1.942657 CTGTGTGCTACTGCTTGTTGT 59.057 47.619 0.00 0.00 40.48 3.32
4205 5826 4.666512 AGTTAATCCCAAATCTGTGTGCT 58.333 39.130 0.00 0.00 0.00 4.40
4238 5859 7.881775 ATAATACCTGGATTTTGAGTGTTCC 57.118 36.000 0.00 0.00 0.00 3.62
4239 5860 9.573133 CAAATAATACCTGGATTTTGAGTGTTC 57.427 33.333 0.00 0.00 0.00 3.18
4269 5890 8.491331 AATTGTTGAGCTTGTTGTTGTTTTAT 57.509 26.923 0.00 0.00 0.00 1.40
4279 5900 6.273071 GTGACCTAAAATTGTTGAGCTTGTT 58.727 36.000 0.00 0.00 0.00 2.83
4288 5909 5.417580 ACATATGGCGTGACCTAAAATTGTT 59.582 36.000 7.80 0.00 40.22 2.83
4296 5917 3.527533 GAAACACATATGGCGTGACCTA 58.472 45.455 7.80 0.00 40.22 3.08
4298 5919 1.400494 GGAAACACATATGGCGTGACC 59.600 52.381 7.80 7.39 37.80 4.02
4347 5968 3.638860 ACACCCATTACCGTCATCTAGA 58.361 45.455 0.00 0.00 0.00 2.43
4374 5995 1.264295 TTGCATGCAGGGCAATACAA 58.736 45.000 21.50 3.91 45.57 2.41


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

AutoCloner maintained by Alex Coulton.