Multiple sequence alignment - TraesCS4B01G316500

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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 TraesCS4B01G316500 chr4B 100.000 3830 0 0 1540 5369 605939804 605943633 0.000000e+00 7073
1 TraesCS4B01G316500 chr4B 100.000 1076 0 0 1 1076 605938265 605939340 0.000000e+00 1988
2 TraesCS4B01G316500 chr4D 95.712 1819 71 3 1619 3436 479363637 479365449 0.000000e+00 2920
3 TraesCS4B01G316500 chr4D 96.154 1560 43 6 3464 5011 479365435 479366989 0.000000e+00 2532
4 TraesCS4B01G316500 chr4D 89.354 263 15 6 827 1076 479362860 479363122 8.680000e-83 318
5 TraesCS4B01G316500 chr4D 82.051 351 36 12 156 497 479360461 479360793 1.910000e-69 274
6 TraesCS4B01G316500 chr4D 89.116 147 16 0 5023 5169 479367081 479367227 3.300000e-42 183
7 TraesCS4B01G316500 chr4D 94.068 118 5 2 5252 5369 479367226 479367341 1.540000e-40 178
8 TraesCS4B01G316500 chr4D 97.778 90 2 0 5165 5254 5081664 5081575 7.200000e-34 156
9 TraesCS4B01G316500 chr4D 81.967 122 20 2 498 618 479361033 479361153 9.510000e-18 102
10 TraesCS4B01G316500 chr4A 93.363 1823 84 8 1628 3436 685749129 685750928 0.000000e+00 2662
11 TraesCS4B01G316500 chr4A 92.180 844 50 9 3653 4480 685751179 685752022 0.000000e+00 1179
12 TraesCS4B01G316500 chr4A 89.227 724 53 10 1 718 685747535 685748239 0.000000e+00 881
13 TraesCS4B01G316500 chr4A 87.209 344 15 9 753 1075 685748360 685748695 1.100000e-96 364
14 TraesCS4B01G316500 chr4A 86.254 291 35 4 4726 5011 685752195 685752485 1.450000e-80 311
15 TraesCS4B01G316500 chr4A 93.583 187 8 1 3464 3650 685750914 685751096 5.300000e-70 276
16 TraesCS4B01G316500 chr4A 89.604 202 13 4 4497 4697 685752007 685752201 3.210000e-62 250
17 TraesCS4B01G316500 chr7D 98.864 88 1 0 5167 5254 98621973 98621886 2.000000e-34 158
18 TraesCS4B01G316500 chr7B 97.778 90 2 0 5168 5257 506378357 506378268 7.200000e-34 156
19 TraesCS4B01G316500 chr6D 97.778 90 2 0 5167 5256 434509264 434509353 7.200000e-34 156
20 TraesCS4B01G316500 chr6D 96.629 89 3 0 5167 5255 255011992 255012080 1.200000e-31 148
21 TraesCS4B01G316500 chr5B 96.774 93 3 0 5165 5257 689662093 689662001 7.200000e-34 156
22 TraesCS4B01G316500 chr1B 97.778 90 2 0 5168 5257 618002463 618002552 7.200000e-34 156
23 TraesCS4B01G316500 chr5D 95.833 96 3 1 5164 5258 504797542 504797637 2.590000e-33 154
24 TraesCS4B01G316500 chr3B 94.000 100 4 2 5164 5262 605277781 605277879 3.350000e-32 150


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 TraesCS4B01G316500 chr4B 605938265 605943633 5368 False 4530.500000 7073 100.000000 1 5369 2 chr4B.!!$F1 5368
1 TraesCS4B01G316500 chr4D 479360461 479367341 6880 False 929.571429 2920 89.774571 156 5369 7 chr4D.!!$F1 5213
2 TraesCS4B01G316500 chr4A 685747535 685752485 4950 False 846.142857 2662 90.202857 1 5011 7 chr4A.!!$F1 5010

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
736 2418 0.039035 AAGCATACGGCCCAAGGAAA 59.961 50.0 0.00 0.00 46.50 3.13 F
740 2422 0.107848 ATACGGCCCAAGGAAAGACG 60.108 55.0 0.00 0.00 0.00 4.18 F
751 2433 0.249398 GGAAAGACGGCTAAGCAGGA 59.751 55.0 0.00 0.00 0.00 3.86 F
952 2845 0.251474 GTTCCCCGGCTTAAACCCTT 60.251 55.0 0.00 0.00 0.00 3.95 F
2203 4527 0.108041 CGTGGTTGCTTATACCGGGT 60.108 55.0 6.32 4.46 38.55 5.28 F
2760 5084 0.538287 AGAACTGCTTTGGACCTGCC 60.538 55.0 0.00 0.00 37.10 4.85 F
3141 5478 0.097674 ACTGCGCGATTTTGAGATGC 59.902 50.0 12.10 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 4395 0.111061 TCAAAGCACAGCACTCCCAT 59.889 50.000 0.00 0.0 0.00 4.00 R
2072 4396 0.111061 ATCAAAGCACAGCACTCCCA 59.889 50.000 0.00 0.0 0.00 4.37 R
2076 4400 1.815003 GCCTTATCAAAGCACAGCACT 59.185 47.619 0.00 0.0 0.00 4.40 R
2505 4829 1.876416 GCAACCCGCTCAGAGTTTACA 60.876 52.381 0.00 0.0 37.77 2.41 R
3100 5435 0.388134 GTTTCTACGACGGCAGAGCA 60.388 55.000 0.00 0.0 0.00 4.26 R
3728 6147 2.300152 TGGAGTGTGCTCGAGAAAGATT 59.700 45.455 18.75 0.0 42.53 2.40 R
4817 7260 0.537188 ATAGTCAGAGCACCCAACCG 59.463 55.000 0.00 0.0 0.00 4.44 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
29 30 9.778993 CATCAATTTATGTATTATGCCTAGCAC 57.221 33.333 0.00 0.00 43.04 4.40
36 37 4.573201 TGTATTATGCCTAGCACGTTTTCC 59.427 41.667 0.00 0.00 43.04 3.13
37 38 2.032680 TATGCCTAGCACGTTTTCCC 57.967 50.000 0.00 0.00 43.04 3.97
41 42 1.294138 CTAGCACGTTTTCCCCCGA 59.706 57.895 0.00 0.00 0.00 5.14
97 98 1.539388 GCGTGTCACATCCCAATTGAA 59.461 47.619 7.12 0.00 0.00 2.69
103 104 5.882557 GTGTCACATCCCAATTGAAGATACT 59.117 40.000 7.12 0.00 0.00 2.12
104 105 7.047891 GTGTCACATCCCAATTGAAGATACTA 58.952 38.462 7.12 0.00 0.00 1.82
105 106 7.552687 GTGTCACATCCCAATTGAAGATACTAA 59.447 37.037 7.12 0.00 0.00 2.24
106 107 7.552687 TGTCACATCCCAATTGAAGATACTAAC 59.447 37.037 7.12 6.33 0.00 2.34
107 108 7.552687 GTCACATCCCAATTGAAGATACTAACA 59.447 37.037 7.12 0.00 0.00 2.41
108 109 7.770433 TCACATCCCAATTGAAGATACTAACAG 59.230 37.037 7.12 0.00 0.00 3.16
109 110 7.770433 CACATCCCAATTGAAGATACTAACAGA 59.230 37.037 7.12 0.00 0.00 3.41
110 111 7.989741 ACATCCCAATTGAAGATACTAACAGAG 59.010 37.037 7.12 0.00 0.00 3.35
125 126 7.286215 ACTAACAGAGTAACAGTCAGCTTTA 57.714 36.000 0.00 0.00 36.27 1.85
151 152 8.299570 AGATTTGCAATCTACCTTTGTTTACAG 58.700 33.333 0.00 0.00 0.00 2.74
159 160 4.584327 ACCTTTGTTTACAGCACAATCC 57.416 40.909 0.00 0.00 34.13 3.01
183 184 6.209391 CCCCAATAATATTGACTCCCATCAAC 59.791 42.308 14.10 0.00 41.29 3.18
215 216 4.754372 TGCTTATATACGTACGGGTCTG 57.246 45.455 21.06 4.57 0.00 3.51
217 218 4.580167 TGCTTATATACGTACGGGTCTGTT 59.420 41.667 21.06 0.00 0.00 3.16
218 219 4.913924 GCTTATATACGTACGGGTCTGTTG 59.086 45.833 21.06 4.56 0.00 3.33
225 226 4.379652 ACGTACGGGTCTGTTGTTAAATT 58.620 39.130 21.06 0.00 0.00 1.82
232 233 3.500680 GGTCTGTTGTTAAATTCGAGCCA 59.499 43.478 0.00 0.00 0.00 4.75
289 290 0.813610 CGTGGATTAATGCGAGGCCA 60.814 55.000 5.01 0.00 0.00 5.36
296 297 5.127845 TGGATTAATGCGAGGCCAAAAATAA 59.872 36.000 5.01 0.00 0.00 1.40
401 408 6.018994 GTGACCGTTGGAATCATAGTATGTTC 60.019 42.308 9.94 11.82 0.00 3.18
406 413 7.116948 CCGTTGGAATCATAGTATGTTCTCATC 59.883 40.741 9.94 10.18 35.70 2.92
422 429 2.064628 ATCTGGAGATGATGGCGGG 58.935 57.895 0.00 0.00 32.68 6.13
423 430 1.486997 ATCTGGAGATGATGGCGGGG 61.487 60.000 0.00 0.00 32.68 5.73
424 431 2.366837 TGGAGATGATGGCGGGGT 60.367 61.111 0.00 0.00 0.00 4.95
425 432 2.111878 GGAGATGATGGCGGGGTG 59.888 66.667 0.00 0.00 0.00 4.61
426 433 2.746375 GGAGATGATGGCGGGGTGT 61.746 63.158 0.00 0.00 0.00 4.16
427 434 1.227674 GAGATGATGGCGGGGTGTC 60.228 63.158 0.00 0.00 0.00 3.67
428 435 1.690219 GAGATGATGGCGGGGTGTCT 61.690 60.000 0.00 0.00 0.00 3.41
566 813 0.698238 TTCTGTGCAACCTAGGCCAT 59.302 50.000 9.30 0.00 34.36 4.40
705 2387 4.362932 CTTTAAGCTGAAAAGCTAGCCC 57.637 45.455 12.13 0.00 45.54 5.19
723 2405 3.345737 CGAGAGGAACGCAAGCATA 57.654 52.632 0.00 0.00 45.62 3.14
724 2406 0.924090 CGAGAGGAACGCAAGCATAC 59.076 55.000 0.00 0.00 45.62 2.39
726 2408 0.460284 AGAGGAACGCAAGCATACGG 60.460 55.000 0.00 0.00 45.62 4.02
728 2410 2.403586 GAACGCAAGCATACGGCC 59.596 61.111 0.00 0.00 46.50 6.13
729 2411 3.108357 GAACGCAAGCATACGGCCC 62.108 63.158 0.00 0.00 46.50 5.80
730 2412 3.910914 AACGCAAGCATACGGCCCA 62.911 57.895 0.00 0.00 46.50 5.36
731 2413 3.130819 CGCAAGCATACGGCCCAA 61.131 61.111 0.00 0.00 46.50 4.12
732 2414 2.800736 GCAAGCATACGGCCCAAG 59.199 61.111 0.00 0.00 46.50 3.61
733 2415 2.774799 GCAAGCATACGGCCCAAGG 61.775 63.158 0.00 0.00 46.50 3.61
735 2417 0.679640 CAAGCATACGGCCCAAGGAA 60.680 55.000 0.00 0.00 46.50 3.36
736 2418 0.039035 AAGCATACGGCCCAAGGAAA 59.961 50.000 0.00 0.00 46.50 3.13
738 2420 0.393808 GCATACGGCCCAAGGAAAGA 60.394 55.000 0.00 0.00 36.11 2.52
739 2421 1.379527 CATACGGCCCAAGGAAAGAC 58.620 55.000 0.00 0.00 0.00 3.01
740 2422 0.107848 ATACGGCCCAAGGAAAGACG 60.108 55.000 0.00 0.00 0.00 4.18
742 2424 3.062466 GGCCCAAGGAAAGACGGC 61.062 66.667 0.00 0.00 38.96 5.68
743 2425 2.034221 GCCCAAGGAAAGACGGCT 59.966 61.111 0.00 0.00 36.65 5.52
744 2426 1.298667 GCCCAAGGAAAGACGGCTA 59.701 57.895 0.00 0.00 36.65 3.93
745 2427 0.322187 GCCCAAGGAAAGACGGCTAA 60.322 55.000 0.00 0.00 36.65 3.09
746 2428 1.739067 CCCAAGGAAAGACGGCTAAG 58.261 55.000 0.00 0.00 0.00 2.18
747 2429 1.087501 CCAAGGAAAGACGGCTAAGC 58.912 55.000 0.00 0.00 0.00 3.09
748 2430 1.610624 CCAAGGAAAGACGGCTAAGCA 60.611 52.381 0.00 0.00 0.00 3.91
749 2431 1.734465 CAAGGAAAGACGGCTAAGCAG 59.266 52.381 0.00 0.00 0.00 4.24
751 2433 0.249398 GGAAAGACGGCTAAGCAGGA 59.751 55.000 0.00 0.00 0.00 3.86
778 2649 1.889573 GTGGCCTGCTAATCCGAGC 60.890 63.158 3.32 0.00 43.16 5.03
803 2674 2.404186 GGCCATTCGACCGGGAAAC 61.404 63.158 6.32 0.00 0.00 2.78
901 2794 2.405143 TCCGCGTAGGATCTGACTG 58.595 57.895 4.92 0.00 45.98 3.51
952 2845 0.251474 GTTCCCCGGCTTAAACCCTT 60.251 55.000 0.00 0.00 0.00 3.95
964 2857 0.545548 AAACCCTTCTCCTCCTCGCT 60.546 55.000 0.00 0.00 0.00 4.93
1600 3493 2.303549 CTTCTCCACCGCAGCCCTAG 62.304 65.000 0.00 0.00 0.00 3.02
2009 4333 2.042259 CGCTGGAGCTGAAATGCCA 61.042 57.895 0.00 0.00 39.32 4.92
2013 4337 1.891150 CTGGAGCTGAAATGCCAGTTT 59.109 47.619 8.40 0.00 42.26 2.66
2072 4396 3.900892 CGCCGCCGAGACCTACAT 61.901 66.667 0.00 0.00 36.29 2.29
2076 4400 2.125326 CGCCGAGACCTACATGGGA 61.125 63.158 0.00 0.00 41.11 4.37
2130 4454 0.250684 TGAAGGCGTTGGAGATTGCA 60.251 50.000 0.00 0.00 0.00 4.08
2142 4466 0.459237 AGATTGCAGAGAAGCGGTCG 60.459 55.000 0.00 0.00 37.31 4.79
2156 4480 3.319198 GTCGGGTGAGGGCTCCAA 61.319 66.667 0.00 0.00 0.00 3.53
2203 4527 0.108041 CGTGGTTGCTTATACCGGGT 60.108 55.000 6.32 4.46 38.55 5.28
2268 4592 2.940514 TGGAGTATGAGAGGTTGGGA 57.059 50.000 0.00 0.00 0.00 4.37
2505 4829 2.481952 GACTCTTGATGCAAAGCGTTCT 59.518 45.455 0.00 0.00 0.00 3.01
2512 4836 3.563808 TGATGCAAAGCGTTCTGTAAACT 59.436 39.130 0.00 0.00 0.00 2.66
2523 4847 1.968493 TCTGTAAACTCTGAGCGGGTT 59.032 47.619 4.19 0.00 0.00 4.11
2728 5052 3.885297 TGTTCCTTTTCTGGAGAAAGCTG 59.115 43.478 2.25 0.00 43.90 4.24
2757 5081 2.952310 GTTGAAGAACTGCTTTGGACCT 59.048 45.455 0.00 0.00 36.83 3.85
2758 5082 2.575532 TGAAGAACTGCTTTGGACCTG 58.424 47.619 0.00 0.00 36.83 4.00
2759 5083 1.268079 GAAGAACTGCTTTGGACCTGC 59.732 52.381 0.00 0.00 36.83 4.85
2760 5084 0.538287 AGAACTGCTTTGGACCTGCC 60.538 55.000 0.00 0.00 37.10 4.85
2882 5206 2.767394 TCATTAATGCTGCATTTGGGCT 59.233 40.909 30.35 10.13 35.54 5.19
3015 5350 8.090250 AGATGCTACTATCTTGTAGAGTTACG 57.910 38.462 5.94 0.00 41.63 3.18
3025 5360 5.939883 TCTTGTAGAGTTACGTGTAGGCTAA 59.060 40.000 0.00 0.00 32.21 3.09
3073 5408 3.700538 ACTGAAGGCAGCATGGAAAATA 58.299 40.909 0.00 0.00 46.26 1.40
3126 5463 1.337821 CCGTCGTAGAAACTGACTGC 58.662 55.000 0.00 0.00 39.69 4.40
3140 5477 1.394572 TGACTGCGCGATTTTGAGATG 59.605 47.619 12.10 0.00 0.00 2.90
3141 5478 0.097674 ACTGCGCGATTTTGAGATGC 59.902 50.000 12.10 0.00 0.00 3.91
3147 5484 2.778659 GCGATTTTGAGATGCTGTCAC 58.221 47.619 0.00 0.00 0.00 3.67
3188 5525 5.840243 ATATGTGTTATGTTGTGCAGCAT 57.160 34.783 0.00 6.74 36.26 3.79
3349 5686 4.928615 GCTGTTGGTGCTTGCAAAATAATA 59.071 37.500 0.00 0.00 0.00 0.98
3350 5687 5.407995 GCTGTTGGTGCTTGCAAAATAATAA 59.592 36.000 0.00 0.00 0.00 1.40
3420 5757 2.543861 CCATATCGTTCTGGTGGTCTCG 60.544 54.545 0.00 0.00 0.00 4.04
3436 5773 6.208994 GGTGGTCTCGTAGATGAAATATAGGT 59.791 42.308 0.00 0.00 33.89 3.08
3437 5774 7.392673 GGTGGTCTCGTAGATGAAATATAGGTA 59.607 40.741 0.00 0.00 33.89 3.08
3438 5775 8.235905 GTGGTCTCGTAGATGAAATATAGGTAC 58.764 40.741 0.00 0.00 33.89 3.34
3439 5776 7.118825 TGGTCTCGTAGATGAAATATAGGTACG 59.881 40.741 0.00 0.00 33.89 3.67
3440 5777 7.332926 GGTCTCGTAGATGAAATATAGGTACGA 59.667 40.741 0.00 0.00 38.66 3.43
3442 5779 8.254178 CTCGTAGATGAAATATAGGTACGAGT 57.746 38.462 16.84 0.00 46.71 4.18
3443 5780 8.249327 TCGTAGATGAAATATAGGTACGAGTC 57.751 38.462 0.00 0.00 36.73 3.36
3444 5781 7.874528 TCGTAGATGAAATATAGGTACGAGTCA 59.125 37.037 0.00 0.00 36.73 3.41
3445 5782 8.169910 CGTAGATGAAATATAGGTACGAGTCAG 58.830 40.741 0.00 0.00 35.04 3.51
3446 5783 7.455641 AGATGAAATATAGGTACGAGTCAGG 57.544 40.000 0.00 0.00 0.00 3.86
3447 5784 6.434652 AGATGAAATATAGGTACGAGTCAGGG 59.565 42.308 0.00 0.00 0.00 4.45
3448 5785 4.280174 TGAAATATAGGTACGAGTCAGGGC 59.720 45.833 0.00 0.00 0.00 5.19
3449 5786 3.520691 ATATAGGTACGAGTCAGGGCA 57.479 47.619 0.00 0.00 0.00 5.36
3450 5787 2.154567 ATAGGTACGAGTCAGGGCAA 57.845 50.000 0.00 0.00 0.00 4.52
3451 5788 1.927487 TAGGTACGAGTCAGGGCAAA 58.073 50.000 0.00 0.00 0.00 3.68
3452 5789 1.276622 AGGTACGAGTCAGGGCAAAT 58.723 50.000 0.00 0.00 0.00 2.32
3453 5790 2.463752 AGGTACGAGTCAGGGCAAATA 58.536 47.619 0.00 0.00 0.00 1.40
3454 5791 3.039011 AGGTACGAGTCAGGGCAAATAT 58.961 45.455 0.00 0.00 0.00 1.28
3455 5792 4.220724 AGGTACGAGTCAGGGCAAATATA 58.779 43.478 0.00 0.00 0.00 0.86
3456 5793 4.281182 AGGTACGAGTCAGGGCAAATATAG 59.719 45.833 0.00 0.00 0.00 1.31
3457 5794 3.753294 ACGAGTCAGGGCAAATATAGG 57.247 47.619 0.00 0.00 0.00 2.57
3458 5795 3.039011 ACGAGTCAGGGCAAATATAGGT 58.961 45.455 0.00 0.00 0.00 3.08
3459 5796 3.181465 ACGAGTCAGGGCAAATATAGGTG 60.181 47.826 0.00 0.00 0.00 4.00
3460 5797 3.142174 GAGTCAGGGCAAATATAGGTGC 58.858 50.000 2.48 2.48 40.14 5.01
3461 5798 2.780010 AGTCAGGGCAAATATAGGTGCT 59.220 45.455 9.57 0.00 40.70 4.40
3462 5799 2.880890 GTCAGGGCAAATATAGGTGCTG 59.119 50.000 9.57 3.01 40.70 4.41
3463 5800 2.509548 TCAGGGCAAATATAGGTGCTGT 59.490 45.455 9.57 0.00 40.70 4.40
3464 5801 3.714280 TCAGGGCAAATATAGGTGCTGTA 59.286 43.478 9.57 0.00 40.70 2.74
3465 5802 4.067896 CAGGGCAAATATAGGTGCTGTAG 58.932 47.826 9.57 0.00 40.70 2.74
3466 5803 3.973973 AGGGCAAATATAGGTGCTGTAGA 59.026 43.478 9.57 0.00 40.70 2.59
3467 5804 4.599241 AGGGCAAATATAGGTGCTGTAGAT 59.401 41.667 9.57 0.00 40.70 1.98
3468 5805 4.697352 GGGCAAATATAGGTGCTGTAGATG 59.303 45.833 9.57 0.00 40.70 2.90
3469 5806 5.513094 GGGCAAATATAGGTGCTGTAGATGA 60.513 44.000 9.57 0.00 40.70 2.92
3470 5807 5.997746 GGCAAATATAGGTGCTGTAGATGAA 59.002 40.000 9.57 0.00 40.70 2.57
3471 5808 6.486657 GGCAAATATAGGTGCTGTAGATGAAA 59.513 38.462 9.57 0.00 40.70 2.69
3472 5809 7.175641 GGCAAATATAGGTGCTGTAGATGAAAT 59.824 37.037 9.57 0.00 40.70 2.17
3473 5810 9.219603 GCAAATATAGGTGCTGTAGATGAAATA 57.780 33.333 3.70 0.00 37.78 1.40
3478 5815 8.901472 ATAGGTGCTGTAGATGAAATATAGGA 57.099 34.615 0.00 0.00 0.00 2.94
3479 5816 7.618019 AGGTGCTGTAGATGAAATATAGGAA 57.382 36.000 0.00 0.00 0.00 3.36
3480 5817 7.675062 AGGTGCTGTAGATGAAATATAGGAAG 58.325 38.462 0.00 0.00 0.00 3.46
3481 5818 7.510685 AGGTGCTGTAGATGAAATATAGGAAGA 59.489 37.037 0.00 0.00 0.00 2.87
3547 5886 8.494433 AGCCCTACATTGAGATAGAAAATAACA 58.506 33.333 0.00 0.00 0.00 2.41
3602 5941 6.433093 CAGCACAGTTTAACCTTATAAACCCT 59.567 38.462 6.37 0.00 43.57 4.34
3773 6192 2.238144 CCTACCTGCAGATATGGATGGG 59.762 54.545 17.39 0.00 0.00 4.00
3840 6259 2.564062 AGATCCCATGTTTGGTGCTTTG 59.436 45.455 0.00 0.00 41.91 2.77
3865 6284 8.970020 TGTGCCTTTATGACTAATGAATGAATT 58.030 29.630 0.00 0.00 0.00 2.17
3927 6346 3.761218 TGTTCTGTTGGTTTGTGTGATGT 59.239 39.130 0.00 0.00 0.00 3.06
3951 6370 3.928375 GTCAGCATTTTGCCGAATTGAAT 59.072 39.130 0.00 0.00 46.52 2.57
4075 6500 5.705609 ATGTTTTGTGGGTTATGTCTGTC 57.294 39.130 0.00 0.00 0.00 3.51
4488 6926 7.933033 GCCCAATGTCATTATATGGTTCATTTT 59.067 33.333 0.00 0.00 30.69 1.82
4489 6927 9.263538 CCCAATGTCATTATATGGTTCATTTTG 57.736 33.333 0.00 0.00 30.69 2.44
4513 6951 8.958119 TGTACTTACCAATGGAATTAGATGTC 57.042 34.615 6.16 0.00 32.46 3.06
4611 7053 6.899393 ATGGTTGTACACAGTTTTCATCAT 57.101 33.333 0.00 0.00 0.00 2.45
4612 7054 6.312399 TGGTTGTACACAGTTTTCATCATC 57.688 37.500 0.00 0.00 0.00 2.92
4613 7055 5.825151 TGGTTGTACACAGTTTTCATCATCA 59.175 36.000 0.00 0.00 0.00 3.07
4746 7188 5.185454 TGTGGTTGAATCAGCTACCATTAG 58.815 41.667 10.64 0.00 43.58 1.73
4817 7260 2.380084 TAAACATCACTCACGGGCTC 57.620 50.000 0.00 0.00 0.00 4.70
4840 7283 3.388024 GGTTGGGTGCTCTGACTATATCA 59.612 47.826 0.00 0.00 35.45 2.15
4912 7356 7.068103 CCAGTTCCAAATGGCAATACAACTATA 59.932 37.037 0.00 0.00 37.34 1.31
4920 7364 3.251004 GGCAATACAACTATAGCCTGCAC 59.749 47.826 0.00 0.00 39.02 4.57
4921 7365 3.876914 GCAATACAACTATAGCCTGCACA 59.123 43.478 0.00 0.00 0.00 4.57
4926 7370 3.244561 ACAACTATAGCCTGCACAAGTGT 60.245 43.478 0.00 0.00 0.00 3.55
4952 7399 5.816449 TGTATTAGGTTGTGCATCACATG 57.184 39.130 0.11 0.00 44.16 3.21
5011 7458 2.500098 TCGTGTAATCTCCCTTGGGAAG 59.500 50.000 9.93 4.61 0.00 3.46
5012 7459 2.500098 CGTGTAATCTCCCTTGGGAAGA 59.500 50.000 9.93 9.52 0.00 2.87
5013 7460 3.055385 CGTGTAATCTCCCTTGGGAAGAA 60.055 47.826 9.93 0.00 0.00 2.52
5015 7462 4.019231 GTGTAATCTCCCTTGGGAAGAAGT 60.019 45.833 9.93 0.95 0.00 3.01
5017 7464 2.118403 TCTCCCTTGGGAAGAAGTGT 57.882 50.000 9.93 0.00 0.00 3.55
5018 7465 1.978580 TCTCCCTTGGGAAGAAGTGTC 59.021 52.381 9.93 0.00 0.00 3.67
5019 7466 1.981495 CTCCCTTGGGAAGAAGTGTCT 59.019 52.381 9.93 0.00 34.72 3.41
5020 7467 3.173965 CTCCCTTGGGAAGAAGTGTCTA 58.826 50.000 9.93 0.00 32.16 2.59
5021 7468 3.777522 CTCCCTTGGGAAGAAGTGTCTAT 59.222 47.826 9.93 0.00 32.16 1.98
5028 7555 7.201911 CCTTGGGAAGAAGTGTCTATTTTTGTT 60.202 37.037 0.00 0.00 32.16 2.83
5040 7567 6.716628 TGTCTATTTTTGTTCTCTGGATGCTT 59.283 34.615 0.00 0.00 0.00 3.91
5052 7579 7.418337 TCTCTGGATGCTTAGTTACATGTAA 57.582 36.000 14.35 14.35 0.00 2.41
5071 7598 6.182507 TGTAAAATAGTGTCCAAGTCAGGT 57.817 37.500 0.00 0.00 0.00 4.00
5082 7609 3.202151 TCCAAGTCAGGTGTTTTTCCTCT 59.798 43.478 0.00 0.00 32.37 3.69
5085 7612 2.106684 AGTCAGGTGTTTTTCCTCTCCC 59.893 50.000 0.00 0.00 32.37 4.30
5087 7614 1.425448 CAGGTGTTTTTCCTCTCCCCT 59.575 52.381 0.00 0.00 32.37 4.79
5097 7624 4.354208 TTCCTCTCCCCTTGAGTAGATT 57.646 45.455 0.00 0.00 42.12 2.40
5099 7626 2.703007 CCTCTCCCCTTGAGTAGATTGG 59.297 54.545 0.00 0.00 42.12 3.16
5103 7630 4.410228 TCTCCCCTTGAGTAGATTGGAATG 59.590 45.833 0.00 0.00 42.12 2.67
5111 7638 5.809001 TGAGTAGATTGGAATGACAAAGCT 58.191 37.500 0.00 0.00 33.48 3.74
5113 7640 7.568349 TGAGTAGATTGGAATGACAAAGCTAT 58.432 34.615 0.00 0.00 33.48 2.97
5132 7659 1.761711 TGTCCCATAAAAGGTCCCCA 58.238 50.000 0.00 0.00 0.00 4.96
5137 7664 2.225267 CCCATAAAAGGTCCCCACACTT 60.225 50.000 0.00 0.00 0.00 3.16
5140 7667 4.263771 CCATAAAAGGTCCCCACACTTACT 60.264 45.833 0.00 0.00 0.00 2.24
5169 7696 7.341445 TGGCAATGTTTCTATACCCAAATAC 57.659 36.000 0.00 0.00 0.00 1.89
5170 7697 7.122715 TGGCAATGTTTCTATACCCAAATACT 58.877 34.615 0.00 0.00 0.00 2.12
5171 7698 7.284489 TGGCAATGTTTCTATACCCAAATACTC 59.716 37.037 0.00 0.00 0.00 2.59
5172 7699 7.255486 GGCAATGTTTCTATACCCAAATACTCC 60.255 40.741 0.00 0.00 0.00 3.85
5173 7700 7.255486 GCAATGTTTCTATACCCAAATACTCCC 60.255 40.741 0.00 0.00 0.00 4.30
5174 7701 7.707467 ATGTTTCTATACCCAAATACTCCCT 57.293 36.000 0.00 0.00 0.00 4.20
5175 7702 7.133133 TGTTTCTATACCCAAATACTCCCTC 57.867 40.000 0.00 0.00 0.00 4.30
5176 7703 6.100714 TGTTTCTATACCCAAATACTCCCTCC 59.899 42.308 0.00 0.00 0.00 4.30
5177 7704 4.413760 TCTATACCCAAATACTCCCTCCG 58.586 47.826 0.00 0.00 0.00 4.63
5178 7705 2.555732 TACCCAAATACTCCCTCCGT 57.444 50.000 0.00 0.00 0.00 4.69
5179 7706 1.665137 ACCCAAATACTCCCTCCGTT 58.335 50.000 0.00 0.00 0.00 4.44
5180 7707 1.558294 ACCCAAATACTCCCTCCGTTC 59.442 52.381 0.00 0.00 0.00 3.95
5181 7708 1.134189 CCCAAATACTCCCTCCGTTCC 60.134 57.143 0.00 0.00 0.00 3.62
5182 7709 1.557832 CCAAATACTCCCTCCGTTCCA 59.442 52.381 0.00 0.00 0.00 3.53
5183 7710 2.026636 CCAAATACTCCCTCCGTTCCAA 60.027 50.000 0.00 0.00 0.00 3.53
5184 7711 3.560453 CCAAATACTCCCTCCGTTCCAAA 60.560 47.826 0.00 0.00 0.00 3.28
5185 7712 4.270008 CAAATACTCCCTCCGTTCCAAAT 58.730 43.478 0.00 0.00 0.00 2.32
5186 7713 4.586306 AATACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
5187 7714 5.703730 AATACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
5188 7715 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
5189 7716 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
5190 7717 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
5191 7718 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
5192 7719 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
5193 7720 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
5194 7721 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
5195 7722 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
5196 7723 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
5197 7724 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
5198 7725 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
5199 7726 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
5200 7727 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
5201 7728 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
5202 7729 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
5203 7730 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
5204 7731 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
5205 7732 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
5206 7733 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
5207 7734 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
5208 7735 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
5209 7736 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
5210 7737 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
5211 7738 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
5212 7739 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
5213 7740 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
5214 7741 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
5215 7742 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
5229 7756 7.922505 TCAAATTTGAACTAAAACCATGACG 57.077 32.000 18.45 0.00 33.55 4.35
5230 7757 7.708051 TCAAATTTGAACTAAAACCATGACGA 58.292 30.769 18.45 0.00 33.55 4.20
5231 7758 7.860373 TCAAATTTGAACTAAAACCATGACGAG 59.140 33.333 18.45 0.00 33.55 4.18
5232 7759 6.877611 ATTTGAACTAAAACCATGACGAGT 57.122 33.333 0.00 0.00 0.00 4.18
5233 7760 7.972832 ATTTGAACTAAAACCATGACGAGTA 57.027 32.000 0.00 0.00 0.00 2.59
5234 7761 7.789273 TTTGAACTAAAACCATGACGAGTAA 57.211 32.000 0.00 0.00 0.00 2.24
5235 7762 7.972832 TTGAACTAAAACCATGACGAGTAAT 57.027 32.000 0.00 0.00 0.00 1.89
5236 7763 7.972832 TGAACTAAAACCATGACGAGTAATT 57.027 32.000 0.00 0.00 0.00 1.40
5237 7764 8.385898 TGAACTAAAACCATGACGAGTAATTT 57.614 30.769 0.00 0.00 0.00 1.82
5238 7765 8.286800 TGAACTAAAACCATGACGAGTAATTTG 58.713 33.333 0.00 0.00 0.00 2.32
5239 7766 7.141100 ACTAAAACCATGACGAGTAATTTGG 57.859 36.000 0.00 0.00 0.00 3.28
5240 7767 6.938030 ACTAAAACCATGACGAGTAATTTGGA 59.062 34.615 0.00 0.00 0.00 3.53
5241 7768 5.880054 AAACCATGACGAGTAATTTGGAG 57.120 39.130 0.00 0.00 0.00 3.86
5242 7769 3.270877 ACCATGACGAGTAATTTGGAGC 58.729 45.455 0.00 0.00 0.00 4.70
5243 7770 2.285220 CCATGACGAGTAATTTGGAGCG 59.715 50.000 0.00 0.00 0.00 5.03
5244 7771 2.004583 TGACGAGTAATTTGGAGCGG 57.995 50.000 0.00 0.00 0.00 5.52
5245 7772 1.546923 TGACGAGTAATTTGGAGCGGA 59.453 47.619 0.00 0.00 0.00 5.54
5246 7773 2.194271 GACGAGTAATTTGGAGCGGAG 58.806 52.381 0.00 0.00 0.00 4.63
5247 7774 1.134788 ACGAGTAATTTGGAGCGGAGG 60.135 52.381 0.00 0.00 0.00 4.30
5248 7775 1.806623 CGAGTAATTTGGAGCGGAGGG 60.807 57.143 0.00 0.00 0.00 4.30
5249 7776 1.485066 GAGTAATTTGGAGCGGAGGGA 59.515 52.381 0.00 0.00 0.00 4.20
5250 7777 1.486726 AGTAATTTGGAGCGGAGGGAG 59.513 52.381 0.00 0.00 0.00 4.30
5251 7778 1.209747 GTAATTTGGAGCGGAGGGAGT 59.790 52.381 0.00 0.00 0.00 3.85
5252 7779 1.580059 AATTTGGAGCGGAGGGAGTA 58.420 50.000 0.00 0.00 0.00 2.59
5310 7837 5.841267 AACATGTACATATATGAGGCCCA 57.159 39.130 19.63 8.04 0.00 5.36
5351 7878 0.585357 CAGTTGAGGCTCATATGCGC 59.415 55.000 19.50 9.23 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.280321 ACGTGTCGGGGGAAAACG 60.280 61.111 0.00 0.00 40.00 3.60
36 37 3.834799 GGCTAGGACGTGTCGGGG 61.835 72.222 0.00 0.00 0.00 5.73
37 38 2.348888 AAGGCTAGGACGTGTCGGG 61.349 63.158 0.00 0.00 0.00 5.14
41 42 0.320771 CTTGCAAGGCTAGGACGTGT 60.321 55.000 19.14 0.00 0.00 4.49
61 62 2.514013 CGCGTAAGGATGCACGTCC 61.514 63.158 0.00 0.26 40.25 4.79
97 98 6.887545 AGCTGACTGTTACTCTGTTAGTATCT 59.112 38.462 0.00 0.00 40.41 1.98
103 104 7.520451 TCTAAAGCTGACTGTTACTCTGTTA 57.480 36.000 0.00 0.00 0.00 2.41
104 105 6.406692 TCTAAAGCTGACTGTTACTCTGTT 57.593 37.500 0.00 0.00 0.00 3.16
105 106 6.597832 ATCTAAAGCTGACTGTTACTCTGT 57.402 37.500 0.00 0.00 0.00 3.41
106 107 7.623089 GCAAATCTAAAGCTGACTGTTACTCTG 60.623 40.741 0.00 0.00 0.00 3.35
107 108 6.370166 GCAAATCTAAAGCTGACTGTTACTCT 59.630 38.462 0.00 0.00 0.00 3.24
108 109 6.147821 TGCAAATCTAAAGCTGACTGTTACTC 59.852 38.462 0.00 0.00 0.00 2.59
109 110 5.997746 TGCAAATCTAAAGCTGACTGTTACT 59.002 36.000 0.00 0.00 0.00 2.24
110 111 6.241207 TGCAAATCTAAAGCTGACTGTTAC 57.759 37.500 0.00 0.00 0.00 2.50
125 126 8.177119 TGTAAACAAAGGTAGATTGCAAATCT 57.823 30.769 1.71 9.71 0.00 2.40
148 149 6.040842 GTCAATATTATTGGGGATTGTGCTGT 59.959 38.462 14.80 0.00 32.33 4.40
151 152 6.294731 GGAGTCAATATTATTGGGGATTGTGC 60.295 42.308 14.80 0.00 32.33 4.57
159 160 7.006509 AGTTGATGGGAGTCAATATTATTGGG 58.993 38.462 14.80 0.00 39.99 4.12
183 184 4.937620 ACGTATATAAGCATGCAATCCCAG 59.062 41.667 21.98 7.21 0.00 4.45
191 192 3.841643 ACCCGTACGTATATAAGCATGC 58.158 45.455 15.21 10.51 0.00 4.06
215 216 8.856490 ATTATTCATGGCTCGAATTTAACAAC 57.144 30.769 7.16 0.00 34.89 3.32
225 226 9.500785 TTGTTTGATATATTATTCATGGCTCGA 57.499 29.630 0.00 0.00 0.00 4.04
263 264 1.192312 CGCATTAATCCACGTCATCGG 59.808 52.381 0.00 0.00 41.85 4.18
264 265 2.124122 TCGCATTAATCCACGTCATCG 58.876 47.619 0.00 0.00 43.34 3.84
269 270 0.814010 GGCCTCGCATTAATCCACGT 60.814 55.000 0.00 0.00 0.00 4.49
406 413 2.429058 CCCCGCCATCATCTCCAG 59.571 66.667 0.00 0.00 0.00 3.86
412 419 0.039618 AAAAGACACCCCGCCATCAT 59.960 50.000 0.00 0.00 0.00 2.45
566 813 1.153449 GTAGGCGTGCATACTGCCA 60.153 57.895 19.86 7.34 44.23 4.92
705 2387 0.924090 GTATGCTTGCGTTCCTCTCG 59.076 55.000 0.00 0.00 0.00 4.04
718 2400 0.394352 CTTTCCTTGGGCCGTATGCT 60.394 55.000 0.00 0.00 40.92 3.79
723 2405 2.032071 CGTCTTTCCTTGGGCCGT 59.968 61.111 0.00 0.00 0.00 5.68
724 2406 2.746277 CCGTCTTTCCTTGGGCCG 60.746 66.667 0.00 0.00 0.00 6.13
726 2408 0.322187 TTAGCCGTCTTTCCTTGGGC 60.322 55.000 0.00 0.00 44.07 5.36
728 2410 1.087501 GCTTAGCCGTCTTTCCTTGG 58.912 55.000 0.00 0.00 0.00 3.61
729 2411 1.734465 CTGCTTAGCCGTCTTTCCTTG 59.266 52.381 0.29 0.00 0.00 3.61
730 2412 1.339151 CCTGCTTAGCCGTCTTTCCTT 60.339 52.381 0.29 0.00 0.00 3.36
731 2413 0.250513 CCTGCTTAGCCGTCTTTCCT 59.749 55.000 0.29 0.00 0.00 3.36
732 2414 0.249398 TCCTGCTTAGCCGTCTTTCC 59.751 55.000 0.29 0.00 0.00 3.13
733 2415 1.066787 ACTCCTGCTTAGCCGTCTTTC 60.067 52.381 0.29 0.00 0.00 2.62
735 2417 0.533032 GACTCCTGCTTAGCCGTCTT 59.467 55.000 0.29 0.00 0.00 3.01
736 2418 0.612174 TGACTCCTGCTTAGCCGTCT 60.612 55.000 0.29 0.00 0.00 4.18
738 2420 1.592223 GTGACTCCTGCTTAGCCGT 59.408 57.895 0.29 0.00 0.00 5.68
739 2421 1.517257 CGTGACTCCTGCTTAGCCG 60.517 63.158 0.29 0.00 0.00 5.52
740 2422 1.811679 GCGTGACTCCTGCTTAGCC 60.812 63.158 0.29 0.00 0.00 3.93
742 2424 0.244994 ACTGCGTGACTCCTGCTTAG 59.755 55.000 0.00 0.00 0.00 2.18
743 2425 0.038251 CACTGCGTGACTCCTGCTTA 60.038 55.000 3.04 0.00 35.23 3.09
744 2426 1.301244 CACTGCGTGACTCCTGCTT 60.301 57.895 3.04 0.00 35.23 3.91
745 2427 2.341543 CACTGCGTGACTCCTGCT 59.658 61.111 3.04 0.00 35.23 4.24
746 2428 2.740055 CCACTGCGTGACTCCTGC 60.740 66.667 9.75 0.00 35.23 4.85
747 2429 2.740055 GCCACTGCGTGACTCCTG 60.740 66.667 9.75 0.00 35.23 3.86
748 2430 4.008933 GGCCACTGCGTGACTCCT 62.009 66.667 0.00 0.00 38.85 3.69
749 2431 4.008933 AGGCCACTGCGTGACTCC 62.009 66.667 5.01 7.87 38.85 3.85
931 2824 2.693762 GGTTTAAGCCGGGGAACGC 61.694 63.158 2.18 0.00 42.52 4.84
952 2845 2.598467 GAGGGAGCGAGGAGGAGA 59.402 66.667 0.00 0.00 0.00 3.71
2009 4333 1.062488 ACTCCCTGCACCCAGAAACT 61.062 55.000 0.00 0.00 41.77 2.66
2013 4337 3.640407 GCACTCCCTGCACCCAGA 61.640 66.667 0.00 0.00 46.29 3.86
2065 4389 0.615331 CACAGCACTCCCATGTAGGT 59.385 55.000 0.00 0.00 34.66 3.08
2071 4395 0.111061 TCAAAGCACAGCACTCCCAT 59.889 50.000 0.00 0.00 0.00 4.00
2072 4396 0.111061 ATCAAAGCACAGCACTCCCA 59.889 50.000 0.00 0.00 0.00 4.37
2076 4400 1.815003 GCCTTATCAAAGCACAGCACT 59.185 47.619 0.00 0.00 0.00 4.40
2130 4454 2.282958 TCACCCGACCGCTTCTCT 60.283 61.111 0.00 0.00 0.00 3.10
2142 4466 2.610859 TCCTTGGAGCCCTCACCC 60.611 66.667 0.00 0.00 0.00 4.61
2155 4479 4.035102 GACCTTGGCCGCCTCCTT 62.035 66.667 11.61 0.00 0.00 3.36
2203 4527 2.342279 CTCCTCGTTGCGACCCAA 59.658 61.111 0.00 0.00 0.00 4.12
2268 4592 2.399916 GAGAAAGCTCTGCATCCAGT 57.600 50.000 0.00 0.00 40.09 4.00
2505 4829 1.876416 GCAACCCGCTCAGAGTTTACA 60.876 52.381 0.00 0.00 37.77 2.41
2538 4862 7.510549 TGACTCATACAACATCGATATCTCA 57.489 36.000 0.00 0.00 0.00 3.27
2728 5052 5.491635 AAGCAGTTCTTCAACTTCTCAAC 57.508 39.130 0.00 0.00 41.24 3.18
2760 5084 4.824479 AGCAAATCCTAACCCAAAATGG 57.176 40.909 0.00 0.00 37.25 3.16
2882 5206 5.818887 TCTCAATGGAATCCTCATGTTTCA 58.181 37.500 0.00 0.00 0.00 2.69
2997 5332 6.038050 GCCTACACGTAACTCTACAAGATAGT 59.962 42.308 0.00 0.00 0.00 2.12
3003 5338 6.764308 ATTAGCCTACACGTAACTCTACAA 57.236 37.500 0.00 0.00 0.00 2.41
3015 5350 7.953752 ACTCTGGATAACTTATTAGCCTACAC 58.046 38.462 3.27 0.00 45.57 2.90
3092 5427 1.319541 GACGGCAGAGCAGGAGTATA 58.680 55.000 0.00 0.00 0.00 1.47
3093 5428 1.729470 CGACGGCAGAGCAGGAGTAT 61.729 60.000 0.00 0.00 0.00 2.12
3094 5429 2.407428 CGACGGCAGAGCAGGAGTA 61.407 63.158 0.00 0.00 0.00 2.59
3100 5435 0.388134 GTTTCTACGACGGCAGAGCA 60.388 55.000 0.00 0.00 0.00 4.26
3126 5463 1.394572 TGACAGCATCTCAAAATCGCG 59.605 47.619 0.00 0.00 0.00 5.87
3140 5477 4.661993 TGTTGACGATATTTGTGACAGC 57.338 40.909 0.00 0.00 0.00 4.40
3141 5478 7.065216 AGAATGTTGACGATATTTGTGACAG 57.935 36.000 0.00 0.00 0.00 3.51
3420 5757 8.452534 CCTGACTCGTACCTATATTTCATCTAC 58.547 40.741 0.00 0.00 0.00 2.59
3436 5773 4.038763 CACCTATATTTGCCCTGACTCGTA 59.961 45.833 0.00 0.00 0.00 3.43
3437 5774 3.039011 ACCTATATTTGCCCTGACTCGT 58.961 45.455 0.00 0.00 0.00 4.18
3438 5775 3.393800 CACCTATATTTGCCCTGACTCG 58.606 50.000 0.00 0.00 0.00 4.18
3439 5776 3.142174 GCACCTATATTTGCCCTGACTC 58.858 50.000 0.00 0.00 32.21 3.36
3440 5777 2.780010 AGCACCTATATTTGCCCTGACT 59.220 45.455 2.78 0.00 39.75 3.41
3441 5778 2.880890 CAGCACCTATATTTGCCCTGAC 59.119 50.000 2.78 0.00 39.75 3.51
3442 5779 2.509548 ACAGCACCTATATTTGCCCTGA 59.490 45.455 2.78 0.00 39.75 3.86
3443 5780 2.936202 ACAGCACCTATATTTGCCCTG 58.064 47.619 2.78 0.00 39.75 4.45
3444 5781 3.973973 TCTACAGCACCTATATTTGCCCT 59.026 43.478 2.78 0.00 39.75 5.19
3445 5782 4.351874 TCTACAGCACCTATATTTGCCC 57.648 45.455 2.78 0.00 39.75 5.36
3446 5783 5.551233 TCATCTACAGCACCTATATTTGCC 58.449 41.667 2.78 0.00 39.75 4.52
3447 5784 7.496529 TTTCATCTACAGCACCTATATTTGC 57.503 36.000 0.00 0.00 39.16 3.68
3452 5789 9.990868 TCCTATATTTCATCTACAGCACCTATA 57.009 33.333 0.00 0.00 0.00 1.31
3453 5790 8.901472 TCCTATATTTCATCTACAGCACCTAT 57.099 34.615 0.00 0.00 0.00 2.57
3454 5791 8.721133 TTCCTATATTTCATCTACAGCACCTA 57.279 34.615 0.00 0.00 0.00 3.08
3455 5792 7.510685 TCTTCCTATATTTCATCTACAGCACCT 59.489 37.037 0.00 0.00 0.00 4.00
3456 5793 7.671302 TCTTCCTATATTTCATCTACAGCACC 58.329 38.462 0.00 0.00 0.00 5.01
3457 5794 9.547753 TTTCTTCCTATATTTCATCTACAGCAC 57.452 33.333 0.00 0.00 0.00 4.40
3493 5832 6.316390 CCCTTGCTGTATTAGGAAACAACTAG 59.684 42.308 0.00 0.00 36.22 2.57
3547 5886 7.112779 CAGGATTTCCCTTCTAATTGTGTACT 58.887 38.462 0.00 0.00 44.85 2.73
3602 5941 5.828859 TGGCCAAGCTTAAGTTTACACTTTA 59.171 36.000 0.61 0.00 40.66 1.85
3728 6147 2.300152 TGGAGTGTGCTCGAGAAAGATT 59.700 45.455 18.75 0.00 42.53 2.40
3798 6217 9.436957 GGATCTTCAGTTTTTCATACAAGAGTA 57.563 33.333 0.00 0.00 34.10 2.59
3840 6259 9.455847 GAATTCATTCATTAGTCATAAAGGCAC 57.544 33.333 0.00 0.00 36.80 5.01
3865 6284 9.745880 GATAGTTCAACTTGGATATAGTTTCGA 57.254 33.333 0.00 0.00 33.73 3.71
4069 6494 3.126001 TCCACTTGTTCCATGACAGAC 57.874 47.619 0.00 0.00 0.00 3.51
4075 6500 3.880047 ATTGCATCCACTTGTTCCATG 57.120 42.857 0.00 0.00 0.00 3.66
4085 6510 3.940209 TGGTCAGAAAATTGCATCCAC 57.060 42.857 0.00 0.00 0.00 4.02
4488 6926 8.544622 TGACATCTAATTCCATTGGTAAGTACA 58.455 33.333 1.86 0.00 0.00 2.90
4489 6927 8.958119 TGACATCTAATTCCATTGGTAAGTAC 57.042 34.615 1.86 0.00 0.00 2.73
4670 7112 8.112822 TCAATCCAGTCCAACCAGAAATAATTA 58.887 33.333 0.00 0.00 0.00 1.40
4817 7260 0.537188 ATAGTCAGAGCACCCAACCG 59.463 55.000 0.00 0.00 0.00 4.44
4829 7272 5.873712 GGGCAGATGTGAATGATATAGTCAG 59.126 44.000 0.00 0.00 40.92 3.51
4912 7356 1.076777 AACCACACTTGTGCAGGCT 60.077 52.632 3.68 0.00 44.34 4.58
4920 7364 5.757886 CACAACCTAATACAACCACACTTG 58.242 41.667 0.00 0.00 0.00 3.16
4921 7365 4.277423 GCACAACCTAATACAACCACACTT 59.723 41.667 0.00 0.00 0.00 3.16
4926 7370 4.457603 GTGATGCACAACCTAATACAACCA 59.542 41.667 0.00 0.00 34.08 3.67
4952 7399 1.210155 GGGCACAGCGAATCAACAC 59.790 57.895 0.00 0.00 0.00 3.32
4992 7439 4.019231 ACTTCTTCCCAAGGGAGATTACAC 60.019 45.833 8.06 0.00 46.06 2.90
5011 7458 7.730364 TCCAGAGAACAAAAATAGACACTTC 57.270 36.000 0.00 0.00 0.00 3.01
5012 7459 7.308830 GCATCCAGAGAACAAAAATAGACACTT 60.309 37.037 0.00 0.00 0.00 3.16
5013 7460 6.150140 GCATCCAGAGAACAAAAATAGACACT 59.850 38.462 0.00 0.00 0.00 3.55
5015 7462 6.240894 AGCATCCAGAGAACAAAAATAGACA 58.759 36.000 0.00 0.00 0.00 3.41
5017 7464 8.103305 ACTAAGCATCCAGAGAACAAAAATAGA 58.897 33.333 0.00 0.00 0.00 1.98
5018 7465 8.273780 ACTAAGCATCCAGAGAACAAAAATAG 57.726 34.615 0.00 0.00 0.00 1.73
5019 7466 8.635765 AACTAAGCATCCAGAGAACAAAAATA 57.364 30.769 0.00 0.00 0.00 1.40
5020 7467 7.530426 AACTAAGCATCCAGAGAACAAAAAT 57.470 32.000 0.00 0.00 0.00 1.82
5021 7468 6.959639 AACTAAGCATCCAGAGAACAAAAA 57.040 33.333 0.00 0.00 0.00 1.94
5028 7555 5.939764 ACATGTAACTAAGCATCCAGAGA 57.060 39.130 0.00 0.00 0.00 3.10
5052 7579 4.706842 ACACCTGACTTGGACACTATTT 57.293 40.909 0.00 0.00 0.00 1.40
5082 7609 4.164221 GTCATTCCAATCTACTCAAGGGGA 59.836 45.833 0.00 0.00 0.00 4.81
5085 7612 6.404074 GCTTTGTCATTCCAATCTACTCAAGG 60.404 42.308 0.00 0.00 0.00 3.61
5087 7614 6.240894 AGCTTTGTCATTCCAATCTACTCAA 58.759 36.000 0.00 0.00 0.00 3.02
5097 7624 3.010027 TGGGACATAGCTTTGTCATTCCA 59.990 43.478 30.26 25.53 46.32 3.53
5137 7664 2.862541 AGAAACATTGCCAGCACAGTA 58.137 42.857 0.00 0.00 0.00 2.74
5140 7667 3.694072 GGTATAGAAACATTGCCAGCACA 59.306 43.478 0.00 0.00 0.00 4.57
5169 7696 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
5170 7697 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
5171 7698 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5172 7699 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5173 7700 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
5174 7701 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
5175 7702 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
5176 7703 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
5177 7704 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
5178 7705 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
5179 7706 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
5180 7707 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
5181 7708 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
5182 7709 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
5183 7710 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
5184 7711 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
5185 7712 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
5186 7713 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
5187 7714 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
5188 7715 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
5189 7716 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
5190 7717 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
5191 7718 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
5204 7731 8.191446 TCGTCATGGTTTTAGTTCAAATTTGAA 58.809 29.630 26.01 26.01 44.31 2.69
5205 7732 7.708051 TCGTCATGGTTTTAGTTCAAATTTGA 58.292 30.769 16.91 16.91 34.92 2.69
5206 7733 7.647715 ACTCGTCATGGTTTTAGTTCAAATTTG 59.352 33.333 12.15 12.15 0.00 2.32
5207 7734 7.712797 ACTCGTCATGGTTTTAGTTCAAATTT 58.287 30.769 0.00 0.00 0.00 1.82
5208 7735 7.272037 ACTCGTCATGGTTTTAGTTCAAATT 57.728 32.000 0.00 0.00 0.00 1.82
5209 7736 6.877611 ACTCGTCATGGTTTTAGTTCAAAT 57.122 33.333 0.00 0.00 0.00 2.32
5210 7737 7.789273 TTACTCGTCATGGTTTTAGTTCAAA 57.211 32.000 0.00 0.00 0.00 2.69
5211 7738 7.972832 ATTACTCGTCATGGTTTTAGTTCAA 57.027 32.000 0.00 0.00 0.00 2.69
5212 7739 7.972832 AATTACTCGTCATGGTTTTAGTTCA 57.027 32.000 0.00 0.00 0.00 3.18
5213 7740 7.749126 CCAAATTACTCGTCATGGTTTTAGTTC 59.251 37.037 0.00 0.00 0.00 3.01
5214 7741 7.446013 TCCAAATTACTCGTCATGGTTTTAGTT 59.554 33.333 0.00 0.00 0.00 2.24
5215 7742 6.938030 TCCAAATTACTCGTCATGGTTTTAGT 59.062 34.615 0.00 0.00 0.00 2.24
5216 7743 7.372451 TCCAAATTACTCGTCATGGTTTTAG 57.628 36.000 0.00 0.00 0.00 1.85
5217 7744 6.128117 GCTCCAAATTACTCGTCATGGTTTTA 60.128 38.462 0.00 0.00 0.00 1.52
5218 7745 5.335661 GCTCCAAATTACTCGTCATGGTTTT 60.336 40.000 0.00 0.00 0.00 2.43
5219 7746 4.156008 GCTCCAAATTACTCGTCATGGTTT 59.844 41.667 0.00 0.00 0.00 3.27
5220 7747 3.689649 GCTCCAAATTACTCGTCATGGTT 59.310 43.478 0.00 0.00 0.00 3.67
5221 7748 3.270877 GCTCCAAATTACTCGTCATGGT 58.729 45.455 0.00 0.00 0.00 3.55
5222 7749 2.285220 CGCTCCAAATTACTCGTCATGG 59.715 50.000 0.00 0.00 0.00 3.66
5223 7750 2.285220 CCGCTCCAAATTACTCGTCATG 59.715 50.000 0.00 0.00 0.00 3.07
5224 7751 2.167693 TCCGCTCCAAATTACTCGTCAT 59.832 45.455 0.00 0.00 0.00 3.06
5225 7752 1.546923 TCCGCTCCAAATTACTCGTCA 59.453 47.619 0.00 0.00 0.00 4.35
5226 7753 2.194271 CTCCGCTCCAAATTACTCGTC 58.806 52.381 0.00 0.00 0.00 4.20
5227 7754 1.134788 CCTCCGCTCCAAATTACTCGT 60.135 52.381 0.00 0.00 0.00 4.18
5228 7755 1.571919 CCTCCGCTCCAAATTACTCG 58.428 55.000 0.00 0.00 0.00 4.18
5229 7756 1.485066 TCCCTCCGCTCCAAATTACTC 59.515 52.381 0.00 0.00 0.00 2.59
5230 7757 1.486726 CTCCCTCCGCTCCAAATTACT 59.513 52.381 0.00 0.00 0.00 2.24
5231 7758 1.209747 ACTCCCTCCGCTCCAAATTAC 59.790 52.381 0.00 0.00 0.00 1.89
5232 7759 1.580059 ACTCCCTCCGCTCCAAATTA 58.420 50.000 0.00 0.00 0.00 1.40
5233 7760 1.486726 CTACTCCCTCCGCTCCAAATT 59.513 52.381 0.00 0.00 0.00 1.82
5234 7761 1.123928 CTACTCCCTCCGCTCCAAAT 58.876 55.000 0.00 0.00 0.00 2.32
5235 7762 0.252103 ACTACTCCCTCCGCTCCAAA 60.252 55.000 0.00 0.00 0.00 3.28
5236 7763 0.252103 AACTACTCCCTCCGCTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
5237 7764 0.252103 AAACTACTCCCTCCGCTCCA 60.252 55.000 0.00 0.00 0.00 3.86
5238 7765 0.175989 CAAACTACTCCCTCCGCTCC 59.824 60.000 0.00 0.00 0.00 4.70
5239 7766 0.175989 CCAAACTACTCCCTCCGCTC 59.824 60.000 0.00 0.00 0.00 5.03
5240 7767 0.544595 ACCAAACTACTCCCTCCGCT 60.545 55.000 0.00 0.00 0.00 5.52
5241 7768 1.136500 CTACCAAACTACTCCCTCCGC 59.864 57.143 0.00 0.00 0.00 5.54
5242 7769 1.755380 CCTACCAAACTACTCCCTCCG 59.245 57.143 0.00 0.00 0.00 4.63
5243 7770 2.830293 ACCTACCAAACTACTCCCTCC 58.170 52.381 0.00 0.00 0.00 4.30
5244 7771 6.346896 CATTTACCTACCAAACTACTCCCTC 58.653 44.000 0.00 0.00 0.00 4.30
5245 7772 5.338953 GCATTTACCTACCAAACTACTCCCT 60.339 44.000 0.00 0.00 0.00 4.20
5246 7773 4.880120 GCATTTACCTACCAAACTACTCCC 59.120 45.833 0.00 0.00 0.00 4.30
5247 7774 5.493809 TGCATTTACCTACCAAACTACTCC 58.506 41.667 0.00 0.00 0.00 3.85
5248 7775 7.625828 AATGCATTTACCTACCAAACTACTC 57.374 36.000 5.99 0.00 0.00 2.59
5249 7776 8.417273 AAAATGCATTTACCTACCAAACTACT 57.583 30.769 24.35 0.72 0.00 2.57
5288 7815 5.073008 TGTGGGCCTCATATATGTACATGTT 59.927 40.000 18.81 8.33 0.00 2.71
5339 7866 0.250295 TTGGGTAGCGCATATGAGCC 60.250 55.000 25.33 14.36 41.94 4.70


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

AutoCloner maintained by Alex Coulton.