Multiple sequence alignment - TraesCS1A01G370800

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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 TraesCS1A01G370800 chr1A 100.000 5911 0 0 1 5911 547963048 547968958 0.000000e+00 10916.0
1 TraesCS1A01G370800 chr1B 93.594 5526 253 46 1 5484 623726473 623731939 0.000000e+00 8150.0
2 TraesCS1A01G370800 chr1D 94.207 5248 209 42 1 5213 453273106 453278293 0.000000e+00 7919.0
3 TraesCS1A01G370800 chr1D 92.056 214 11 5 5218 5430 453278365 453278573 4.480000e-76 296.0
4 TraesCS1A01G370800 chr1D 91.667 108 7 2 5684 5791 453278685 453278790 1.330000e-31 148.0
5 TraesCS1A01G370800 chr1D 100.000 34 0 0 5878 5911 453278792 453278825 4.950000e-06 63.9
6 TraesCS1A01G370800 chrUn 98.886 449 5 0 3557 4005 475776442 475775994 0.000000e+00 802.0
7 TraesCS1A01G370800 chr3D 88.485 165 18 1 5491 5655 293809716 293809879 1.300000e-46 198.0
8 TraesCS1A01G370800 chr3D 90.426 94 7 2 5792 5884 567196559 567196651 8.040000e-24 122.0
9 TraesCS1A01G370800 chr3B 86.310 168 21 1 5491 5658 809833709 809833874 1.310000e-41 182.0
10 TraesCS1A01G370800 chr3B 88.000 100 12 0 5786 5885 827494370 827494469 1.040000e-22 119.0
11 TraesCS1A01G370800 chr3B 88.000 100 12 0 5786 5885 830634392 830634293 1.040000e-22 119.0
12 TraesCS1A01G370800 chr4D 85.882 170 20 3 5491 5658 65101297 65101464 1.690000e-40 178.0
13 TraesCS1A01G370800 chr7D 86.127 173 13 9 5491 5657 5492045 5492212 6.090000e-40 176.0
14 TraesCS1A01G370800 chr7B 85.799 169 20 4 5488 5654 207126202 207126368 6.090000e-40 176.0
15 TraesCS1A01G370800 chr6A 85.976 164 21 2 5491 5654 108924033 108924194 2.190000e-39 174.0
16 TraesCS1A01G370800 chr2D 85.976 164 20 3 5485 5648 617215182 617215342 7.880000e-39 172.0
17 TraesCS1A01G370800 chr2D 92.941 85 6 0 5799 5883 36796299 36796215 2.240000e-24 124.0
18 TraesCS1A01G370800 chr2D 87.379 103 11 2 5795 5897 643235908 643235808 3.740000e-22 117.0
19 TraesCS1A01G370800 chr2D 92.105 38 3 0 812 849 16666404 16666441 3.000000e-03 54.7
20 TraesCS1A01G370800 chr2B 85.294 170 21 4 5485 5653 752925044 752925210 7.880000e-39 172.0
21 TraesCS1A01G370800 chr2B 84.000 175 24 4 5491 5665 212934823 212934993 1.320000e-36 165.0
22 TraesCS1A01G370800 chr2B 90.323 93 9 0 5795 5887 142869605 142869513 8.040000e-24 122.0
23 TraesCS1A01G370800 chr6B 89.796 98 9 1 5785 5882 48874132 48874036 2.240000e-24 124.0
24 TraesCS1A01G370800 chr6B 89.796 98 9 1 5785 5882 48981525 48981429 2.240000e-24 124.0
25 TraesCS1A01G370800 chr6B 88.776 98 10 1 5785 5882 48938458 48938362 1.040000e-22 119.0
26 TraesCS1A01G370800 chr6B 97.143 35 1 0 5680 5714 668902939 668902905 6.400000e-05 60.2
27 TraesCS1A01G370800 chr7A 92.157 51 3 1 5680 5730 732577163 732577114 2.960000e-08 71.3
28 TraesCS1A01G370800 chr3A 100.000 28 0 0 822 849 526839853 526839880 1.100000e-02 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 TraesCS1A01G370800 chr1A 547963048 547968958 5910 False 10916.000 10916 100.0000 1 5911 1 chr1A.!!$F1 5910
1 TraesCS1A01G370800 chr1B 623726473 623731939 5466 False 8150.000 8150 93.5940 1 5484 1 chr1B.!!$F1 5483
2 TraesCS1A01G370800 chr1D 453273106 453278825 5719 False 2106.725 7919 94.4825 1 5911 4 chr1D.!!$F1 5910

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
374 400 0.035317 TGATGCTCGGTCTGCAAACT 59.965 50.0 0.0 0.0 44.01 2.66 F
1982 2033 0.391263 CCTAAGACGCCACCTTCACC 60.391 60.0 0.0 0.0 0.00 4.02 F
2639 2694 0.106819 GCTGGAATCATCCTGGCTGT 60.107 55.0 0.0 0.0 46.70 4.40 F
3369 3424 0.035630 CTTCACTGCCTCCCCTTGAG 60.036 60.0 0.0 0.0 41.07 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2200 0.034337 GTAGTTGGCCACGGAAGACA 59.966 55.000 3.88 0.0 0.00 3.41 R
2986 3041 0.389391 CCCGTATCCTCTGTCGCAAT 59.611 55.000 0.00 0.0 0.00 3.56 R
4391 4446 3.266510 TCTTGCTACCCATGTAAGCTG 57.733 47.619 11.16 5.9 0.00 4.24 R
5182 5238 2.290705 GGCTTGAACCCTGCCTAACTAA 60.291 50.000 0.00 0.0 43.05 2.24 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
85 87 3.590630 AGGATCTACATCATCCCCCAATG 59.409 47.826 0.00 0.00 40.90 2.82
133 135 7.366513 TGATATGATTCTTCTCTCTTGCGTAG 58.633 38.462 0.00 0.00 0.00 3.51
159 161 0.618458 TAGATTCTTTGGGGCGTGCT 59.382 50.000 0.00 0.00 0.00 4.40
169 171 1.376683 GGGCGTGCTCACATACCAA 60.377 57.895 0.69 0.00 0.00 3.67
184 186 9.800433 CTCACATACCAATGCATTACAAAATAA 57.200 29.630 12.53 0.00 36.50 1.40
228 230 4.460382 GCCTTCCAAAGTGATTTGATCTCA 59.540 41.667 2.38 0.00 33.95 3.27
232 234 6.957920 TCCAAAGTGATTTGATCTCACAAA 57.042 33.333 14.08 0.00 44.37 2.83
237 239 3.502211 GTGATTTGATCTCACAAACCGGT 59.498 43.478 0.00 0.00 42.08 5.28
251 253 2.814280 ACCGGTTAATCTATCTGCCG 57.186 50.000 0.00 0.00 38.99 5.69
260 262 1.035385 TCTATCTGCCGAACGCTCCA 61.035 55.000 0.00 0.00 38.78 3.86
319 345 2.790433 TGGGCCACTACTTCACAAATC 58.210 47.619 0.00 0.00 0.00 2.17
337 363 8.998377 TCACAAATCGATTATTTTGTCTTCTCA 58.002 29.630 11.83 0.00 35.54 3.27
374 400 0.035317 TGATGCTCGGTCTGCAAACT 59.965 50.000 0.00 0.00 44.01 2.66
429 455 4.453478 GTGTTCCCCTTCGGTTACTTTTAG 59.547 45.833 0.00 0.00 0.00 1.85
436 462 3.323751 TCGGTTACTTTTAGGACTGCC 57.676 47.619 0.00 0.00 0.00 4.85
446 472 4.341863 TTTAGGACTGCCCCTAACTAGA 57.658 45.455 0.00 0.00 45.59 2.43
448 474 1.062810 AGGACTGCCCCTAACTAGAGG 60.063 57.143 0.00 0.00 34.07 3.69
451 477 2.422165 GCCCCTAACTAGAGGCGC 59.578 66.667 0.00 0.00 37.46 6.53
480 515 2.432146 TGAGTAAGGATTCAGCGCTCAT 59.568 45.455 7.13 1.61 0.00 2.90
552 587 2.030562 CGCTGGTTCTTGGTCGGT 59.969 61.111 0.00 0.00 0.00 4.69
558 593 0.533531 GGTTCTTGGTCGGTCGGTTT 60.534 55.000 0.00 0.00 0.00 3.27
584 619 5.573282 CAGTTAATCGATCGACTGTTGACTT 59.427 40.000 22.06 10.65 35.84 3.01
585 620 5.573282 AGTTAATCGATCGACTGTTGACTTG 59.427 40.000 22.06 0.00 0.00 3.16
715 754 7.064728 GGTCTGTAGATTTGATAAAAGTTCGCT 59.935 37.037 0.00 0.00 0.00 4.93
733 772 5.164606 TCGCTAACTCCAAAAAGTTCAAC 57.835 39.130 0.00 0.00 40.01 3.18
762 802 4.830826 AGAAAAGTTCACGGGATTTGAC 57.169 40.909 0.00 0.00 0.00 3.18
764 804 4.827284 AGAAAAGTTCACGGGATTTGACAT 59.173 37.500 0.00 0.00 0.00 3.06
900 942 3.945285 CCAAAAAGCGAAGGCCTATCTAA 59.055 43.478 5.16 0.00 41.24 2.10
1044 1086 1.841103 GCTCCTCCTCCTGATCCCC 60.841 68.421 0.00 0.00 0.00 4.81
1063 1105 4.208686 CGGTGCTCTCCCCGCTAC 62.209 72.222 0.00 0.00 37.43 3.58
1103 1145 1.448189 CCGTCGCGATTAACCCCAA 60.448 57.895 14.06 0.00 0.00 4.12
1219 1264 6.484364 TTTCTTGCAGAAAGGAAGGATTTT 57.516 33.333 7.09 0.00 44.91 1.82
1344 1390 1.338200 GGCCATAGCGTCAAGGATAGG 60.338 57.143 0.00 0.00 41.24 2.57
1371 1418 5.335348 GCTAAATGCGTTTCCTCTGGTAAAA 60.335 40.000 7.29 0.00 0.00 1.52
1375 1422 5.523438 TGCGTTTCCTCTGGTAAAATTTT 57.477 34.783 8.75 8.75 0.00 1.82
1376 1423 5.525199 TGCGTTTCCTCTGGTAAAATTTTC 58.475 37.500 6.72 0.00 0.00 2.29
1377 1424 5.300792 TGCGTTTCCTCTGGTAAAATTTTCT 59.699 36.000 6.72 0.00 0.00 2.52
1378 1425 5.629435 GCGTTTCCTCTGGTAAAATTTTCTG 59.371 40.000 6.72 0.00 0.00 3.02
1452 1501 6.432403 AAACTCTGAGTTCTCTGAAGGAAT 57.568 37.500 22.24 0.66 37.47 3.01
1529 1578 3.050275 GCGGACCAAGGTGTGCTC 61.050 66.667 0.00 0.00 0.00 4.26
1530 1579 2.738521 CGGACCAAGGTGTGCTCG 60.739 66.667 0.00 0.00 0.00 5.03
1537 1588 3.482436 ACCAAGGTGTGCTCGATTTTTA 58.518 40.909 0.00 0.00 0.00 1.52
1550 1601 6.156519 GCTCGATTTTTATCTTGGTTTTGGT 58.843 36.000 0.00 0.00 0.00 3.67
1570 1621 8.967664 TTTGGTAAATGTTACACTGTACTCTT 57.032 30.769 0.00 0.00 0.00 2.85
1647 1698 1.486726 AGAATTGCTACCGGGGAAGAG 59.513 52.381 6.32 0.00 0.00 2.85
1648 1699 1.485066 GAATTGCTACCGGGGAAGAGA 59.515 52.381 6.32 0.00 0.00 3.10
1705 1756 1.004277 GGTGCTGTATTGAAGGGTGGA 59.996 52.381 0.00 0.00 0.00 4.02
1739 1790 4.680237 TGACAAGGCGGACGGCAG 62.680 66.667 20.23 13.94 46.16 4.85
1772 1823 1.069090 GCGACGGGCTCAATGGATA 59.931 57.895 0.00 0.00 39.11 2.59
1925 1976 2.201022 CCGGGACCGCTACTATGCT 61.201 63.158 4.98 0.00 38.24 3.79
1933 1984 3.754323 GACCGCTACTATGCTGATCTAGT 59.246 47.826 0.00 0.00 33.02 2.57
1982 2033 0.391263 CCTAAGACGCCACCTTCACC 60.391 60.000 0.00 0.00 0.00 4.02
1986 2037 3.168528 ACGCCACCTTCACCCAGT 61.169 61.111 0.00 0.00 0.00 4.00
2015 2066 1.443322 CCAACGTGCACACCATGTCA 61.443 55.000 18.64 0.00 42.76 3.58
2100 2151 9.921637 AACAACTTCAAAGAGTCAAATTTAACA 57.078 25.926 0.00 0.00 0.00 2.41
2149 2200 4.509580 ACGTTGGGCCCACCGTTT 62.510 61.111 38.58 20.17 42.11 3.60
2167 2218 0.759959 TTGTCTTCCGTGGCCAACTA 59.240 50.000 7.24 0.00 0.00 2.24
2174 2225 1.671742 CGTGGCCAACTACCTCAGT 59.328 57.895 7.24 0.00 40.05 3.41
2331 2384 0.909610 TCTGGAGATTTGGCTCGGGT 60.910 55.000 0.00 0.00 35.74 5.28
2393 2446 2.348888 CGGTCTTACACGAGGGCCT 61.349 63.158 5.25 5.25 0.00 5.19
2401 2454 3.941188 ACGAGGGCCTGGTGTGTG 61.941 66.667 21.21 0.00 0.00 3.82
2408 2461 2.508928 CCTGGTGTGTGTTCGGGT 59.491 61.111 0.00 0.00 0.00 5.28
2409 2462 1.597027 CCTGGTGTGTGTTCGGGTC 60.597 63.158 0.00 0.00 0.00 4.46
2410 2463 1.145156 CTGGTGTGTGTTCGGGTCA 59.855 57.895 0.00 0.00 0.00 4.02
2411 2464 1.153329 TGGTGTGTGTTCGGGTCAC 60.153 57.895 0.00 0.00 36.48 3.67
2412 2465 1.145377 GGTGTGTGTTCGGGTCACT 59.855 57.895 0.00 0.00 36.83 3.41
2413 2466 0.878961 GGTGTGTGTTCGGGTCACTC 60.879 60.000 0.00 0.00 36.83 3.51
2414 2467 1.066752 TGTGTGTTCGGGTCACTCG 59.933 57.895 0.00 0.00 36.83 4.18
2432 2487 4.454161 CACTCGTTTGATGATACCACCAAA 59.546 41.667 0.00 0.00 0.00 3.28
2441 2496 2.311542 TGATACCACCAAAGCATCCCTT 59.688 45.455 0.00 0.00 34.51 3.95
2478 2533 0.112218 ACCACATTGTAGGCAAGGCA 59.888 50.000 0.00 0.00 39.72 4.75
2479 2534 1.272648 ACCACATTGTAGGCAAGGCAT 60.273 47.619 0.00 0.00 39.72 4.40
2480 2535 2.025416 ACCACATTGTAGGCAAGGCATA 60.025 45.455 0.00 0.00 39.72 3.14
2481 2536 2.358898 CCACATTGTAGGCAAGGCATAC 59.641 50.000 6.12 6.12 44.56 2.39
2482 2537 3.282021 CACATTGTAGGCAAGGCATACT 58.718 45.455 13.23 0.00 44.59 2.12
2483 2538 3.696051 CACATTGTAGGCAAGGCATACTT 59.304 43.478 13.23 0.21 44.59 2.24
2484 2539 4.158394 CACATTGTAGGCAAGGCATACTTT 59.842 41.667 13.23 0.00 44.59 2.66
2485 2540 4.399303 ACATTGTAGGCAAGGCATACTTTC 59.601 41.667 13.23 0.00 44.59 2.62
2486 2541 2.999331 TGTAGGCAAGGCATACTTTCC 58.001 47.619 13.23 0.00 44.59 3.13
2490 2545 2.576615 GGCAAGGCATACTTTCCTAGG 58.423 52.381 0.82 0.82 39.15 3.02
2491 2546 2.172717 GGCAAGGCATACTTTCCTAGGA 59.827 50.000 7.62 7.62 39.15 2.94
2492 2547 3.371595 GGCAAGGCATACTTTCCTAGGAA 60.372 47.826 20.72 20.72 39.15 3.36
2493 2548 4.270008 GCAAGGCATACTTTCCTAGGAAA 58.730 43.478 30.53 30.53 41.22 3.13
2494 2549 4.889995 GCAAGGCATACTTTCCTAGGAAAT 59.110 41.667 32.18 23.89 42.34 2.17
2495 2550 5.221126 GCAAGGCATACTTTCCTAGGAAATG 60.221 44.000 32.18 27.38 42.34 2.32
2496 2551 5.975988 AGGCATACTTTCCTAGGAAATGA 57.024 39.130 32.18 23.76 42.34 2.57
2512 2567 7.781324 AGGAAATGAACCAATAAACTCATGT 57.219 32.000 0.00 0.00 0.00 3.21
2554 2609 2.099652 TTGCTGCACTGGCGACTAGT 62.100 55.000 0.00 0.00 45.35 2.57
2572 2627 4.997395 ACTAGTGCATTAGTTTGGTCAGTG 59.003 41.667 15.56 0.00 29.72 3.66
2639 2694 0.106819 GCTGGAATCATCCTGGCTGT 60.107 55.000 0.00 0.00 46.70 4.40
2756 2811 7.936496 TGATTTCTTGCCACATAACTTCATA 57.064 32.000 0.00 0.00 0.00 2.15
2866 2921 4.746611 CCTCAAAAAGAAAACACAGATGGC 59.253 41.667 0.00 0.00 0.00 4.40
2986 3041 4.628715 GCAAATCCTCAATACCTCAGGGAA 60.629 45.833 0.00 0.00 36.25 3.97
2995 3050 0.036010 ACCTCAGGGAATTGCGACAG 60.036 55.000 0.00 0.00 36.25 3.51
2996 3051 0.250234 CCTCAGGGAATTGCGACAGA 59.750 55.000 0.00 0.00 33.58 3.41
3052 3107 3.757947 TCCAAGGACTCTGATCTACCA 57.242 47.619 0.00 0.00 0.00 3.25
3055 3110 4.467795 TCCAAGGACTCTGATCTACCAAAG 59.532 45.833 0.00 0.00 0.00 2.77
3064 3119 6.098982 ACTCTGATCTACCAAAGAAGTATGGG 59.901 42.308 0.00 0.00 41.17 4.00
3065 3120 5.964477 TCTGATCTACCAAAGAAGTATGGGT 59.036 40.000 0.00 0.00 41.17 4.51
3083 3138 3.430453 GGGTCTCCCAAATGTTCATGAA 58.570 45.455 3.38 3.38 44.65 2.57
3088 3143 7.310361 GGGTCTCCCAAATGTTCATGAATTTTA 60.310 37.037 12.12 0.00 44.65 1.52
3093 3148 9.270640 TCCCAAATGTTCATGAATTTTAAAGTG 57.729 29.630 12.12 4.13 0.00 3.16
3369 3424 0.035630 CTTCACTGCCTCCCCTTGAG 60.036 60.000 0.00 0.00 41.07 3.02
3451 3506 6.431234 AGAAACTTGATGATCCCAAACTGTAC 59.569 38.462 0.00 0.00 0.00 2.90
3618 3673 0.108472 TGCAGCATCCTTCTCGTCAG 60.108 55.000 0.00 0.00 0.00 3.51
3913 3968 4.878397 AGATTTATCCAAAGCTCGACAAGG 59.122 41.667 0.00 0.00 35.50 3.61
3929 3984 4.036262 CGACAAGGTGGTTTTTCTTGATGA 59.964 41.667 8.95 0.00 39.97 2.92
3930 3985 5.278463 CGACAAGGTGGTTTTTCTTGATGAT 60.278 40.000 8.95 0.00 39.97 2.45
4027 4082 2.235898 ACTTGTGGAGAGAGCTTCCATC 59.764 50.000 8.84 4.26 35.82 3.51
4325 4380 4.082274 TGTGCAATGCTGAGTTTATTCG 57.918 40.909 6.82 0.00 0.00 3.34
4354 4409 7.235606 TCCCTCTATAAGGTTCTCCATGTTATG 59.764 40.741 0.00 0.00 44.56 1.90
4547 4602 7.500892 TGTCAATGACTTGGAAGCTTTTAACTA 59.499 33.333 14.97 0.00 33.15 2.24
4569 4624 8.398878 ACTACATCCTTTGTTTTATTTCGGAA 57.601 30.769 0.00 0.00 39.87 4.30
4570 4625 8.512138 ACTACATCCTTTGTTTTATTTCGGAAG 58.488 33.333 0.00 0.00 39.87 3.46
4620 4675 9.247126 TGCATTCCATTTGATAAATATTTGTCG 57.753 29.630 17.05 5.73 31.81 4.35
4728 4783 1.478105 CCCTCGATCGATCATGGCATA 59.522 52.381 24.40 0.00 0.00 3.14
4768 4823 2.027192 ACCCACATGTAAGCAGTAGTGG 60.027 50.000 0.00 0.00 41.54 4.00
4958 5013 6.183360 CCATTCTGACATCTCTAGCCTAGTTT 60.183 42.308 0.00 0.00 0.00 2.66
4980 5035 8.603181 AGTTTGTTCAGTGTTTGATTTATTTGC 58.397 29.630 0.00 0.00 35.27 3.68
5047 5102 3.653164 TGAGATTACATGCCAGTAGGGA 58.347 45.455 0.00 0.00 40.01 4.20
5052 5107 5.888161 AGATTACATGCCAGTAGGGAAAAAG 59.112 40.000 0.00 0.00 39.40 2.27
5055 5110 4.677182 ACATGCCAGTAGGGAAAAAGAAT 58.323 39.130 0.00 0.00 39.40 2.40
5056 5111 5.826643 ACATGCCAGTAGGGAAAAAGAATA 58.173 37.500 0.00 0.00 39.40 1.75
5068 5123 6.494835 AGGGAAAAAGAATAATTCTGCAGTGT 59.505 34.615 14.67 0.18 40.59 3.55
5154 5209 7.970102 TGTAACAGGGAAGTTAGAAATACACT 58.030 34.615 0.00 0.00 34.85 3.55
5164 5220 9.924650 GAAGTTAGAAATACACTAGAAAGACCA 57.075 33.333 0.00 0.00 0.00 4.02
5286 5414 6.164176 TCTAAGTACTTGGCTTCTTGTTAGC 58.836 40.000 18.56 0.00 37.91 3.09
5307 5437 3.619242 GCTGGAAACTAACCTCACCTACC 60.619 52.174 0.00 0.00 0.00 3.18
5424 5555 6.895607 TTCAATACGTTCAATCGCTCATAA 57.104 33.333 0.00 0.00 0.00 1.90
5450 5581 9.846248 ACATGCTGAAAACAATCTACTATTTTC 57.154 29.630 0.00 0.00 40.09 2.29
5453 5584 9.897744 TGCTGAAAACAATCTACTATTTTCTTG 57.102 29.630 9.08 4.58 40.25 3.02
5454 5585 9.899226 GCTGAAAACAATCTACTATTTTCTTGT 57.101 29.630 9.08 0.00 40.25 3.16
5479 5610 8.344831 GTTTGCTGTTGATATCATGCATACTTA 58.655 33.333 24.39 12.93 32.48 2.24
5503 5634 6.682423 GTACTCTTAGTACTCCCTCACTTC 57.318 45.833 0.00 0.00 45.70 3.01
5515 5646 9.145442 GTACTCCCTCACTTCCTAAATATAAGT 57.855 37.037 0.00 0.00 33.82 2.24
5519 5650 8.925338 TCCCTCACTTCCTAAATATAAGTCTTC 58.075 37.037 0.00 0.00 31.21 2.87
5537 5668 8.879342 AAGTCTTCTTACAGATTTCGATATGG 57.121 34.615 0.00 0.00 31.46 2.74
5538 5669 8.239038 AGTCTTCTTACAGATTTCGATATGGA 57.761 34.615 0.00 0.00 0.00 3.41
5539 5670 8.138712 AGTCTTCTTACAGATTTCGATATGGAC 58.861 37.037 0.00 0.00 0.00 4.02
5540 5671 8.138712 GTCTTCTTACAGATTTCGATATGGACT 58.861 37.037 0.00 0.00 0.00 3.85
5541 5672 9.350951 TCTTCTTACAGATTTCGATATGGACTA 57.649 33.333 0.00 0.00 0.00 2.59
5542 5673 9.400638 CTTCTTACAGATTTCGATATGGACTAC 57.599 37.037 0.00 0.00 0.00 2.73
5543 5674 8.459911 TCTTACAGATTTCGATATGGACTACA 57.540 34.615 0.00 0.00 0.00 2.74
5544 5675 9.078990 TCTTACAGATTTCGATATGGACTACAT 57.921 33.333 0.00 0.00 43.68 2.29
5547 5678 7.306213 ACAGATTTCGATATGGACTACATACG 58.694 38.462 0.00 0.00 44.41 3.06
5548 5679 6.747739 CAGATTTCGATATGGACTACATACGG 59.252 42.308 0.00 0.00 44.41 4.02
5549 5680 6.657966 AGATTTCGATATGGACTACATACGGA 59.342 38.462 0.00 0.00 44.41 4.69
5550 5681 5.874895 TTCGATATGGACTACATACGGAG 57.125 43.478 0.00 0.00 44.41 4.63
5551 5682 3.688185 TCGATATGGACTACATACGGAGC 59.312 47.826 0.00 0.00 44.41 4.70
5552 5683 3.439129 CGATATGGACTACATACGGAGCA 59.561 47.826 0.00 0.00 44.41 4.26
5553 5684 4.082949 CGATATGGACTACATACGGAGCAA 60.083 45.833 0.00 0.00 44.41 3.91
5554 5685 5.564063 CGATATGGACTACATACGGAGCAAA 60.564 44.000 0.00 0.00 44.41 3.68
5555 5686 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
5556 5687 3.592059 TGGACTACATACGGAGCAAAAC 58.408 45.455 0.00 0.00 0.00 2.43
5557 5688 2.601763 GGACTACATACGGAGCAAAACG 59.398 50.000 0.00 0.00 0.00 3.60
5558 5689 3.504863 GACTACATACGGAGCAAAACGA 58.495 45.455 0.00 0.00 0.00 3.85
5559 5690 3.508762 ACTACATACGGAGCAAAACGAG 58.491 45.455 0.00 0.00 0.00 4.18
5560 5691 2.450609 ACATACGGAGCAAAACGAGT 57.549 45.000 0.00 0.00 0.00 4.18
5561 5692 2.066262 ACATACGGAGCAAAACGAGTG 58.934 47.619 0.00 0.00 0.00 3.51
5562 5693 2.288579 ACATACGGAGCAAAACGAGTGA 60.289 45.455 0.00 0.00 0.00 3.41
5563 5694 2.512485 TACGGAGCAAAACGAGTGAA 57.488 45.000 0.00 0.00 0.00 3.18
5564 5695 1.878953 ACGGAGCAAAACGAGTGAAT 58.121 45.000 0.00 0.00 0.00 2.57
5565 5696 1.798813 ACGGAGCAAAACGAGTGAATC 59.201 47.619 0.00 0.00 0.00 2.52
5566 5697 2.069273 CGGAGCAAAACGAGTGAATCT 58.931 47.619 0.00 0.00 0.00 2.40
5567 5698 3.250744 CGGAGCAAAACGAGTGAATCTA 58.749 45.455 0.00 0.00 0.00 1.98
5568 5699 3.865745 CGGAGCAAAACGAGTGAATCTAT 59.134 43.478 0.00 0.00 0.00 1.98
5569 5700 5.041287 CGGAGCAAAACGAGTGAATCTATA 58.959 41.667 0.00 0.00 0.00 1.31
5570 5701 5.051641 CGGAGCAAAACGAGTGAATCTATAC 60.052 44.000 0.00 0.00 0.00 1.47
5571 5702 6.043411 GGAGCAAAACGAGTGAATCTATACT 58.957 40.000 0.00 0.00 0.00 2.12
5572 5703 6.199342 GGAGCAAAACGAGTGAATCTATACTC 59.801 42.308 0.00 0.00 39.86 2.59
5573 5704 6.868622 AGCAAAACGAGTGAATCTATACTCT 58.131 36.000 0.00 0.00 40.82 3.24
5574 5705 7.997482 AGCAAAACGAGTGAATCTATACTCTA 58.003 34.615 0.00 0.00 40.82 2.43
5575 5706 8.467598 AGCAAAACGAGTGAATCTATACTCTAA 58.532 33.333 0.00 0.00 40.82 2.10
5576 5707 9.084164 GCAAAACGAGTGAATCTATACTCTAAA 57.916 33.333 0.00 0.00 40.82 1.85
5667 5798 7.714703 ACGGAGGAAGTACAATTCTTATACTC 58.285 38.462 0.00 0.00 0.00 2.59
5668 5799 7.146648 CGGAGGAAGTACAATTCTTATACTCC 58.853 42.308 0.00 0.00 37.23 3.85
5669 5800 7.201884 CGGAGGAAGTACAATTCTTATACTCCA 60.202 40.741 15.70 0.00 38.64 3.86
5670 5801 8.652290 GGAGGAAGTACAATTCTTATACTCCAT 58.348 37.037 0.00 0.00 38.62 3.41
5671 5802 9.699703 GAGGAAGTACAATTCTTATACTCCATC 57.300 37.037 0.00 0.00 0.00 3.51
5672 5803 8.652290 AGGAAGTACAATTCTTATACTCCATCC 58.348 37.037 0.00 0.00 0.00 3.51
5673 5804 8.429641 GGAAGTACAATTCTTATACTCCATCCA 58.570 37.037 0.00 0.00 29.42 3.41
5674 5805 9.832445 GAAGTACAATTCTTATACTCCATCCAA 57.168 33.333 0.00 0.00 0.00 3.53
5677 5808 9.778741 GTACAATTCTTATACTCCATCCAATCA 57.221 33.333 0.00 0.00 0.00 2.57
5693 5824 9.396022 CCATCCAATCATAAAGTTGTACTAAGT 57.604 33.333 0.00 0.00 0.00 2.24
5700 5831 6.702723 TCATAAAGTTGTACTAAGTGTGCGTT 59.297 34.615 0.00 0.00 33.83 4.84
5716 5847 8.445275 AGTGTGCGTTAATTAATATGGATTGA 57.555 30.769 0.31 0.00 0.00 2.57
5791 5922 5.662456 TGCACACACGCCTAGTATTATTAA 58.338 37.500 0.00 0.00 0.00 1.40
5792 5923 6.285224 TGCACACACGCCTAGTATTATTAAT 58.715 36.000 0.00 0.00 0.00 1.40
5793 5924 6.764085 TGCACACACGCCTAGTATTATTAATT 59.236 34.615 0.00 0.00 0.00 1.40
5794 5925 7.281324 TGCACACACGCCTAGTATTATTAATTT 59.719 33.333 0.00 0.00 0.00 1.82
5795 5926 8.767085 GCACACACGCCTAGTATTATTAATTTA 58.233 33.333 0.00 0.00 0.00 1.40
5797 5928 9.264719 ACACACGCCTAGTATTATTAATTTACC 57.735 33.333 0.00 0.00 0.00 2.85
5798 5929 8.715088 CACACGCCTAGTATTATTAATTTACCC 58.285 37.037 0.00 0.00 0.00 3.69
5799 5930 7.879677 ACACGCCTAGTATTATTAATTTACCCC 59.120 37.037 0.00 0.00 0.00 4.95
5800 5931 7.335171 CACGCCTAGTATTATTAATTTACCCCC 59.665 40.741 0.00 0.00 0.00 5.40
5801 5932 7.238305 ACGCCTAGTATTATTAATTTACCCCCT 59.762 37.037 0.00 0.00 0.00 4.79
5802 5933 7.767659 CGCCTAGTATTATTAATTTACCCCCTC 59.232 40.741 0.00 0.00 0.00 4.30
5803 5934 8.051535 GCCTAGTATTATTAATTTACCCCCTCC 58.948 40.741 0.00 0.00 0.00 4.30
5804 5935 8.262933 CCTAGTATTATTAATTTACCCCCTCCG 58.737 40.741 0.00 0.00 0.00 4.63
5805 5936 6.479006 AGTATTATTAATTTACCCCCTCCGC 58.521 40.000 0.00 0.00 0.00 5.54
5806 5937 4.792513 TTATTAATTTACCCCCTCCGCA 57.207 40.909 0.00 0.00 0.00 5.69
5807 5938 3.673543 ATTAATTTACCCCCTCCGCAA 57.326 42.857 0.00 0.00 0.00 4.85
5808 5939 3.453059 TTAATTTACCCCCTCCGCAAA 57.547 42.857 0.00 0.00 0.00 3.68
5809 5940 1.847328 AATTTACCCCCTCCGCAAAG 58.153 50.000 0.00 0.00 0.00 2.77
5810 5941 0.996583 ATTTACCCCCTCCGCAAAGA 59.003 50.000 0.00 0.00 0.00 2.52
5811 5942 0.772384 TTTACCCCCTCCGCAAAGAA 59.228 50.000 0.00 0.00 0.00 2.52
5812 5943 0.772384 TTACCCCCTCCGCAAAGAAA 59.228 50.000 0.00 0.00 0.00 2.52
5813 5944 0.996583 TACCCCCTCCGCAAAGAAAT 59.003 50.000 0.00 0.00 0.00 2.17
5814 5945 0.996583 ACCCCCTCCGCAAAGAAATA 59.003 50.000 0.00 0.00 0.00 1.40
5815 5946 1.569072 ACCCCCTCCGCAAAGAAATAT 59.431 47.619 0.00 0.00 0.00 1.28
5816 5947 2.781174 ACCCCCTCCGCAAAGAAATATA 59.219 45.455 0.00 0.00 0.00 0.86
5817 5948 3.203487 ACCCCCTCCGCAAAGAAATATAA 59.797 43.478 0.00 0.00 0.00 0.98
5818 5949 4.141018 ACCCCCTCCGCAAAGAAATATAAT 60.141 41.667 0.00 0.00 0.00 1.28
5819 5950 5.073965 ACCCCCTCCGCAAAGAAATATAATA 59.926 40.000 0.00 0.00 0.00 0.98
5820 5951 5.648092 CCCCCTCCGCAAAGAAATATAATAG 59.352 44.000 0.00 0.00 0.00 1.73
5821 5952 5.123979 CCCCTCCGCAAAGAAATATAATAGC 59.876 44.000 0.00 0.00 0.00 2.97
5822 5953 5.163854 CCCTCCGCAAAGAAATATAATAGCG 60.164 44.000 0.00 0.00 43.13 4.26
5823 5954 5.408604 CCTCCGCAAAGAAATATAATAGCGT 59.591 40.000 0.00 0.00 42.08 5.07
5824 5955 6.073222 CCTCCGCAAAGAAATATAATAGCGTT 60.073 38.462 0.00 0.00 42.08 4.84
5825 5956 7.254227 TCCGCAAAGAAATATAATAGCGTTT 57.746 32.000 0.00 0.00 42.08 3.60
5826 5957 8.367943 TCCGCAAAGAAATATAATAGCGTTTA 57.632 30.769 0.00 0.00 42.08 2.01
5827 5958 8.492748 TCCGCAAAGAAATATAATAGCGTTTAG 58.507 33.333 0.00 0.00 42.08 1.85
5828 5959 8.492748 CCGCAAAGAAATATAATAGCGTTTAGA 58.507 33.333 0.00 0.00 42.08 2.10
5841 5972 7.969536 ATAGCGTTTAGATCATTGCATTAGT 57.030 32.000 0.00 0.00 0.00 2.24
5842 5973 6.052840 AGCGTTTAGATCATTGCATTAGTG 57.947 37.500 0.00 0.00 0.00 2.74
5843 5974 5.817296 AGCGTTTAGATCATTGCATTAGTGA 59.183 36.000 0.00 0.00 0.00 3.41
5844 5975 6.484643 AGCGTTTAGATCATTGCATTAGTGAT 59.515 34.615 0.00 0.00 38.32 3.06
5845 5976 6.794158 GCGTTTAGATCATTGCATTAGTGATC 59.206 38.462 17.32 17.32 46.97 2.92
5852 5983 8.670804 GATCATTGCATTAGTGATCTAAATGC 57.329 34.615 22.49 22.49 44.63 3.56
5853 5984 7.812690 TCATTGCATTAGTGATCTAAATGCT 57.187 32.000 26.08 14.02 39.23 3.79
5854 5985 7.868775 TCATTGCATTAGTGATCTAAATGCTC 58.131 34.615 26.08 10.92 39.23 4.26
5855 5986 7.718314 TCATTGCATTAGTGATCTAAATGCTCT 59.282 33.333 26.08 17.09 39.23 4.09
5856 5987 7.870509 TTGCATTAGTGATCTAAATGCTCTT 57.129 32.000 26.08 0.00 39.23 2.85
5857 5988 8.962884 TTGCATTAGTGATCTAAATGCTCTTA 57.037 30.769 26.08 13.32 39.23 2.10
5858 5989 9.565090 TTGCATTAGTGATCTAAATGCTCTTAT 57.435 29.630 26.08 2.12 39.23 1.73
5874 6005 9.525826 AATGCTCTTATATTTCTTTATGGAGGG 57.474 33.333 0.00 0.00 0.00 4.30
5875 6006 8.275187 TGCTCTTATATTTCTTTATGGAGGGA 57.725 34.615 0.00 0.00 0.00 4.20
5876 6007 8.378565 TGCTCTTATATTTCTTTATGGAGGGAG 58.621 37.037 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 4.853050 AGAGGAGCATGCTGGCGC 62.853 66.667 28.27 10.59 36.27 6.53
133 135 2.625314 GCCCCAAAGAATCTATCAAGCC 59.375 50.000 0.00 0.00 0.00 4.35
184 186 2.509964 CCCCTAGGTGGCTCAGTTTTAT 59.490 50.000 8.29 0.00 0.00 1.40
228 230 4.196971 GGCAGATAGATTAACCGGTTTGT 58.803 43.478 27.64 14.69 0.00 2.83
232 234 2.313317 TCGGCAGATAGATTAACCGGT 58.687 47.619 0.00 0.00 40.95 5.28
251 253 0.827368 AAGGGAGATCTGGAGCGTTC 59.173 55.000 0.00 0.00 0.00 3.95
286 288 2.316867 GGCCCATTTTTGTGCACGC 61.317 57.895 13.13 6.45 0.00 5.34
319 345 7.850982 CCGGTTAATGAGAAGACAAAATAATCG 59.149 37.037 0.00 0.00 0.00 3.34
374 400 3.981071 AGATGAAACTTGATGGGTCGA 57.019 42.857 0.00 0.00 0.00 4.20
414 440 3.683340 GGCAGTCCTAAAAGTAACCGAAG 59.317 47.826 0.00 0.00 0.00 3.79
429 455 1.415200 CCTCTAGTTAGGGGCAGTCC 58.585 60.000 0.00 0.00 37.09 3.85
436 462 0.105039 CAAGGCGCCTCTAGTTAGGG 59.895 60.000 32.93 7.01 37.11 3.53
450 476 1.739067 ATCCTTACTCAACGCAAGGC 58.261 50.000 0.00 0.00 46.39 4.35
451 477 3.334691 TGAATCCTTACTCAACGCAAGG 58.665 45.455 0.00 0.00 46.39 3.61
458 493 2.233676 TGAGCGCTGAATCCTTACTCAA 59.766 45.455 18.48 0.00 30.24 3.02
552 587 2.601314 CGATCGATTAACTGCAAACCGA 59.399 45.455 10.26 0.00 0.00 4.69
558 593 3.503827 ACAGTCGATCGATTAACTGCA 57.496 42.857 27.64 0.00 42.23 4.41
584 619 9.850628 TTTCAAAATTTTGCATTTTCATCAACA 57.149 22.222 23.36 1.16 38.05 3.33
690 729 7.965045 AGCGAACTTTTATCAAATCTACAGAC 58.035 34.615 0.00 0.00 0.00 3.51
733 772 6.126568 TCCCGTGAACTTTTCTTTAAACTG 57.873 37.500 0.00 0.00 0.00 3.16
857 898 2.985847 GGCTTGCCTGCTCCGTTT 60.986 61.111 4.11 0.00 0.00 3.60
900 942 4.820173 CGGGTTTCTAGAAGGAAGTGTTTT 59.180 41.667 5.12 0.00 0.00 2.43
957 999 0.038159 CCTCTTCCGCTCGTCAAACT 60.038 55.000 0.00 0.00 0.00 2.66
1219 1264 2.284798 GACTCGCAATCTCGGCAGGA 62.285 60.000 0.00 0.00 0.00 3.86
1344 1390 3.181506 CCAGAGGAAACGCATTTAGCTTC 60.182 47.826 0.00 0.00 42.61 3.86
1371 1418 9.520204 CAAGACACAAGAAACATAACAGAAAAT 57.480 29.630 0.00 0.00 0.00 1.82
1375 1422 5.008613 GCCAAGACACAAGAAACATAACAGA 59.991 40.000 0.00 0.00 0.00 3.41
1376 1423 5.215160 GCCAAGACACAAGAAACATAACAG 58.785 41.667 0.00 0.00 0.00 3.16
1377 1424 4.037446 GGCCAAGACACAAGAAACATAACA 59.963 41.667 0.00 0.00 0.00 2.41
1378 1425 4.037446 TGGCCAAGACACAAGAAACATAAC 59.963 41.667 0.61 0.00 0.00 1.89
1452 1501 1.133598 CACTAATACGGCACCGACAGA 59.866 52.381 17.40 0.00 42.83 3.41
1483 1532 2.285083 TCGAATCGTTGGCTAAATGGG 58.715 47.619 1.52 0.00 0.00 4.00
1537 1588 8.141268 CAGTGTAACATTTACCAAAACCAAGAT 58.859 33.333 0.00 0.00 41.43 2.40
1589 1640 6.491745 TGTGCAAACCATCTAAGGACAAAATA 59.508 34.615 0.00 0.00 0.00 1.40
1590 1641 5.304101 TGTGCAAACCATCTAAGGACAAAAT 59.696 36.000 0.00 0.00 0.00 1.82
1592 1643 4.211125 TGTGCAAACCATCTAAGGACAAA 58.789 39.130 0.00 0.00 0.00 2.83
1593 1644 3.826524 TGTGCAAACCATCTAAGGACAA 58.173 40.909 0.00 0.00 0.00 3.18
1647 1698 2.079925 CAGAAAGCACCCTGTTAGCTC 58.920 52.381 0.00 0.00 37.70 4.09
1648 1699 1.699634 TCAGAAAGCACCCTGTTAGCT 59.300 47.619 0.00 0.00 41.03 3.32
1705 1756 1.546476 GTCACTTGGTCGATCAGGTCT 59.454 52.381 10.95 0.00 0.00 3.85
1739 1790 0.521735 GTCGCCAAACCACCATCTTC 59.478 55.000 0.00 0.00 0.00 2.87
1772 1823 0.250640 CCTGTGTGCTTCTCCTGCTT 60.251 55.000 0.00 0.00 0.00 3.91
1916 1967 7.609918 AGTGGATGTACTAGATCAGCATAGTAG 59.390 40.741 0.00 0.00 35.66 2.57
1933 1984 1.408969 TGCGGATGCTAGTGGATGTA 58.591 50.000 0.00 0.00 43.34 2.29
1982 2033 1.282248 CGTTGGCACGTCTACACTGG 61.282 60.000 0.00 0.00 41.84 4.00
2007 2058 2.233271 CTTGCTTTCCACTGACATGGT 58.767 47.619 0.00 0.00 40.95 3.55
2015 2066 3.077359 GCTGTGATACTTGCTTTCCACT 58.923 45.455 0.00 0.00 0.00 4.00
2100 2151 7.287696 GGAATGACCCTTGTATTGTATCCATTT 59.712 37.037 0.00 0.00 0.00 2.32
2149 2200 0.034337 GTAGTTGGCCACGGAAGACA 59.966 55.000 3.88 0.00 0.00 3.41
2167 2218 1.209019 GATCCAGCATCACACTGAGGT 59.791 52.381 0.00 0.00 37.32 3.85
2174 2225 2.927028 CTCAATGGATCCAGCATCACA 58.073 47.619 21.33 0.00 32.33 3.58
2317 2370 1.299976 GACCACCCGAGCCAAATCT 59.700 57.895 0.00 0.00 0.00 2.40
2331 2384 1.460273 GGAAAAAGCCGCTTGGACCA 61.460 55.000 6.34 0.00 33.02 4.02
2381 2434 2.203728 ACACCAGGCCCTCGTGTA 60.204 61.111 12.80 0.00 38.91 2.90
2393 2446 1.153329 GTGACCCGAACACACACCA 60.153 57.895 0.00 0.00 38.05 4.17
2401 2454 1.459592 CATCAAACGAGTGACCCGAAC 59.540 52.381 0.00 0.00 0.00 3.95
2408 2461 3.259625 TGGTGGTATCATCAAACGAGTGA 59.740 43.478 0.00 0.00 29.80 3.41
2409 2462 3.595173 TGGTGGTATCATCAAACGAGTG 58.405 45.455 0.00 0.00 29.80 3.51
2410 2463 3.973206 TGGTGGTATCATCAAACGAGT 57.027 42.857 0.00 0.00 29.80 4.18
2411 2464 4.437390 GCTTTGGTGGTATCATCAAACGAG 60.437 45.833 10.43 2.72 45.78 4.18
2412 2465 3.438781 GCTTTGGTGGTATCATCAAACGA 59.561 43.478 10.43 0.00 45.78 3.85
2413 2466 3.190327 TGCTTTGGTGGTATCATCAAACG 59.810 43.478 10.43 8.23 45.78 3.60
2414 2467 4.782019 TGCTTTGGTGGTATCATCAAAC 57.218 40.909 10.43 8.45 45.78 2.93
2432 2487 6.731467 TCCTTATAAAAACTGAAGGGATGCT 58.269 36.000 0.00 0.00 39.20 3.79
2480 2535 8.803235 GTTTATTGGTTCATTTCCTAGGAAAGT 58.197 33.333 34.12 22.25 45.66 2.66
2481 2536 9.025041 AGTTTATTGGTTCATTTCCTAGGAAAG 57.975 33.333 34.12 26.21 45.66 2.62
2482 2537 8.950007 AGTTTATTGGTTCATTTCCTAGGAAA 57.050 30.769 33.59 33.59 46.37 3.13
2483 2538 8.167392 TGAGTTTATTGGTTCATTTCCTAGGAA 58.833 33.333 20.72 20.72 0.00 3.36
2484 2539 7.695055 TGAGTTTATTGGTTCATTTCCTAGGA 58.305 34.615 7.62 7.62 0.00 2.94
2485 2540 7.938140 TGAGTTTATTGGTTCATTTCCTAGG 57.062 36.000 0.82 0.82 0.00 3.02
2486 2541 8.960591 ACATGAGTTTATTGGTTCATTTCCTAG 58.039 33.333 0.00 0.00 0.00 3.02
2487 2542 8.739039 CACATGAGTTTATTGGTTCATTTCCTA 58.261 33.333 0.00 0.00 0.00 2.94
2488 2543 7.233348 ACACATGAGTTTATTGGTTCATTTCCT 59.767 33.333 0.00 0.00 0.00 3.36
2489 2544 7.378181 ACACATGAGTTTATTGGTTCATTTCC 58.622 34.615 0.00 0.00 0.00 3.13
2490 2545 8.816640 AACACATGAGTTTATTGGTTCATTTC 57.183 30.769 0.00 0.00 0.00 2.17
2491 2546 8.420222 TGAACACATGAGTTTATTGGTTCATTT 58.580 29.630 9.96 0.00 38.61 2.32
2492 2547 7.867403 GTGAACACATGAGTTTATTGGTTCATT 59.133 33.333 9.96 0.00 43.33 2.57
2493 2548 7.014134 TGTGAACACATGAGTTTATTGGTTCAT 59.986 33.333 9.96 0.00 43.33 2.57
2494 2549 6.319911 TGTGAACACATGAGTTTATTGGTTCA 59.680 34.615 9.96 0.00 40.49 3.18
2495 2550 6.734137 TGTGAACACATGAGTTTATTGGTTC 58.266 36.000 9.96 0.00 36.21 3.62
2496 2551 6.545666 TCTGTGAACACATGAGTTTATTGGTT 59.454 34.615 9.96 0.00 41.01 3.67
2512 2567 3.006940 GTGTTCCAAGTGTCTGTGAACA 58.993 45.455 0.00 0.00 41.99 3.18
2554 2609 3.550820 ACACACTGACCAAACTAATGCA 58.449 40.909 0.00 0.00 0.00 3.96
2639 2694 1.406887 GCCCAAATTCCGCAGAGAGTA 60.407 52.381 0.00 0.00 0.00 2.59
2756 2811 5.874261 GCAAATACAAGCCCACACAATTTAT 59.126 36.000 0.00 0.00 0.00 1.40
2866 2921 5.276868 CGACGAAGCCATATTTTTACTCCTG 60.277 44.000 0.00 0.00 0.00 3.86
2986 3041 0.389391 CCCGTATCCTCTGTCGCAAT 59.611 55.000 0.00 0.00 0.00 3.56
2995 3050 3.939592 CCTTTTGAACTTCCCGTATCCTC 59.060 47.826 0.00 0.00 0.00 3.71
2996 3051 3.329814 ACCTTTTGAACTTCCCGTATCCT 59.670 43.478 0.00 0.00 0.00 3.24
3064 3119 9.487790 TTTAAAATTCATGAACATTTGGGAGAC 57.512 29.630 22.24 0.00 0.00 3.36
3065 3120 9.709495 CTTTAAAATTCATGAACATTTGGGAGA 57.291 29.630 22.24 7.27 0.00 3.71
3083 3138 7.763985 GCCCACAATATGCTAACACTTTAAAAT 59.236 33.333 0.00 0.00 0.00 1.82
3088 3143 4.085733 TGCCCACAATATGCTAACACTTT 58.914 39.130 0.00 0.00 0.00 2.66
3093 3148 4.270808 GCAAAATGCCCACAATATGCTAAC 59.729 41.667 0.00 0.00 37.42 2.34
3097 3152 2.610374 CTGCAAAATGCCCACAATATGC 59.390 45.455 0.00 0.00 44.23 3.14
3319 3374 0.463620 GGGTTTTGGCTGCAAGTTGA 59.536 50.000 7.16 0.00 35.30 3.18
3369 3424 8.078596 CCAATGAAAAGTATTCATTAGCTAGCC 58.921 37.037 12.13 0.00 44.60 3.93
3451 3506 3.616956 TCTGAGAACAAGGCATAGTGG 57.383 47.619 0.00 0.00 0.00 4.00
3618 3673 6.147328 GTCTGTCAGTTACTATGTGGAAAACC 59.853 42.308 0.00 0.00 0.00 3.27
3913 3968 7.820648 ACTACATCATCATCAAGAAAAACCAC 58.179 34.615 0.00 0.00 0.00 4.16
4027 4082 4.500703 AATTCAAGTAACGATCGAAGCG 57.499 40.909 24.34 9.17 0.00 4.68
4273 4328 9.827411 CTTTAGTTCAAAACTTTATCAGCCTAC 57.173 33.333 0.00 0.00 42.81 3.18
4354 4409 4.882671 AATTACATGGACAATCTGCGAC 57.117 40.909 0.00 0.00 0.00 5.19
4391 4446 3.266510 TCTTGCTACCCATGTAAGCTG 57.733 47.619 11.16 5.90 0.00 4.24
4434 4489 9.445786 ACAAATTTTGAAACTCTGTACAATACG 57.554 29.630 15.81 0.00 0.00 3.06
4547 4602 7.368059 GTCTTCCGAAATAAAACAAAGGATGT 58.632 34.615 0.00 0.00 46.82 3.06
4566 4621 4.918810 AACAACAAATGACAGGTCTTCC 57.081 40.909 0.65 0.00 0.00 3.46
4569 4624 6.530019 AAGAAAACAACAAATGACAGGTCT 57.470 33.333 0.65 0.00 0.00 3.85
4570 4625 7.455447 CAAAAGAAAACAACAAATGACAGGTC 58.545 34.615 0.00 0.00 0.00 3.85
4620 4675 5.566774 CGTCTTCATTCTGCAATCAAAAGTC 59.433 40.000 0.00 0.00 0.00 3.01
4728 4783 4.732672 GGTTGTAACCTAGACCGAGAAT 57.267 45.455 6.54 0.00 45.75 2.40
4958 5013 5.689514 CGGCAAATAAATCAAACACTGAACA 59.310 36.000 0.00 0.00 37.67 3.18
5052 5107 8.693542 AAAGCATTTACACTGCAGAATTATTC 57.306 30.769 23.35 0.00 42.15 1.75
5055 5110 7.384660 CCAAAAAGCATTTACACTGCAGAATTA 59.615 33.333 23.35 5.13 37.28 1.40
5056 5111 6.203338 CCAAAAAGCATTTACACTGCAGAATT 59.797 34.615 23.35 6.21 37.28 2.17
5154 5209 3.010138 CCCAGGGTCATTTGGTCTTTCTA 59.990 47.826 0.00 0.00 32.40 2.10
5182 5238 2.290705 GGCTTGAACCCTGCCTAACTAA 60.291 50.000 0.00 0.00 43.05 2.24
5260 5386 7.172703 GCTAACAAGAAGCCAAGTACTTAGAAA 59.827 37.037 8.04 0.00 33.73 2.52
5261 5387 6.649557 GCTAACAAGAAGCCAAGTACTTAGAA 59.350 38.462 8.04 0.00 33.73 2.10
5263 5389 6.091441 CAGCTAACAAGAAGCCAAGTACTTAG 59.909 42.308 8.04 1.59 41.02 2.18
5286 5414 3.581332 TGGTAGGTGAGGTTAGTTTCCAG 59.419 47.826 0.00 0.00 0.00 3.86
5410 5541 4.190772 TCAGCATGTTATGAGCGATTGAA 58.809 39.130 0.00 0.00 37.40 2.69
5424 5555 9.846248 GAAAATAGTAGATTGTTTTCAGCATGT 57.154 29.630 0.00 0.00 39.27 3.21
5446 5577 7.116662 GCATGATATCAACAGCAAACAAGAAAA 59.883 33.333 9.99 0.00 0.00 2.29
5447 5578 6.587226 GCATGATATCAACAGCAAACAAGAAA 59.413 34.615 9.99 0.00 0.00 2.52
5450 5581 5.404096 TGCATGATATCAACAGCAAACAAG 58.596 37.500 21.33 0.73 32.22 3.16
5452 5583 5.585820 ATGCATGATATCAACAGCAAACA 57.414 34.783 24.97 10.58 36.39 2.83
5453 5584 6.732154 AGTATGCATGATATCAACAGCAAAC 58.268 36.000 24.97 15.70 36.39 2.93
5454 5585 6.947644 AGTATGCATGATATCAACAGCAAA 57.052 33.333 24.97 10.87 36.39 3.68
5458 5589 9.920133 AGTACTAAGTATGCATGATATCAACAG 57.080 33.333 9.99 4.27 0.00 3.16
5488 5619 9.369672 CTTATATTTAGGAAGTGAGGGAGTACT 57.630 37.037 0.00 0.00 0.00 2.73
5489 5620 9.145442 ACTTATATTTAGGAAGTGAGGGAGTAC 57.855 37.037 0.00 0.00 32.25 2.73
5490 5621 9.364653 GACTTATATTTAGGAAGTGAGGGAGTA 57.635 37.037 0.00 0.00 33.61 2.59
5491 5622 8.068733 AGACTTATATTTAGGAAGTGAGGGAGT 58.931 37.037 0.00 0.00 33.61 3.85
5492 5623 8.485578 AGACTTATATTTAGGAAGTGAGGGAG 57.514 38.462 0.00 0.00 33.61 4.30
5493 5624 8.855804 AAGACTTATATTTAGGAAGTGAGGGA 57.144 34.615 0.00 0.00 33.61 4.20
5494 5625 8.929487 AGAAGACTTATATTTAGGAAGTGAGGG 58.071 37.037 0.00 0.00 33.61 4.30
5522 5653 7.306213 CGTATGTAGTCCATATCGAAATCTGT 58.694 38.462 0.00 0.00 38.29 3.41
5523 5654 6.747739 CCGTATGTAGTCCATATCGAAATCTG 59.252 42.308 0.00 0.00 38.29 2.90
5524 5655 6.657966 TCCGTATGTAGTCCATATCGAAATCT 59.342 38.462 0.00 0.00 38.29 2.40
5525 5656 6.849502 TCCGTATGTAGTCCATATCGAAATC 58.150 40.000 0.00 0.00 38.29 2.17
5526 5657 6.625300 GCTCCGTATGTAGTCCATATCGAAAT 60.625 42.308 0.00 0.00 38.29 2.17
5528 5659 4.155462 GCTCCGTATGTAGTCCATATCGAA 59.845 45.833 0.00 0.00 38.29 3.71
5529 5660 3.688185 GCTCCGTATGTAGTCCATATCGA 59.312 47.826 0.00 0.00 38.29 3.59
5530 5661 3.439129 TGCTCCGTATGTAGTCCATATCG 59.561 47.826 0.00 0.00 38.29 2.92
5531 5662 5.386958 TTGCTCCGTATGTAGTCCATATC 57.613 43.478 0.00 0.00 38.29 1.63
5532 5663 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
5533 5664 5.353938 GTTTTGCTCCGTATGTAGTCCATA 58.646 41.667 0.00 0.00 34.86 2.74
5534 5665 4.189231 GTTTTGCTCCGTATGTAGTCCAT 58.811 43.478 0.00 0.00 37.58 3.41
5535 5666 3.592059 GTTTTGCTCCGTATGTAGTCCA 58.408 45.455 0.00 0.00 0.00 4.02
5536 5667 2.601763 CGTTTTGCTCCGTATGTAGTCC 59.398 50.000 0.00 0.00 0.00 3.85
5537 5668 3.504863 TCGTTTTGCTCCGTATGTAGTC 58.495 45.455 0.00 0.00 0.00 2.59
5538 5669 3.057033 ACTCGTTTTGCTCCGTATGTAGT 60.057 43.478 0.00 0.00 0.00 2.73
5539 5670 3.303495 CACTCGTTTTGCTCCGTATGTAG 59.697 47.826 0.00 0.00 0.00 2.74
5540 5671 3.057386 TCACTCGTTTTGCTCCGTATGTA 60.057 43.478 0.00 0.00 0.00 2.29
5541 5672 2.066262 CACTCGTTTTGCTCCGTATGT 58.934 47.619 0.00 0.00 0.00 2.29
5542 5673 2.333926 TCACTCGTTTTGCTCCGTATG 58.666 47.619 0.00 0.00 0.00 2.39
5543 5674 2.736144 TCACTCGTTTTGCTCCGTAT 57.264 45.000 0.00 0.00 0.00 3.06
5544 5675 2.512485 TTCACTCGTTTTGCTCCGTA 57.488 45.000 0.00 0.00 0.00 4.02
5545 5676 1.798813 GATTCACTCGTTTTGCTCCGT 59.201 47.619 0.00 0.00 0.00 4.69
5546 5677 2.069273 AGATTCACTCGTTTTGCTCCG 58.931 47.619 0.00 0.00 0.00 4.63
5547 5678 6.043411 AGTATAGATTCACTCGTTTTGCTCC 58.957 40.000 0.00 0.00 0.00 4.70
5548 5679 6.975772 AGAGTATAGATTCACTCGTTTTGCTC 59.024 38.462 0.00 0.00 44.77 4.26
5549 5680 6.868622 AGAGTATAGATTCACTCGTTTTGCT 58.131 36.000 0.00 0.00 44.77 3.91
5550 5681 8.630278 TTAGAGTATAGATTCACTCGTTTTGC 57.370 34.615 0.00 0.00 44.77 3.68
5640 5771 8.713737 GTATAAGAATTGTACTTCCTCCGTTT 57.286 34.615 0.00 0.00 39.28 3.60
5667 5798 9.396022 ACTTAGTACAACTTTATGATTGGATGG 57.604 33.333 0.00 0.00 0.00 3.51
5669 5800 9.959721 ACACTTAGTACAACTTTATGATTGGAT 57.040 29.630 0.00 0.00 0.00 3.41
5670 5801 9.214957 CACACTTAGTACAACTTTATGATTGGA 57.785 33.333 0.00 0.00 0.00 3.53
5671 5802 7.962918 GCACACTTAGTACAACTTTATGATTGG 59.037 37.037 0.00 0.00 0.00 3.16
5672 5803 7.688167 CGCACACTTAGTACAACTTTATGATTG 59.312 37.037 0.00 0.00 0.00 2.67
5673 5804 7.386848 ACGCACACTTAGTACAACTTTATGATT 59.613 33.333 0.00 0.00 0.00 2.57
5674 5805 6.872020 ACGCACACTTAGTACAACTTTATGAT 59.128 34.615 0.00 0.00 0.00 2.45
5675 5806 6.218019 ACGCACACTTAGTACAACTTTATGA 58.782 36.000 0.00 0.00 0.00 2.15
5676 5807 6.462073 ACGCACACTTAGTACAACTTTATG 57.538 37.500 0.00 0.00 0.00 1.90
5677 5808 8.592105 TTAACGCACACTTAGTACAACTTTAT 57.408 30.769 0.00 0.00 0.00 1.40
5678 5809 8.592105 ATTAACGCACACTTAGTACAACTTTA 57.408 30.769 0.00 0.00 0.00 1.85
5679 5810 6.907206 TTAACGCACACTTAGTACAACTTT 57.093 33.333 0.00 0.00 0.00 2.66
5680 5811 7.486802 AATTAACGCACACTTAGTACAACTT 57.513 32.000 0.00 0.00 0.00 2.66
5681 5812 8.592105 TTAATTAACGCACACTTAGTACAACT 57.408 30.769 0.00 0.00 0.00 3.16
5687 5818 8.951787 TCCATATTAATTAACGCACACTTAGT 57.048 30.769 0.00 0.00 0.00 2.24
5693 5824 8.349245 CCTTCAATCCATATTAATTAACGCACA 58.651 33.333 0.00 0.00 0.00 4.57
5708 5839 7.184862 AGAAAAATGTACTCCCTTCAATCCAT 58.815 34.615 0.00 0.00 0.00 3.41
5714 5845 9.581289 TTCAAATAGAAAAATGTACTCCCTTCA 57.419 29.630 0.00 0.00 32.05 3.02
5771 5902 9.264719 GGTAAATTAATAATACTAGGCGTGTGT 57.735 33.333 9.80 0.00 0.00 3.72
5777 5908 8.051535 GGAGGGGGTAAATTAATAATACTAGGC 58.948 40.741 9.80 0.00 0.00 3.93
5791 5922 0.996583 TCTTTGCGGAGGGGGTAAAT 59.003 50.000 0.00 0.00 0.00 1.40
5792 5923 0.772384 TTCTTTGCGGAGGGGGTAAA 59.228 50.000 0.00 0.00 0.00 2.01
5793 5924 0.772384 TTTCTTTGCGGAGGGGGTAA 59.228 50.000 0.00 0.00 0.00 2.85
5794 5925 0.996583 ATTTCTTTGCGGAGGGGGTA 59.003 50.000 0.00 0.00 0.00 3.69
5795 5926 0.996583 TATTTCTTTGCGGAGGGGGT 59.003 50.000 0.00 0.00 0.00 4.95
5796 5927 2.364972 ATATTTCTTTGCGGAGGGGG 57.635 50.000 0.00 0.00 0.00 5.40
5797 5928 5.123979 GCTATTATATTTCTTTGCGGAGGGG 59.876 44.000 0.00 0.00 0.00 4.79
5798 5929 5.163854 CGCTATTATATTTCTTTGCGGAGGG 60.164 44.000 0.00 0.00 38.74 4.30
5799 5930 5.408604 ACGCTATTATATTTCTTTGCGGAGG 59.591 40.000 0.00 0.00 45.26 4.30
5800 5931 6.467723 ACGCTATTATATTTCTTTGCGGAG 57.532 37.500 0.00 0.00 45.26 4.63
5801 5932 6.854496 AACGCTATTATATTTCTTTGCGGA 57.146 33.333 0.00 0.00 45.26 5.54
5802 5933 8.492748 TCTAAACGCTATTATATTTCTTTGCGG 58.507 33.333 0.00 0.00 45.26 5.69
5815 5946 9.489084 ACTAATGCAATGATCTAAACGCTATTA 57.511 29.630 0.00 0.00 0.00 0.98
5816 5947 8.285394 CACTAATGCAATGATCTAAACGCTATT 58.715 33.333 0.00 0.00 0.00 1.73
5817 5948 7.657354 TCACTAATGCAATGATCTAAACGCTAT 59.343 33.333 0.00 0.00 0.00 2.97
5818 5949 6.983890 TCACTAATGCAATGATCTAAACGCTA 59.016 34.615 0.00 0.00 0.00 4.26
5819 5950 5.817296 TCACTAATGCAATGATCTAAACGCT 59.183 36.000 0.00 0.00 0.00 5.07
5820 5951 6.048073 TCACTAATGCAATGATCTAAACGC 57.952 37.500 0.00 0.00 0.00 4.84
5827 5958 8.512956 AGCATTTAGATCACTAATGCAATGATC 58.487 33.333 26.88 18.66 46.04 2.92
5828 5959 8.405418 AGCATTTAGATCACTAATGCAATGAT 57.595 30.769 26.88 13.13 40.77 2.45
5829 5960 7.718314 AGAGCATTTAGATCACTAATGCAATGA 59.282 33.333 26.88 0.00 40.77 2.57
5830 5961 7.872881 AGAGCATTTAGATCACTAATGCAATG 58.127 34.615 26.88 12.18 40.77 2.82
5831 5962 8.461249 AAGAGCATTTAGATCACTAATGCAAT 57.539 30.769 26.88 18.00 40.77 3.56
5832 5963 7.870509 AAGAGCATTTAGATCACTAATGCAA 57.129 32.000 26.88 0.83 40.77 4.08
5848 5979 9.525826 CCCTCCATAAAGAAATATAAGAGCATT 57.474 33.333 0.00 0.00 0.00 3.56
5849 5980 8.894592 TCCCTCCATAAAGAAATATAAGAGCAT 58.105 33.333 0.00 0.00 0.00 3.79
5850 5981 8.275187 TCCCTCCATAAAGAAATATAAGAGCA 57.725 34.615 0.00 0.00 0.00 4.26
5851 5982 8.379331 ACTCCCTCCATAAAGAAATATAAGAGC 58.621 37.037 0.00 0.00 0.00 4.09
5859 5990 9.225682 TGAATAGTACTCCCTCCATAAAGAAAT 57.774 33.333 0.00 0.00 0.00 2.17
5860 5991 8.618240 TGAATAGTACTCCCTCCATAAAGAAA 57.382 34.615 0.00 0.00 0.00 2.52
5861 5992 8.798975 ATGAATAGTACTCCCTCCATAAAGAA 57.201 34.615 0.00 0.00 0.00 2.52
5862 5993 8.010697 TGATGAATAGTACTCCCTCCATAAAGA 58.989 37.037 0.00 0.00 0.00 2.52
5863 5994 8.195165 TGATGAATAGTACTCCCTCCATAAAG 57.805 38.462 0.00 0.00 0.00 1.85
5864 5995 8.561536 TTGATGAATAGTACTCCCTCCATAAA 57.438 34.615 0.00 0.00 0.00 1.40
5865 5996 8.561536 TTTGATGAATAGTACTCCCTCCATAA 57.438 34.615 0.00 0.00 0.00 1.90
5866 5997 7.789831 ACTTTGATGAATAGTACTCCCTCCATA 59.210 37.037 0.00 0.00 0.00 2.74
5867 5998 6.617371 ACTTTGATGAATAGTACTCCCTCCAT 59.383 38.462 0.00 0.00 0.00 3.41
5868 5999 5.964477 ACTTTGATGAATAGTACTCCCTCCA 59.036 40.000 0.00 0.00 0.00 3.86
5869 6000 6.487299 ACTTTGATGAATAGTACTCCCTCC 57.513 41.667 0.00 0.00 0.00 4.30
5870 6001 8.008513 TGTACTTTGATGAATAGTACTCCCTC 57.991 38.462 0.00 0.00 42.85 4.30
5871 6002 7.973048 TGTACTTTGATGAATAGTACTCCCT 57.027 36.000 0.00 0.00 42.85 4.20


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

AutoCloner maintained by Alex Coulton.