Multiple sequence alignment - TraesCS4D01G345500

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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 TraesCS4D01G345500 chr4D 100.000 3005 0 0 1 3005 500039414 500042418 0.000000e+00 5550.0
1 TraesCS4D01G345500 chr3D 97.566 2670 48 5 1 2657 281084448 281087113 0.000000e+00 4554.0
2 TraesCS4D01G345500 chr3D 97.107 2662 65 8 1 2660 450572976 450570325 0.000000e+00 4479.0
3 TraesCS4D01G345500 chr1A 97.353 2153 37 7 1 2146 493290300 493292439 0.000000e+00 3642.0
4 TraesCS4D01G345500 chr1A 96.386 498 15 3 2167 2663 493292561 493293056 0.000000e+00 817.0
5 TraesCS4D01G345500 chr1A 87.069 116 15 0 2783 2898 21645631 21645746 6.760000e-27 132.0
6 TraesCS4D01G345500 chr1B 90.000 1120 82 13 958 2077 601257570 601258659 0.000000e+00 1421.0
7 TraesCS4D01G345500 chr4A 90.698 817 69 5 955 1770 519159506 519160316 0.000000e+00 1081.0
8 TraesCS4D01G345500 chr5D 87.302 819 87 8 961 1770 558499136 558498326 0.000000e+00 920.0
9 TraesCS4D01G345500 chr5D 86.560 439 32 11 220 657 524597969 524598381 2.730000e-125 459.0
10 TraesCS4D01G345500 chr5D 89.431 123 13 0 846 968 558499612 558499490 4.010000e-34 156.0
11 TraesCS4D01G345500 chr2A 86.497 785 90 13 1299 2076 692641808 692641033 0.000000e+00 848.0
12 TraesCS4D01G345500 chr2D 86.224 784 93 13 1299 2076 551871494 551870720 0.000000e+00 835.0
13 TraesCS4D01G345500 chr2D 89.456 607 57 5 963 1568 211559853 211559253 0.000000e+00 760.0
14 TraesCS4D01G345500 chr2B 86.817 531 56 10 958 1487 652282593 652283110 5.580000e-162 580.0
15 TraesCS4D01G345500 chr2B 90.068 443 40 2 1631 2072 652283132 652283571 3.360000e-159 571.0
16 TraesCS4D01G345500 chr2B 84.821 448 56 9 1629 2072 657077355 657076916 9.890000e-120 440.0
17 TraesCS4D01G345500 chr2B 89.150 341 33 4 966 1305 657078011 657077674 3.580000e-114 422.0
18 TraesCS4D01G345500 chr2B 81.452 124 23 0 2775 2898 31510154 31510277 5.300000e-18 102.0
19 TraesCS4D01G345500 chr2B 81.452 124 23 0 2775 2898 31511156 31511279 5.300000e-18 102.0
20 TraesCS4D01G345500 chrUn 90.873 252 19 4 492 742 31916731 31916979 4.800000e-88 335.0
21 TraesCS4D01G345500 chrUn 88.043 276 21 5 235 498 31913440 31913715 1.740000e-82 316.0
22 TraesCS4D01G345500 chrUn 92.965 199 11 2 2657 2853 249202029 249201832 1.360000e-73 287.0
23 TraesCS4D01G345500 chrUn 92.965 199 11 2 2657 2853 277823400 277823597 1.360000e-73 287.0
24 TraesCS4D01G345500 chrUn 90.588 170 8 2 81 250 31913259 31913420 5.040000e-53 219.0
25 TraesCS4D01G345500 chrUn 81.452 124 23 0 2775 2898 334928922 334928799 5.300000e-18 102.0
26 TraesCS4D01G345500 chr6B 92.754 207 13 2 446 652 257587344 257587140 6.300000e-77 298.0
27 TraesCS4D01G345500 chr6B 93.277 119 7 1 274 391 257596177 257596059 1.110000e-39 174.0
28 TraesCS4D01G345500 chr6B 98.507 67 1 0 222 288 257597152 257597086 5.260000e-23 119.0
29 TraesCS4D01G345500 chr1D 83.032 277 34 10 2150 2422 42068414 42068147 3.870000e-59 239.0
30 TraesCS4D01G345500 chr7D 81.618 272 37 10 2150 2417 46087244 46086982 2.350000e-51 213.0
31 TraesCS4D01G345500 chr7D 100.000 34 0 0 905 938 502878986 502879019 2.500000e-06 63.9
32 TraesCS4D01G345500 chr6A 93.496 123 5 1 2776 2898 119759988 119759869 2.380000e-41 180.0
33 TraesCS4D01G345500 chr6A 100.000 36 0 0 179 214 146741431 146741466 1.930000e-07 67.6
34 TraesCS4D01G345500 chr6D 91.870 123 6 2 2780 2898 472907184 472907062 5.150000e-38 169.0
35 TraesCS4D01G345500 chr7B 100.000 34 0 0 905 938 531660351 531660384 2.500000e-06 63.9
36 TraesCS4D01G345500 chr7A 97.059 34 1 0 905 938 570117978 570118011 1.160000e-04 58.4


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 TraesCS4D01G345500 chr4D 500039414 500042418 3004 False 5550.0 5550 100.000000 1 3005 1 chr4D.!!$F1 3004
1 TraesCS4D01G345500 chr3D 281084448 281087113 2665 False 4554.0 4554 97.566000 1 2657 1 chr3D.!!$F1 2656
2 TraesCS4D01G345500 chr3D 450570325 450572976 2651 True 4479.0 4479 97.107000 1 2660 1 chr3D.!!$R1 2659
3 TraesCS4D01G345500 chr1A 493290300 493293056 2756 False 2229.5 3642 96.869500 1 2663 2 chr1A.!!$F2 2662
4 TraesCS4D01G345500 chr1B 601257570 601258659 1089 False 1421.0 1421 90.000000 958 2077 1 chr1B.!!$F1 1119
5 TraesCS4D01G345500 chr4A 519159506 519160316 810 False 1081.0 1081 90.698000 955 1770 1 chr4A.!!$F1 815
6 TraesCS4D01G345500 chr5D 558498326 558499612 1286 True 538.0 920 88.366500 846 1770 2 chr5D.!!$R1 924
7 TraesCS4D01G345500 chr2A 692641033 692641808 775 True 848.0 848 86.497000 1299 2076 1 chr2A.!!$R1 777
8 TraesCS4D01G345500 chr2D 551870720 551871494 774 True 835.0 835 86.224000 1299 2076 1 chr2D.!!$R2 777
9 TraesCS4D01G345500 chr2D 211559253 211559853 600 True 760.0 760 89.456000 963 1568 1 chr2D.!!$R1 605
10 TraesCS4D01G345500 chr2B 652282593 652283571 978 False 575.5 580 88.442500 958 2072 2 chr2B.!!$F2 1114
11 TraesCS4D01G345500 chr2B 657076916 657078011 1095 True 431.0 440 86.985500 966 2072 2 chr2B.!!$R1 1106
12 TraesCS4D01G345500 chrUn 31913259 31916979 3720 False 290.0 335 89.834667 81 742 3 chrUn.!!$F2 661

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
66 67 2.392662 AGGCAGCACTCTTATCAGCTA 58.607 47.619 0.00 0.00 35.19 3.32 F
566 3634 3.342719 TCAAACAACACAACTCAGCTGA 58.657 40.909 17.19 17.19 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1127 4562 4.019321 CCCTCCCATCCGTGACATTTATAT 60.019 45.833 0.0 0.0 0.00 0.86 R
2190 5853 0.029834 CACAACAACAGGCAGAGTGC 59.970 55.000 0.0 0.0 44.08 4.40 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 9.696917 TTTTCTTATTTCTTTCTGGAAAGCATC 57.303 29.630 15.76 0.00 45.48 3.91
66 67 2.392662 AGGCAGCACTCTTATCAGCTA 58.607 47.619 0.00 0.00 35.19 3.32
566 3634 3.342719 TCAAACAACACAACTCAGCTGA 58.657 40.909 17.19 17.19 0.00 4.26
952 4026 6.496144 ACTTTGTCCTCTAGGTACAAAAGT 57.504 37.500 18.72 15.26 40.79 2.66
1127 4562 1.482182 CCTGTATGGCAGCTACACTCA 59.518 52.381 0.00 0.00 43.71 3.41
1229 4664 2.019984 GCACCTCATCCAAACCATCTC 58.980 52.381 0.00 0.00 0.00 2.75
2044 5606 4.478203 TCCAATTGGAATGGAGTTGTTGA 58.522 39.130 25.13 0.00 41.98 3.18
2177 5840 4.866508 TCTCAGACCACTGTCGTAAATT 57.133 40.909 0.00 0.00 46.51 1.82
2190 5853 6.260050 ACTGTCGTAAATTATTATGGCACTGG 59.740 38.462 0.00 0.00 37.64 4.00
2402 6065 6.156949 GGGAGTATGATCCTCCTATATTTGCA 59.843 42.308 14.06 0.00 46.43 4.08
2417 6080 2.728690 TTGCATGCTTGTAGCTTTGG 57.271 45.000 20.33 0.00 42.97 3.28
2437 6100 8.028938 GCTTTGGTCTATTTTATGAATGTGTGT 58.971 33.333 0.00 0.00 0.00 3.72
2530 6194 9.700831 AGCACTAAGGGATTTCAGTTATAATTT 57.299 29.630 0.00 0.00 0.00 1.82
2658 6322 1.153429 GCGCCCCAACCACTAGTAG 60.153 63.158 0.00 0.00 0.00 2.57
2661 6325 1.276989 CGCCCCAACCACTAGTAGAAA 59.723 52.381 3.59 0.00 0.00 2.52
2662 6326 2.677037 CGCCCCAACCACTAGTAGAAAG 60.677 54.545 3.59 0.00 0.00 2.62
2663 6327 2.570302 GCCCCAACCACTAGTAGAAAGA 59.430 50.000 3.59 0.00 0.00 2.52
2664 6328 3.008704 GCCCCAACCACTAGTAGAAAGAA 59.991 47.826 3.59 0.00 0.00 2.52
2665 6329 4.324331 GCCCCAACCACTAGTAGAAAGAAT 60.324 45.833 3.59 0.00 0.00 2.40
2666 6330 5.104652 GCCCCAACCACTAGTAGAAAGAATA 60.105 44.000 3.59 0.00 0.00 1.75
2667 6331 6.346896 CCCCAACCACTAGTAGAAAGAATAC 58.653 44.000 3.59 0.00 0.00 1.89
2668 6332 6.156429 CCCCAACCACTAGTAGAAAGAATACT 59.844 42.308 3.59 0.00 37.29 2.12
2669 6333 7.042335 CCCAACCACTAGTAGAAAGAATACTG 58.958 42.308 3.59 0.00 35.20 2.74
2670 6334 6.535508 CCAACCACTAGTAGAAAGAATACTGC 59.464 42.308 3.59 0.00 35.20 4.40
2671 6335 6.852420 ACCACTAGTAGAAAGAATACTGCA 57.148 37.500 3.59 0.00 35.20 4.41
2672 6336 6.631962 ACCACTAGTAGAAAGAATACTGCAC 58.368 40.000 3.59 0.00 35.20 4.57
2673 6337 6.437793 ACCACTAGTAGAAAGAATACTGCACT 59.562 38.462 3.59 0.00 35.20 4.40
2674 6338 6.975772 CCACTAGTAGAAAGAATACTGCACTC 59.024 42.308 3.59 0.00 35.20 3.51
2675 6339 7.363007 CCACTAGTAGAAAGAATACTGCACTCA 60.363 40.741 3.59 0.00 35.20 3.41
2676 6340 7.700234 CACTAGTAGAAAGAATACTGCACTCAG 59.300 40.741 3.59 0.00 45.71 3.35
2690 6354 3.797331 TCAGTGGCTGAGACTGGG 58.203 61.111 0.00 0.00 41.11 4.45
2691 6355 1.915266 TCAGTGGCTGAGACTGGGG 60.915 63.158 0.00 0.00 41.11 4.96
2692 6356 2.608988 AGTGGCTGAGACTGGGGG 60.609 66.667 0.00 0.00 0.00 5.40
2693 6357 2.607750 GTGGCTGAGACTGGGGGA 60.608 66.667 0.00 0.00 0.00 4.81
2694 6358 1.997874 GTGGCTGAGACTGGGGGAT 60.998 63.158 0.00 0.00 0.00 3.85
2695 6359 1.690633 TGGCTGAGACTGGGGGATC 60.691 63.158 0.00 0.00 0.00 3.36
2696 6360 1.690633 GGCTGAGACTGGGGGATCA 60.691 63.158 0.00 0.00 0.00 2.92
2697 6361 1.274703 GGCTGAGACTGGGGGATCAA 61.275 60.000 0.00 0.00 0.00 2.57
2698 6362 0.107459 GCTGAGACTGGGGGATCAAC 60.107 60.000 0.00 0.00 0.00 3.18
2699 6363 1.279496 CTGAGACTGGGGGATCAACA 58.721 55.000 0.00 0.00 0.00 3.33
2700 6364 0.984230 TGAGACTGGGGGATCAACAC 59.016 55.000 0.00 0.00 0.00 3.32
2701 6365 0.108138 GAGACTGGGGGATCAACACG 60.108 60.000 0.00 0.00 0.00 4.49
2702 6366 1.745489 GACTGGGGGATCAACACGC 60.745 63.158 0.00 0.00 35.31 5.34
2703 6367 2.438434 CTGGGGGATCAACACGCC 60.438 66.667 0.00 0.00 39.88 5.68
2720 6384 2.776963 CCCGGCCCCCTCCTTAAT 60.777 66.667 0.00 0.00 0.00 1.40
2721 6385 1.462627 CCCGGCCCCCTCCTTAATA 60.463 63.158 0.00 0.00 0.00 0.98
2722 6386 1.063654 CCCGGCCCCCTCCTTAATAA 61.064 60.000 0.00 0.00 0.00 1.40
2723 6387 0.109913 CCGGCCCCCTCCTTAATAAC 59.890 60.000 0.00 0.00 0.00 1.89
2724 6388 0.841289 CGGCCCCCTCCTTAATAACA 59.159 55.000 0.00 0.00 0.00 2.41
2725 6389 1.423921 CGGCCCCCTCCTTAATAACAT 59.576 52.381 0.00 0.00 0.00 2.71
2726 6390 2.158519 CGGCCCCCTCCTTAATAACATT 60.159 50.000 0.00 0.00 0.00 2.71
2727 6391 3.230976 GGCCCCCTCCTTAATAACATTG 58.769 50.000 0.00 0.00 0.00 2.82
2728 6392 3.117284 GGCCCCCTCCTTAATAACATTGA 60.117 47.826 0.00 0.00 0.00 2.57
2729 6393 4.145052 GCCCCCTCCTTAATAACATTGAG 58.855 47.826 0.00 0.00 0.00 3.02
2730 6394 4.386424 GCCCCCTCCTTAATAACATTGAGT 60.386 45.833 0.00 0.00 0.00 3.41
2731 6395 5.766590 CCCCCTCCTTAATAACATTGAGTT 58.233 41.667 0.00 0.00 44.27 3.01
2732 6396 6.636336 GCCCCCTCCTTAATAACATTGAGTTA 60.636 42.308 0.00 0.00 46.10 2.24
2733 6397 6.998673 CCCCCTCCTTAATAACATTGAGTTAG 59.001 42.308 0.00 0.00 45.31 2.34
2734 6398 6.998673 CCCCTCCTTAATAACATTGAGTTAGG 59.001 42.308 0.00 0.00 45.31 2.69
2735 6399 6.486993 CCCTCCTTAATAACATTGAGTTAGGC 59.513 42.308 0.00 0.00 45.31 3.93
2736 6400 6.486993 CCTCCTTAATAACATTGAGTTAGGCC 59.513 42.308 0.00 0.00 45.31 5.19
2737 6401 7.208064 TCCTTAATAACATTGAGTTAGGCCT 57.792 36.000 11.78 11.78 45.31 5.19
2738 6402 8.326765 TCCTTAATAACATTGAGTTAGGCCTA 57.673 34.615 8.91 8.91 45.31 3.93
2739 6403 8.774183 TCCTTAATAACATTGAGTTAGGCCTAA 58.226 33.333 21.68 21.68 45.31 2.69
2740 6404 9.574516 CCTTAATAACATTGAGTTAGGCCTAAT 57.425 33.333 27.60 16.33 45.31 1.73
2744 6408 6.884280 AACATTGAGTTAGGCCTAATATGC 57.116 37.500 27.60 14.86 39.09 3.14
2745 6409 5.940617 ACATTGAGTTAGGCCTAATATGCA 58.059 37.500 27.60 18.81 0.00 3.96
2746 6410 6.546484 ACATTGAGTTAGGCCTAATATGCAT 58.454 36.000 27.60 13.47 0.00 3.96
2747 6411 6.432162 ACATTGAGTTAGGCCTAATATGCATG 59.568 38.462 27.60 23.75 0.00 4.06
2748 6412 5.823861 TGAGTTAGGCCTAATATGCATGA 57.176 39.130 27.60 0.00 0.00 3.07
2749 6413 5.798132 TGAGTTAGGCCTAATATGCATGAG 58.202 41.667 27.60 3.79 0.00 2.90
2750 6414 5.171339 AGTTAGGCCTAATATGCATGAGG 57.829 43.478 27.60 13.92 0.00 3.86
2751 6415 4.599241 AGTTAGGCCTAATATGCATGAGGT 59.401 41.667 27.60 8.42 0.00 3.85
2752 6416 5.073691 AGTTAGGCCTAATATGCATGAGGTT 59.926 40.000 27.60 13.29 0.00 3.50
2753 6417 6.272324 AGTTAGGCCTAATATGCATGAGGTTA 59.728 38.462 27.60 12.59 0.00 2.85
2754 6418 5.582950 AGGCCTAATATGCATGAGGTTAA 57.417 39.130 19.56 0.00 0.00 2.01
2755 6419 5.952387 AGGCCTAATATGCATGAGGTTAAA 58.048 37.500 19.56 0.00 0.00 1.52
2756 6420 6.555711 AGGCCTAATATGCATGAGGTTAAAT 58.444 36.000 19.56 0.00 0.00 1.40
2757 6421 6.435277 AGGCCTAATATGCATGAGGTTAAATG 59.565 38.462 19.56 5.11 0.00 2.32
2758 6422 6.350445 GGCCTAATATGCATGAGGTTAAATGG 60.350 42.308 19.56 9.18 0.00 3.16
2759 6423 6.209391 GCCTAATATGCATGAGGTTAAATGGT 59.791 38.462 19.56 0.00 0.00 3.55
2760 6424 7.255942 GCCTAATATGCATGAGGTTAAATGGTT 60.256 37.037 19.56 0.00 0.00 3.67
2761 6425 9.295825 CCTAATATGCATGAGGTTAAATGGTTA 57.704 33.333 10.16 0.00 0.00 2.85
2765 6429 9.985730 ATATGCATGAGGTTAAATGGTTATTTG 57.014 29.630 10.16 0.00 37.12 2.32
2766 6430 6.105333 TGCATGAGGTTAAATGGTTATTTGC 58.895 36.000 0.00 0.00 37.12 3.68
2767 6431 6.070881 TGCATGAGGTTAAATGGTTATTTGCT 60.071 34.615 0.00 0.00 37.12 3.91
2768 6432 6.256321 GCATGAGGTTAAATGGTTATTTGCTG 59.744 38.462 0.00 0.00 37.12 4.41
2769 6433 5.719173 TGAGGTTAAATGGTTATTTGCTGC 58.281 37.500 0.00 0.00 37.12 5.25
2770 6434 5.480073 TGAGGTTAAATGGTTATTTGCTGCT 59.520 36.000 0.00 0.00 37.12 4.24
2771 6435 6.661377 TGAGGTTAAATGGTTATTTGCTGCTA 59.339 34.615 0.00 0.00 37.12 3.49
2772 6436 7.177568 TGAGGTTAAATGGTTATTTGCTGCTAA 59.822 33.333 0.00 0.00 37.12 3.09
2773 6437 7.902087 AGGTTAAATGGTTATTTGCTGCTAAA 58.098 30.769 0.00 0.45 37.12 1.85
2774 6438 8.034804 AGGTTAAATGGTTATTTGCTGCTAAAG 58.965 33.333 0.00 0.00 37.12 1.85
2775 6439 8.032451 GGTTAAATGGTTATTTGCTGCTAAAGA 58.968 33.333 0.00 0.00 37.12 2.52
2776 6440 9.418045 GTTAAATGGTTATTTGCTGCTAAAGAA 57.582 29.630 0.00 1.25 37.12 2.52
2777 6441 9.988815 TTAAATGGTTATTTGCTGCTAAAGAAA 57.011 25.926 0.00 0.00 37.12 2.52
2778 6442 8.538409 AAATGGTTATTTGCTGCTAAAGAAAG 57.462 30.769 0.00 0.00 35.26 2.62
2779 6443 6.892658 TGGTTATTTGCTGCTAAAGAAAGA 57.107 33.333 0.00 0.00 0.00 2.52
2780 6444 7.283625 TGGTTATTTGCTGCTAAAGAAAGAA 57.716 32.000 0.00 0.00 0.00 2.52
2781 6445 7.370383 TGGTTATTTGCTGCTAAAGAAAGAAG 58.630 34.615 0.00 0.00 0.00 2.85
2782 6446 7.014230 TGGTTATTTGCTGCTAAAGAAAGAAGT 59.986 33.333 0.00 0.00 0.00 3.01
2783 6447 7.539022 GGTTATTTGCTGCTAAAGAAAGAAGTC 59.461 37.037 0.00 0.00 0.00 3.01
2784 6448 5.438761 TTTGCTGCTAAAGAAAGAAGTCC 57.561 39.130 0.00 0.00 0.00 3.85
2785 6449 4.085357 TGCTGCTAAAGAAAGAAGTCCA 57.915 40.909 0.00 0.00 0.00 4.02
2786 6450 4.655963 TGCTGCTAAAGAAAGAAGTCCAT 58.344 39.130 0.00 0.00 0.00 3.41
2787 6451 5.072741 TGCTGCTAAAGAAAGAAGTCCATT 58.927 37.500 0.00 0.00 0.00 3.16
2788 6452 5.536161 TGCTGCTAAAGAAAGAAGTCCATTT 59.464 36.000 0.00 0.00 0.00 2.32
2789 6453 6.040842 TGCTGCTAAAGAAAGAAGTCCATTTT 59.959 34.615 0.00 0.00 0.00 1.82
2790 6454 6.925718 GCTGCTAAAGAAAGAAGTCCATTTTT 59.074 34.615 0.00 0.00 0.00 1.94
2791 6455 7.115520 GCTGCTAAAGAAAGAAGTCCATTTTTC 59.884 37.037 0.00 0.00 0.00 2.29
2792 6456 8.006298 TGCTAAAGAAAGAAGTCCATTTTTCA 57.994 30.769 0.00 0.00 33.19 2.69
2793 6457 7.920682 TGCTAAAGAAAGAAGTCCATTTTTCAC 59.079 33.333 0.00 0.00 33.19 3.18
2794 6458 7.382488 GCTAAAGAAAGAAGTCCATTTTTCACC 59.618 37.037 0.00 0.00 33.19 4.02
2795 6459 5.791336 AGAAAGAAGTCCATTTTTCACCC 57.209 39.130 0.00 0.00 33.19 4.61
2796 6460 5.458595 AGAAAGAAGTCCATTTTTCACCCT 58.541 37.500 0.00 0.00 33.19 4.34
2797 6461 6.610830 AGAAAGAAGTCCATTTTTCACCCTA 58.389 36.000 0.00 0.00 33.19 3.53
2798 6462 7.066781 AGAAAGAAGTCCATTTTTCACCCTAA 58.933 34.615 0.00 0.00 33.19 2.69
2799 6463 7.563556 AGAAAGAAGTCCATTTTTCACCCTAAA 59.436 33.333 0.00 0.00 33.19 1.85
2800 6464 7.669089 AAGAAGTCCATTTTTCACCCTAAAA 57.331 32.000 0.00 0.00 0.00 1.52
2801 6465 7.855784 AGAAGTCCATTTTTCACCCTAAAAT 57.144 32.000 0.00 0.00 36.03 1.82
2802 6466 7.670364 AGAAGTCCATTTTTCACCCTAAAATG 58.330 34.615 11.96 11.96 45.70 2.32
2803 6467 5.793817 AGTCCATTTTTCACCCTAAAATGC 58.206 37.500 13.00 4.11 45.19 3.56
2804 6468 4.625311 GTCCATTTTTCACCCTAAAATGCG 59.375 41.667 13.00 8.41 45.19 4.73
2805 6469 4.282195 TCCATTTTTCACCCTAAAATGCGT 59.718 37.500 13.00 0.00 45.19 5.24
2806 6470 4.625311 CCATTTTTCACCCTAAAATGCGTC 59.375 41.667 13.00 0.00 45.19 5.19
2807 6471 3.926821 TTTTCACCCTAAAATGCGTCC 57.073 42.857 0.00 0.00 0.00 4.79
2808 6472 2.871096 TTCACCCTAAAATGCGTCCT 57.129 45.000 0.00 0.00 0.00 3.85
2809 6473 2.107950 TCACCCTAAAATGCGTCCTG 57.892 50.000 0.00 0.00 0.00 3.86
2810 6474 1.626321 TCACCCTAAAATGCGTCCTGA 59.374 47.619 0.00 0.00 0.00 3.86
2811 6475 2.238646 TCACCCTAAAATGCGTCCTGAT 59.761 45.455 0.00 0.00 0.00 2.90
2812 6476 2.355756 CACCCTAAAATGCGTCCTGATG 59.644 50.000 0.00 0.00 0.00 3.07
2813 6477 1.949525 CCCTAAAATGCGTCCTGATGG 59.050 52.381 0.00 0.00 0.00 3.51
2814 6478 2.421388 CCCTAAAATGCGTCCTGATGGA 60.421 50.000 0.00 0.00 40.69 3.41
2826 6490 2.777692 TCCTGATGGACAAATACTCCCC 59.222 50.000 0.00 0.00 37.46 4.81
2827 6491 2.780010 CCTGATGGACAAATACTCCCCT 59.220 50.000 0.00 0.00 34.57 4.79
2828 6492 3.181450 CCTGATGGACAAATACTCCCCTC 60.181 52.174 0.00 0.00 34.57 4.30
2829 6493 3.455910 CTGATGGACAAATACTCCCCTCA 59.544 47.826 0.00 0.00 0.00 3.86
2830 6494 3.849574 TGATGGACAAATACTCCCCTCAA 59.150 43.478 0.00 0.00 0.00 3.02
2831 6495 3.713826 TGGACAAATACTCCCCTCAAC 57.286 47.619 0.00 0.00 0.00 3.18
2832 6496 3.256704 TGGACAAATACTCCCCTCAACT 58.743 45.455 0.00 0.00 0.00 3.16
2833 6497 3.655777 TGGACAAATACTCCCCTCAACTT 59.344 43.478 0.00 0.00 0.00 2.66
2834 6498 4.010349 GGACAAATACTCCCCTCAACTTG 58.990 47.826 0.00 0.00 0.00 3.16
2835 6499 4.263331 GGACAAATACTCCCCTCAACTTGA 60.263 45.833 0.00 0.00 0.00 3.02
2836 6500 5.313712 GACAAATACTCCCCTCAACTTGAA 58.686 41.667 0.00 0.00 0.00 2.69
2837 6501 5.892348 ACAAATACTCCCCTCAACTTGAAT 58.108 37.500 0.00 0.00 0.00 2.57
2838 6502 6.314917 ACAAATACTCCCCTCAACTTGAATT 58.685 36.000 0.00 0.00 0.00 2.17
2839 6503 6.782494 ACAAATACTCCCCTCAACTTGAATTT 59.218 34.615 0.00 0.00 0.00 1.82
2840 6504 6.840780 AATACTCCCCTCAACTTGAATTTG 57.159 37.500 0.00 0.00 0.00 2.32
2841 6505 3.500343 ACTCCCCTCAACTTGAATTTGG 58.500 45.455 0.00 0.00 0.00 3.28
2842 6506 3.117131 ACTCCCCTCAACTTGAATTTGGT 60.117 43.478 0.00 0.00 0.00 3.67
2843 6507 4.105697 ACTCCCCTCAACTTGAATTTGGTA 59.894 41.667 0.00 0.00 0.00 3.25
2844 6508 5.222337 ACTCCCCTCAACTTGAATTTGGTAT 60.222 40.000 0.00 0.00 0.00 2.73
2845 6509 5.016173 TCCCCTCAACTTGAATTTGGTATG 58.984 41.667 0.00 0.00 0.00 2.39
2846 6510 5.016173 CCCCTCAACTTGAATTTGGTATGA 58.984 41.667 0.00 0.00 0.00 2.15
2847 6511 5.658190 CCCCTCAACTTGAATTTGGTATGAT 59.342 40.000 0.00 0.00 0.00 2.45
2848 6512 6.155049 CCCCTCAACTTGAATTTGGTATGATT 59.845 38.462 0.00 0.00 0.00 2.57
2849 6513 7.310609 CCCCTCAACTTGAATTTGGTATGATTT 60.311 37.037 0.00 0.00 0.00 2.17
2850 6514 7.761249 CCCTCAACTTGAATTTGGTATGATTTC 59.239 37.037 0.00 0.00 0.00 2.17
2851 6515 8.306038 CCTCAACTTGAATTTGGTATGATTTCA 58.694 33.333 0.00 0.00 0.00 2.69
2852 6516 9.695526 CTCAACTTGAATTTGGTATGATTTCAA 57.304 29.630 0.00 0.00 0.00 2.69
2853 6517 9.474920 TCAACTTGAATTTGGTATGATTTCAAC 57.525 29.630 0.00 0.00 0.00 3.18
2854 6518 8.711457 CAACTTGAATTTGGTATGATTTCAACC 58.289 33.333 0.00 5.49 0.00 3.77
2855 6519 7.386059 ACTTGAATTTGGTATGATTTCAACCC 58.614 34.615 8.47 2.28 31.97 4.11
2856 6520 6.293004 TGAATTTGGTATGATTTCAACCCC 57.707 37.500 8.47 0.36 31.97 4.95
2857 6521 5.188751 TGAATTTGGTATGATTTCAACCCCC 59.811 40.000 8.47 0.00 31.97 5.40
2858 6522 3.835478 TTGGTATGATTTCAACCCCCA 57.165 42.857 8.47 0.00 31.97 4.96
2859 6523 3.835478 TGGTATGATTTCAACCCCCAA 57.165 42.857 8.47 0.00 31.97 4.12
2860 6524 4.133526 TGGTATGATTTCAACCCCCAAA 57.866 40.909 8.47 0.00 31.97 3.28
2861 6525 4.693420 TGGTATGATTTCAACCCCCAAAT 58.307 39.130 8.47 0.00 31.97 2.32
2862 6526 4.714308 TGGTATGATTTCAACCCCCAAATC 59.286 41.667 8.47 0.00 38.83 2.17
2863 6527 4.100963 GGTATGATTTCAACCCCCAAATCC 59.899 45.833 0.00 0.00 37.96 3.01
2864 6528 3.558608 TGATTTCAACCCCCAAATCCT 57.441 42.857 0.00 0.00 37.96 3.24
2865 6529 3.440127 TGATTTCAACCCCCAAATCCTC 58.560 45.455 0.00 0.00 37.96 3.71
2866 6530 3.181413 TGATTTCAACCCCCAAATCCTCA 60.181 43.478 0.00 0.00 37.96 3.86
2867 6531 3.336509 TTTCAACCCCCAAATCCTCAA 57.663 42.857 0.00 0.00 0.00 3.02
2868 6532 3.336509 TTCAACCCCCAAATCCTCAAA 57.663 42.857 0.00 0.00 0.00 2.69
2869 6533 3.336509 TCAACCCCCAAATCCTCAAAA 57.663 42.857 0.00 0.00 0.00 2.44
2870 6534 2.969262 TCAACCCCCAAATCCTCAAAAC 59.031 45.455 0.00 0.00 0.00 2.43
2871 6535 2.024176 ACCCCCAAATCCTCAAAACC 57.976 50.000 0.00 0.00 0.00 3.27
2872 6536 0.894835 CCCCCAAATCCTCAAAACCG 59.105 55.000 0.00 0.00 0.00 4.44
2873 6537 0.894835 CCCCAAATCCTCAAAACCGG 59.105 55.000 0.00 0.00 0.00 5.28
2874 6538 1.549037 CCCCAAATCCTCAAAACCGGA 60.549 52.381 9.46 0.00 0.00 5.14
2875 6539 2.456577 CCCAAATCCTCAAAACCGGAT 58.543 47.619 9.46 0.00 41.68 4.18
2876 6540 2.166254 CCCAAATCCTCAAAACCGGATG 59.834 50.000 9.46 4.12 39.86 3.51
2877 6541 3.088532 CCAAATCCTCAAAACCGGATGA 58.911 45.455 9.46 8.89 39.86 2.92
2878 6542 3.509575 CCAAATCCTCAAAACCGGATGAA 59.490 43.478 9.46 0.00 39.86 2.57
2879 6543 4.160252 CCAAATCCTCAAAACCGGATGAAT 59.840 41.667 9.46 0.00 39.86 2.57
2880 6544 5.343249 CAAATCCTCAAAACCGGATGAATC 58.657 41.667 9.46 0.00 39.86 2.52
2881 6545 4.510167 ATCCTCAAAACCGGATGAATCT 57.490 40.909 9.46 0.00 38.56 2.40
2882 6546 3.873910 TCCTCAAAACCGGATGAATCTC 58.126 45.455 9.46 0.00 0.00 2.75
2883 6547 2.945668 CCTCAAAACCGGATGAATCTCC 59.054 50.000 9.46 0.00 0.00 3.71
2884 6548 2.945668 CTCAAAACCGGATGAATCTCCC 59.054 50.000 9.46 0.00 31.04 4.30
2885 6549 2.024414 CAAAACCGGATGAATCTCCCC 58.976 52.381 9.46 0.00 31.04 4.81
2886 6550 0.551396 AAACCGGATGAATCTCCCCC 59.449 55.000 9.46 0.00 31.04 5.40
2887 6551 0.327576 AACCGGATGAATCTCCCCCT 60.328 55.000 9.46 0.00 31.04 4.79
2888 6552 0.566176 ACCGGATGAATCTCCCCCTA 59.434 55.000 9.46 0.00 31.04 3.53
2889 6553 1.061657 ACCGGATGAATCTCCCCCTAA 60.062 52.381 9.46 0.00 31.04 2.69
2890 6554 1.625818 CCGGATGAATCTCCCCCTAAG 59.374 57.143 0.00 0.00 31.04 2.18
2891 6555 1.625818 CGGATGAATCTCCCCCTAAGG 59.374 57.143 0.00 0.00 31.04 2.69
2892 6556 2.707554 GGATGAATCTCCCCCTAAGGT 58.292 52.381 0.00 0.00 0.00 3.50
2893 6557 2.373502 GGATGAATCTCCCCCTAAGGTG 59.626 54.545 0.00 0.00 0.00 4.00
2894 6558 1.893315 TGAATCTCCCCCTAAGGTGG 58.107 55.000 0.00 0.00 0.00 4.61
2895 6559 1.082194 TGAATCTCCCCCTAAGGTGGT 59.918 52.381 0.00 0.00 0.00 4.16
2896 6560 2.206223 GAATCTCCCCCTAAGGTGGTT 58.794 52.381 0.00 0.00 0.00 3.67
2897 6561 2.378308 ATCTCCCCCTAAGGTGGTTT 57.622 50.000 0.00 0.00 0.00 3.27
2898 6562 1.368374 TCTCCCCCTAAGGTGGTTTG 58.632 55.000 0.00 0.00 0.00 2.93
2899 6563 0.331616 CTCCCCCTAAGGTGGTTTGG 59.668 60.000 0.00 0.00 0.00 3.28
2900 6564 0.403750 TCCCCCTAAGGTGGTTTGGT 60.404 55.000 0.00 0.00 29.52 3.67
2901 6565 0.039180 CCCCCTAAGGTGGTTTGGTC 59.961 60.000 0.00 0.00 29.52 4.02
2902 6566 0.322187 CCCCTAAGGTGGTTTGGTCG 60.322 60.000 0.00 0.00 29.52 4.79
2903 6567 0.322187 CCCTAAGGTGGTTTGGTCGG 60.322 60.000 0.00 0.00 29.52 4.79
2904 6568 0.688487 CCTAAGGTGGTTTGGTCGGA 59.312 55.000 0.00 0.00 0.00 4.55
2905 6569 1.072648 CCTAAGGTGGTTTGGTCGGAA 59.927 52.381 0.00 0.00 0.00 4.30
2906 6570 2.423577 CTAAGGTGGTTTGGTCGGAAG 58.576 52.381 0.00 0.00 0.00 3.46
2907 6571 0.822121 AAGGTGGTTTGGTCGGAAGC 60.822 55.000 0.00 0.00 0.00 3.86
2908 6572 2.613506 GGTGGTTTGGTCGGAAGCG 61.614 63.158 0.00 0.00 0.00 4.68
2909 6573 1.890510 GTGGTTTGGTCGGAAGCGT 60.891 57.895 0.00 0.00 0.00 5.07
2910 6574 1.153127 TGGTTTGGTCGGAAGCGTT 60.153 52.632 0.00 0.00 0.00 4.84
2911 6575 1.281656 GGTTTGGTCGGAAGCGTTG 59.718 57.895 0.00 0.00 0.00 4.10
2912 6576 1.161563 GGTTTGGTCGGAAGCGTTGA 61.162 55.000 0.00 0.00 0.00 3.18
2913 6577 0.234884 GTTTGGTCGGAAGCGTTGAG 59.765 55.000 0.00 0.00 0.00 3.02
2951 6615 3.374330 CGAAGATCGTGTCGCCAC 58.626 61.111 4.03 0.00 38.27 5.01
2952 6616 1.154016 CGAAGATCGTGTCGCCACT 60.154 57.895 0.00 0.00 39.55 4.00
2953 6617 1.406219 CGAAGATCGTGTCGCCACTG 61.406 60.000 0.00 0.00 39.55 3.66
2954 6618 0.388649 GAAGATCGTGTCGCCACTGT 60.389 55.000 0.00 0.00 39.55 3.55
2955 6619 0.388649 AAGATCGTGTCGCCACTGTC 60.389 55.000 0.00 0.00 39.55 3.51
2956 6620 1.805945 GATCGTGTCGCCACTGTCC 60.806 63.158 0.00 0.00 39.55 4.02
2957 6621 3.626680 ATCGTGTCGCCACTGTCCG 62.627 63.158 0.00 0.00 39.55 4.79
2961 6625 4.736896 GTCGCCACTGTCCGGGAC 62.737 72.222 20.36 20.36 35.21 4.46
2981 6645 4.697756 CGCGGCAGGACCTTTCCA 62.698 66.667 0.00 0.00 45.72 3.53
2982 6646 2.044946 GCGGCAGGACCTTTCCAT 60.045 61.111 9.58 0.00 45.72 3.41
2983 6647 2.115291 GCGGCAGGACCTTTCCATC 61.115 63.158 9.58 0.00 45.72 3.51
2984 6648 1.452108 CGGCAGGACCTTTCCATCC 60.452 63.158 9.58 0.00 45.72 3.51
2985 6649 1.691219 GGCAGGACCTTTCCATCCA 59.309 57.895 0.00 0.00 45.72 3.41
2986 6650 0.394899 GGCAGGACCTTTCCATCCAG 60.395 60.000 0.00 0.00 45.72 3.86
2987 6651 0.394899 GCAGGACCTTTCCATCCAGG 60.395 60.000 0.00 0.00 45.72 4.45
2988 6652 0.257039 CAGGACCTTTCCATCCAGGG 59.743 60.000 0.00 0.00 45.72 4.45
2989 6653 0.121197 AGGACCTTTCCATCCAGGGA 59.879 55.000 0.00 0.00 45.72 4.20
2990 6654 0.548510 GGACCTTTCCATCCAGGGAG 59.451 60.000 0.00 0.00 42.30 4.30
2991 6655 0.106967 GACCTTTCCATCCAGGGAGC 60.107 60.000 0.00 0.00 38.42 4.70
2992 6656 0.846427 ACCTTTCCATCCAGGGAGCA 60.846 55.000 0.00 0.00 38.42 4.26
2993 6657 0.554792 CCTTTCCATCCAGGGAGCAT 59.445 55.000 0.00 0.00 38.42 3.79
2994 6658 1.688772 CTTTCCATCCAGGGAGCATG 58.311 55.000 0.00 0.00 38.42 4.06
2995 6659 0.396139 TTTCCATCCAGGGAGCATGC 60.396 55.000 10.51 10.51 38.42 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.731089 TGCCTTTCAATTTCTTTGGCAG 58.269 40.909 0.00 0.00 43.09 4.85
1127 4562 4.019321 CCCTCCCATCCGTGACATTTATAT 60.019 45.833 0.00 0.00 0.00 0.86
1229 4664 5.336372 GGGCTCAGCTTAGACATACATCTAG 60.336 48.000 2.54 0.00 32.78 2.43
1419 4959 4.674475 TGAACATAAAGTACTGCGCGATA 58.326 39.130 12.10 0.00 0.00 2.92
1428 4969 9.180678 CAAACTGGATTGTTGAACATAAAGTAC 57.819 33.333 0.00 0.00 0.00 2.73
1925 5487 5.314923 AGCCATCACATGTGTTGTATTTC 57.685 39.130 27.10 14.76 36.57 2.17
2044 5606 6.321181 TGTTCTTTGGTTATCAGCAAGAAACT 59.679 34.615 14.27 0.00 41.38 2.66
2177 5840 2.746142 GCAGAGTGCCAGTGCCATAATA 60.746 50.000 0.00 0.00 37.42 0.98
2190 5853 0.029834 CACAACAACAGGCAGAGTGC 59.970 55.000 0.00 0.00 44.08 4.40
2227 5890 1.816835 AGGACGTCATCGCTTCAGTTA 59.183 47.619 18.91 0.00 41.18 2.24
2402 6065 6.840780 AAAATAGACCAAAGCTACAAGCAT 57.159 33.333 1.22 0.00 45.56 3.79
2417 6080 7.008628 GCAGCAACACACATTCATAAAATAGAC 59.991 37.037 0.00 0.00 0.00 2.59
2437 6100 6.832520 TGGAAAAATAAGATACAGCAGCAA 57.167 33.333 0.00 0.00 0.00 3.91
2673 6337 1.915266 CCCCAGTCTCAGCCACTGA 60.915 63.158 1.31 0.00 43.54 3.41
2674 6338 2.667418 CCCCAGTCTCAGCCACTG 59.333 66.667 0.00 0.00 40.96 3.66
2675 6339 2.483329 ATCCCCCAGTCTCAGCCACT 62.483 60.000 0.00 0.00 0.00 4.00
2676 6340 1.977293 GATCCCCCAGTCTCAGCCAC 61.977 65.000 0.00 0.00 0.00 5.01
2677 6341 1.690633 GATCCCCCAGTCTCAGCCA 60.691 63.158 0.00 0.00 0.00 4.75
2678 6342 1.274703 TTGATCCCCCAGTCTCAGCC 61.275 60.000 0.00 0.00 0.00 4.85
2679 6343 0.107459 GTTGATCCCCCAGTCTCAGC 60.107 60.000 0.00 0.00 0.00 4.26
2680 6344 1.065854 GTGTTGATCCCCCAGTCTCAG 60.066 57.143 0.00 0.00 0.00 3.35
2681 6345 0.984230 GTGTTGATCCCCCAGTCTCA 59.016 55.000 0.00 0.00 0.00 3.27
2682 6346 0.108138 CGTGTTGATCCCCCAGTCTC 60.108 60.000 0.00 0.00 0.00 3.36
2683 6347 1.983224 CGTGTTGATCCCCCAGTCT 59.017 57.895 0.00 0.00 0.00 3.24
2684 6348 1.745489 GCGTGTTGATCCCCCAGTC 60.745 63.158 0.00 0.00 0.00 3.51
2685 6349 2.351276 GCGTGTTGATCCCCCAGT 59.649 61.111 0.00 0.00 0.00 4.00
2686 6350 2.438434 GGCGTGTTGATCCCCCAG 60.438 66.667 0.00 0.00 0.00 4.45
2687 6351 4.041762 GGGCGTGTTGATCCCCCA 62.042 66.667 0.00 0.00 35.75 4.96
2702 6366 2.994912 TATTAAGGAGGGGGCCGGGG 62.995 65.000 2.18 0.00 0.00 5.73
2703 6367 1.063654 TTATTAAGGAGGGGGCCGGG 61.064 60.000 2.18 0.00 0.00 5.73
2704 6368 0.109913 GTTATTAAGGAGGGGGCCGG 59.890 60.000 0.00 0.00 0.00 6.13
2705 6369 0.841289 TGTTATTAAGGAGGGGGCCG 59.159 55.000 0.00 0.00 0.00 6.13
2706 6370 3.117284 TCAATGTTATTAAGGAGGGGGCC 60.117 47.826 0.00 0.00 0.00 5.80
2707 6371 4.145052 CTCAATGTTATTAAGGAGGGGGC 58.855 47.826 0.00 0.00 0.00 5.80
2708 6372 5.388599 ACTCAATGTTATTAAGGAGGGGG 57.611 43.478 0.00 0.00 0.00 5.40
2709 6373 6.998673 CCTAACTCAATGTTATTAAGGAGGGG 59.001 42.308 0.00 0.00 40.02 4.79
2710 6374 6.486993 GCCTAACTCAATGTTATTAAGGAGGG 59.513 42.308 0.00 0.00 40.02 4.30
2711 6375 6.486993 GGCCTAACTCAATGTTATTAAGGAGG 59.513 42.308 0.00 0.00 40.02 4.30
2712 6376 7.283329 AGGCCTAACTCAATGTTATTAAGGAG 58.717 38.462 1.29 0.00 40.02 3.69
2713 6377 7.208064 AGGCCTAACTCAATGTTATTAAGGA 57.792 36.000 1.29 0.00 40.02 3.36
2714 6378 8.974060 TTAGGCCTAACTCAATGTTATTAAGG 57.026 34.615 21.68 0.00 40.02 2.69
2718 6382 9.014297 GCATATTAGGCCTAACTCAATGTTATT 57.986 33.333 27.46 9.52 40.02 1.40
2719 6383 8.163408 TGCATATTAGGCCTAACTCAATGTTAT 58.837 33.333 27.46 14.95 40.02 1.89
2720 6384 7.513856 TGCATATTAGGCCTAACTCAATGTTA 58.486 34.615 27.46 13.33 39.89 2.41
2721 6385 6.364701 TGCATATTAGGCCTAACTCAATGTT 58.635 36.000 27.46 11.49 42.31 2.71
2722 6386 5.940617 TGCATATTAGGCCTAACTCAATGT 58.059 37.500 27.46 12.23 0.00 2.71
2723 6387 6.656270 TCATGCATATTAGGCCTAACTCAATG 59.344 38.462 27.46 24.43 0.00 2.82
2724 6388 6.782986 TCATGCATATTAGGCCTAACTCAAT 58.217 36.000 27.46 14.75 0.00 2.57
2725 6389 6.186420 TCATGCATATTAGGCCTAACTCAA 57.814 37.500 27.46 13.41 0.00 3.02
2726 6390 5.280164 CCTCATGCATATTAGGCCTAACTCA 60.280 44.000 27.46 20.33 0.00 3.41
2727 6391 5.181748 CCTCATGCATATTAGGCCTAACTC 58.818 45.833 27.46 15.83 0.00 3.01
2728 6392 4.599241 ACCTCATGCATATTAGGCCTAACT 59.401 41.667 27.46 17.72 31.96 2.24
2729 6393 4.911390 ACCTCATGCATATTAGGCCTAAC 58.089 43.478 27.46 14.93 31.96 2.34
2730 6394 5.582950 AACCTCATGCATATTAGGCCTAA 57.417 39.130 27.11 27.11 31.96 2.69
2731 6395 6.696042 TTAACCTCATGCATATTAGGCCTA 57.304 37.500 8.91 8.91 31.96 3.93
2732 6396 5.582950 TTAACCTCATGCATATTAGGCCT 57.417 39.130 11.78 11.78 31.96 5.19
2733 6397 6.350445 CCATTTAACCTCATGCATATTAGGCC 60.350 42.308 17.58 0.00 31.96 5.19
2734 6398 6.209391 ACCATTTAACCTCATGCATATTAGGC 59.791 38.462 17.58 0.00 31.96 3.93
2735 6399 7.765695 ACCATTTAACCTCATGCATATTAGG 57.234 36.000 16.53 16.53 34.46 2.69
2739 6403 9.985730 CAAATAACCATTTAACCTCATGCATAT 57.014 29.630 0.00 0.00 32.96 1.78
2740 6404 7.925483 GCAAATAACCATTTAACCTCATGCATA 59.075 33.333 0.00 0.00 32.96 3.14
2741 6405 6.762661 GCAAATAACCATTTAACCTCATGCAT 59.237 34.615 0.00 0.00 32.96 3.96
2742 6406 6.070881 AGCAAATAACCATTTAACCTCATGCA 60.071 34.615 0.00 0.00 32.96 3.96
2743 6407 6.256321 CAGCAAATAACCATTTAACCTCATGC 59.744 38.462 0.00 0.00 32.96 4.06
2744 6408 6.256321 GCAGCAAATAACCATTTAACCTCATG 59.744 38.462 0.00 0.00 32.96 3.07
2745 6409 6.155049 AGCAGCAAATAACCATTTAACCTCAT 59.845 34.615 0.00 0.00 32.96 2.90
2746 6410 5.480073 AGCAGCAAATAACCATTTAACCTCA 59.520 36.000 0.00 0.00 32.96 3.86
2747 6411 5.965922 AGCAGCAAATAACCATTTAACCTC 58.034 37.500 0.00 0.00 32.96 3.85
2748 6412 7.475137 TTAGCAGCAAATAACCATTTAACCT 57.525 32.000 0.00 0.00 32.96 3.50
2749 6413 8.032451 TCTTTAGCAGCAAATAACCATTTAACC 58.968 33.333 0.00 0.00 32.96 2.85
2750 6414 8.980143 TCTTTAGCAGCAAATAACCATTTAAC 57.020 30.769 0.00 0.00 32.96 2.01
2751 6415 9.988815 TTTCTTTAGCAGCAAATAACCATTTAA 57.011 25.926 0.00 0.00 32.96 1.52
2752 6416 9.638239 CTTTCTTTAGCAGCAAATAACCATTTA 57.362 29.630 0.00 0.00 32.96 1.40
2753 6417 8.367156 TCTTTCTTTAGCAGCAAATAACCATTT 58.633 29.630 0.00 0.00 34.60 2.32
2754 6418 7.895759 TCTTTCTTTAGCAGCAAATAACCATT 58.104 30.769 0.00 0.00 0.00 3.16
2755 6419 7.466746 TCTTTCTTTAGCAGCAAATAACCAT 57.533 32.000 0.00 0.00 0.00 3.55
2756 6420 6.892658 TCTTTCTTTAGCAGCAAATAACCA 57.107 33.333 0.00 0.00 0.00 3.67
2757 6421 7.371159 ACTTCTTTCTTTAGCAGCAAATAACC 58.629 34.615 0.00 0.00 0.00 2.85
2758 6422 7.539022 GGACTTCTTTCTTTAGCAGCAAATAAC 59.461 37.037 0.00 0.00 0.00 1.89
2759 6423 7.230510 TGGACTTCTTTCTTTAGCAGCAAATAA 59.769 33.333 0.00 0.00 0.00 1.40
2760 6424 6.714810 TGGACTTCTTTCTTTAGCAGCAAATA 59.285 34.615 0.00 0.00 0.00 1.40
2761 6425 5.536161 TGGACTTCTTTCTTTAGCAGCAAAT 59.464 36.000 0.00 0.00 0.00 2.32
2762 6426 4.887071 TGGACTTCTTTCTTTAGCAGCAAA 59.113 37.500 0.00 0.00 0.00 3.68
2763 6427 4.460263 TGGACTTCTTTCTTTAGCAGCAA 58.540 39.130 0.00 0.00 0.00 3.91
2764 6428 4.085357 TGGACTTCTTTCTTTAGCAGCA 57.915 40.909 0.00 0.00 0.00 4.41
2765 6429 5.635417 AATGGACTTCTTTCTTTAGCAGC 57.365 39.130 0.00 0.00 0.00 5.25
2766 6430 8.137437 TGAAAAATGGACTTCTTTCTTTAGCAG 58.863 33.333 0.00 0.00 0.00 4.24
2767 6431 7.920682 GTGAAAAATGGACTTCTTTCTTTAGCA 59.079 33.333 0.00 0.00 0.00 3.49
2768 6432 7.382488 GGTGAAAAATGGACTTCTTTCTTTAGC 59.618 37.037 0.00 0.00 0.00 3.09
2769 6433 7.867909 GGGTGAAAAATGGACTTCTTTCTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
2770 6434 7.563556 AGGGTGAAAAATGGACTTCTTTCTTTA 59.436 33.333 0.00 0.00 0.00 1.85
2771 6435 6.384015 AGGGTGAAAAATGGACTTCTTTCTTT 59.616 34.615 0.00 0.00 0.00 2.52
2772 6436 5.899547 AGGGTGAAAAATGGACTTCTTTCTT 59.100 36.000 0.00 0.00 0.00 2.52
2773 6437 5.458595 AGGGTGAAAAATGGACTTCTTTCT 58.541 37.500 0.00 0.00 0.00 2.52
2774 6438 5.791336 AGGGTGAAAAATGGACTTCTTTC 57.209 39.130 0.00 0.00 0.00 2.62
2775 6439 7.669089 TTTAGGGTGAAAAATGGACTTCTTT 57.331 32.000 0.00 0.00 0.00 2.52
2776 6440 7.669089 TTTTAGGGTGAAAAATGGACTTCTT 57.331 32.000 0.00 0.00 0.00 2.52
2777 6441 7.670364 CATTTTAGGGTGAAAAATGGACTTCT 58.330 34.615 11.59 0.00 44.75 2.85
2778 6442 6.368791 GCATTTTAGGGTGAAAAATGGACTTC 59.631 38.462 17.97 3.19 46.86 3.01
2779 6443 6.230472 GCATTTTAGGGTGAAAAATGGACTT 58.770 36.000 17.97 0.00 46.86 3.01
2780 6444 5.566627 CGCATTTTAGGGTGAAAAATGGACT 60.567 40.000 17.97 0.00 46.86 3.85
2781 6445 4.625311 CGCATTTTAGGGTGAAAAATGGAC 59.375 41.667 17.97 6.27 46.86 4.02
2782 6446 4.282195 ACGCATTTTAGGGTGAAAAATGGA 59.718 37.500 17.97 0.00 46.86 3.41
2783 6447 4.565022 ACGCATTTTAGGGTGAAAAATGG 58.435 39.130 17.97 12.41 46.86 3.16
2785 6449 4.526650 AGGACGCATTTTAGGGTGAAAAAT 59.473 37.500 0.00 0.00 37.08 1.82
2786 6450 3.892588 AGGACGCATTTTAGGGTGAAAAA 59.107 39.130 0.00 0.00 34.56 1.94
2787 6451 3.254657 CAGGACGCATTTTAGGGTGAAAA 59.745 43.478 0.00 0.00 34.56 2.29
2788 6452 2.817258 CAGGACGCATTTTAGGGTGAAA 59.183 45.455 0.00 0.00 34.56 2.69
2789 6453 2.039216 TCAGGACGCATTTTAGGGTGAA 59.961 45.455 0.00 0.00 34.56 3.18
2790 6454 1.626321 TCAGGACGCATTTTAGGGTGA 59.374 47.619 0.00 0.00 34.56 4.02
2791 6455 2.107950 TCAGGACGCATTTTAGGGTG 57.892 50.000 0.00 0.00 34.56 4.61
2792 6456 2.643551 CATCAGGACGCATTTTAGGGT 58.356 47.619 0.00 0.00 37.38 4.34
2793 6457 1.949525 CCATCAGGACGCATTTTAGGG 59.050 52.381 0.00 0.00 36.89 3.53
2794 6458 2.917933 TCCATCAGGACGCATTTTAGG 58.082 47.619 0.00 0.00 39.61 2.69
2805 6469 2.777692 GGGGAGTATTTGTCCATCAGGA 59.222 50.000 0.00 0.00 43.21 3.86
2806 6470 2.780010 AGGGGAGTATTTGTCCATCAGG 59.220 50.000 0.00 0.00 35.57 3.86
2807 6471 3.455910 TGAGGGGAGTATTTGTCCATCAG 59.544 47.826 0.00 0.00 35.57 2.90
2808 6472 3.459828 TGAGGGGAGTATTTGTCCATCA 58.540 45.455 0.00 0.00 35.57 3.07
2809 6473 4.080299 AGTTGAGGGGAGTATTTGTCCATC 60.080 45.833 0.00 0.00 35.57 3.51
2810 6474 3.852578 AGTTGAGGGGAGTATTTGTCCAT 59.147 43.478 0.00 0.00 35.57 3.41
2811 6475 3.256704 AGTTGAGGGGAGTATTTGTCCA 58.743 45.455 0.00 0.00 35.57 4.02
2812 6476 4.010349 CAAGTTGAGGGGAGTATTTGTCC 58.990 47.826 0.00 0.00 0.00 4.02
2813 6477 4.906618 TCAAGTTGAGGGGAGTATTTGTC 58.093 43.478 0.08 0.00 0.00 3.18
2814 6478 4.993705 TCAAGTTGAGGGGAGTATTTGT 57.006 40.909 0.08 0.00 0.00 2.83
2815 6479 6.840780 AATTCAAGTTGAGGGGAGTATTTG 57.159 37.500 5.56 0.00 0.00 2.32
2816 6480 6.211384 CCAAATTCAAGTTGAGGGGAGTATTT 59.789 38.462 5.56 4.85 0.00 1.40
2817 6481 5.716703 CCAAATTCAAGTTGAGGGGAGTATT 59.283 40.000 5.56 0.00 0.00 1.89
2818 6482 5.222337 ACCAAATTCAAGTTGAGGGGAGTAT 60.222 40.000 16.36 0.94 0.00 2.12
2819 6483 4.105697 ACCAAATTCAAGTTGAGGGGAGTA 59.894 41.667 16.36 0.00 0.00 2.59
2820 6484 3.117131 ACCAAATTCAAGTTGAGGGGAGT 60.117 43.478 16.36 7.37 0.00 3.85
2821 6485 3.500343 ACCAAATTCAAGTTGAGGGGAG 58.500 45.455 16.36 6.87 0.00 4.30
2822 6486 3.611025 ACCAAATTCAAGTTGAGGGGA 57.389 42.857 16.36 0.33 0.00 4.81
2823 6487 5.016173 TCATACCAAATTCAAGTTGAGGGG 58.984 41.667 5.56 8.76 0.00 4.79
2824 6488 6.780457 ATCATACCAAATTCAAGTTGAGGG 57.220 37.500 5.56 9.09 0.00 4.30
2825 6489 8.306038 TGAAATCATACCAAATTCAAGTTGAGG 58.694 33.333 5.56 6.50 0.00 3.86
2826 6490 9.695526 TTGAAATCATACCAAATTCAAGTTGAG 57.304 29.630 5.56 0.00 35.67 3.02
2827 6491 9.474920 GTTGAAATCATACCAAATTCAAGTTGA 57.525 29.630 0.08 0.08 39.77 3.18
2828 6492 8.711457 GGTTGAAATCATACCAAATTCAAGTTG 58.289 33.333 0.00 0.00 39.77 3.16
2829 6493 7.877612 GGGTTGAAATCATACCAAATTCAAGTT 59.122 33.333 13.20 0.00 39.77 2.66
2830 6494 7.386059 GGGTTGAAATCATACCAAATTCAAGT 58.614 34.615 13.20 0.00 39.77 3.16
2831 6495 6.818142 GGGGTTGAAATCATACCAAATTCAAG 59.182 38.462 13.20 0.00 39.77 3.02
2832 6496 6.296145 GGGGGTTGAAATCATACCAAATTCAA 60.296 38.462 13.20 0.00 37.59 2.69
2833 6497 5.188751 GGGGGTTGAAATCATACCAAATTCA 59.811 40.000 13.20 0.00 32.43 2.57
2834 6498 5.188751 TGGGGGTTGAAATCATACCAAATTC 59.811 40.000 13.20 0.00 32.43 2.17
2835 6499 5.097234 TGGGGGTTGAAATCATACCAAATT 58.903 37.500 13.20 0.00 32.43 1.82
2836 6500 4.693420 TGGGGGTTGAAATCATACCAAAT 58.307 39.130 13.20 0.00 32.43 2.32
2837 6501 4.133526 TGGGGGTTGAAATCATACCAAA 57.866 40.909 13.20 0.00 32.43 3.28
2838 6502 3.835478 TGGGGGTTGAAATCATACCAA 57.165 42.857 13.20 0.00 32.43 3.67
2839 6503 3.835478 TTGGGGGTTGAAATCATACCA 57.165 42.857 13.20 0.00 32.43 3.25
2840 6504 4.100963 GGATTTGGGGGTTGAAATCATACC 59.899 45.833 0.00 6.34 39.40 2.73
2841 6505 4.962362 AGGATTTGGGGGTTGAAATCATAC 59.038 41.667 0.00 0.00 39.40 2.39
2842 6506 5.208121 GAGGATTTGGGGGTTGAAATCATA 58.792 41.667 0.00 0.00 39.40 2.15
2843 6507 4.033009 GAGGATTTGGGGGTTGAAATCAT 58.967 43.478 0.00 0.00 39.40 2.45
2844 6508 3.181413 TGAGGATTTGGGGGTTGAAATCA 60.181 43.478 0.00 0.00 39.40 2.57
2845 6509 3.440127 TGAGGATTTGGGGGTTGAAATC 58.560 45.455 0.00 0.00 37.69 2.17
2846 6510 3.558608 TGAGGATTTGGGGGTTGAAAT 57.441 42.857 0.00 0.00 0.00 2.17
2847 6511 3.336509 TTGAGGATTTGGGGGTTGAAA 57.663 42.857 0.00 0.00 0.00 2.69
2848 6512 3.336509 TTTGAGGATTTGGGGGTTGAA 57.663 42.857 0.00 0.00 0.00 2.69
2849 6513 2.969262 GTTTTGAGGATTTGGGGGTTGA 59.031 45.455 0.00 0.00 0.00 3.18
2850 6514 2.038426 GGTTTTGAGGATTTGGGGGTTG 59.962 50.000 0.00 0.00 0.00 3.77
2851 6515 2.334977 GGTTTTGAGGATTTGGGGGTT 58.665 47.619 0.00 0.00 0.00 4.11
2852 6516 1.825641 CGGTTTTGAGGATTTGGGGGT 60.826 52.381 0.00 0.00 0.00 4.95
2853 6517 0.894835 CGGTTTTGAGGATTTGGGGG 59.105 55.000 0.00 0.00 0.00 5.40
2854 6518 0.894835 CCGGTTTTGAGGATTTGGGG 59.105 55.000 0.00 0.00 0.00 4.96
2855 6519 1.917872 TCCGGTTTTGAGGATTTGGG 58.082 50.000 0.00 0.00 0.00 4.12
2856 6520 3.088532 TCATCCGGTTTTGAGGATTTGG 58.911 45.455 0.00 0.00 44.26 3.28
2857 6521 4.782019 TTCATCCGGTTTTGAGGATTTG 57.218 40.909 0.00 0.00 44.26 2.32
2858 6522 5.264395 AGATTCATCCGGTTTTGAGGATTT 58.736 37.500 0.00 0.00 44.26 2.17
2859 6523 4.860022 AGATTCATCCGGTTTTGAGGATT 58.140 39.130 0.00 0.00 44.26 3.01
2861 6525 3.370527 GGAGATTCATCCGGTTTTGAGGA 60.371 47.826 0.00 0.00 41.30 3.71
2862 6526 2.945668 GGAGATTCATCCGGTTTTGAGG 59.054 50.000 0.00 0.00 0.00 3.86
2863 6527 2.945668 GGGAGATTCATCCGGTTTTGAG 59.054 50.000 0.00 0.00 40.56 3.02
2864 6528 2.356741 GGGGAGATTCATCCGGTTTTGA 60.357 50.000 0.00 0.35 40.56 2.69
2865 6529 2.024414 GGGGAGATTCATCCGGTTTTG 58.976 52.381 0.00 0.00 40.56 2.44
2866 6530 1.063942 GGGGGAGATTCATCCGGTTTT 60.064 52.381 0.00 0.00 40.56 2.43
2867 6531 0.551396 GGGGGAGATTCATCCGGTTT 59.449 55.000 0.00 0.00 40.56 3.27
2868 6532 0.327576 AGGGGGAGATTCATCCGGTT 60.328 55.000 0.00 0.00 40.56 4.44
2869 6533 0.566176 TAGGGGGAGATTCATCCGGT 59.434 55.000 0.00 0.00 40.56 5.28
2870 6534 1.625818 CTTAGGGGGAGATTCATCCGG 59.374 57.143 0.00 0.00 40.56 5.14
2871 6535 1.625818 CCTTAGGGGGAGATTCATCCG 59.374 57.143 0.00 0.00 40.56 4.18
2872 6536 2.373502 CACCTTAGGGGGAGATTCATCC 59.626 54.545 2.32 0.00 38.59 3.51
2873 6537 2.373502 CCACCTTAGGGGGAGATTCATC 59.626 54.545 16.00 0.00 38.59 2.92
2874 6538 2.294536 ACCACCTTAGGGGGAGATTCAT 60.295 50.000 28.75 0.00 38.59 2.57
2875 6539 1.082194 ACCACCTTAGGGGGAGATTCA 59.918 52.381 28.75 0.00 38.59 2.57
2876 6540 1.894699 ACCACCTTAGGGGGAGATTC 58.105 55.000 28.75 0.00 38.59 2.52
2877 6541 2.311841 CAAACCACCTTAGGGGGAGATT 59.688 50.000 28.75 14.81 38.59 2.40
2878 6542 1.923148 CAAACCACCTTAGGGGGAGAT 59.077 52.381 28.75 9.07 38.59 2.75
2879 6543 1.368374 CAAACCACCTTAGGGGGAGA 58.632 55.000 28.75 0.00 38.59 3.71
2880 6544 0.331616 CCAAACCACCTTAGGGGGAG 59.668 60.000 28.75 14.94 38.59 4.30
2881 6545 0.403750 ACCAAACCACCTTAGGGGGA 60.404 55.000 28.75 0.00 38.59 4.81
2882 6546 0.039180 GACCAAACCACCTTAGGGGG 59.961 60.000 19.74 19.74 40.03 5.40
2883 6547 0.322187 CGACCAAACCACCTTAGGGG 60.322 60.000 2.32 0.00 41.89 4.79
2884 6548 0.322187 CCGACCAAACCACCTTAGGG 60.322 60.000 2.32 0.00 38.88 3.53
2885 6549 0.688487 TCCGACCAAACCACCTTAGG 59.312 55.000 0.00 0.00 0.00 2.69
2886 6550 2.423577 CTTCCGACCAAACCACCTTAG 58.576 52.381 0.00 0.00 0.00 2.18
2887 6551 1.543871 GCTTCCGACCAAACCACCTTA 60.544 52.381 0.00 0.00 0.00 2.69
2888 6552 0.822121 GCTTCCGACCAAACCACCTT 60.822 55.000 0.00 0.00 0.00 3.50
2889 6553 1.228154 GCTTCCGACCAAACCACCT 60.228 57.895 0.00 0.00 0.00 4.00
2890 6554 2.613506 CGCTTCCGACCAAACCACC 61.614 63.158 0.00 0.00 36.29 4.61
2891 6555 1.441732 AACGCTTCCGACCAAACCAC 61.442 55.000 0.00 0.00 38.29 4.16
2892 6556 1.153127 AACGCTTCCGACCAAACCA 60.153 52.632 0.00 0.00 38.29 3.67
2893 6557 1.161563 TCAACGCTTCCGACCAAACC 61.162 55.000 0.00 0.00 38.29 3.27
2894 6558 0.234884 CTCAACGCTTCCGACCAAAC 59.765 55.000 0.00 0.00 38.29 2.93
2895 6559 1.503818 GCTCAACGCTTCCGACCAAA 61.504 55.000 0.00 0.00 38.29 3.28
2896 6560 1.959226 GCTCAACGCTTCCGACCAA 60.959 57.895 0.00 0.00 38.29 3.67
2897 6561 2.357034 GCTCAACGCTTCCGACCA 60.357 61.111 0.00 0.00 38.29 4.02
2898 6562 3.479269 CGCTCAACGCTTCCGACC 61.479 66.667 0.00 0.00 38.29 4.79
2944 6608 4.736896 GTCCCGGACAGTGGCGAC 62.737 72.222 13.05 0.00 32.09 5.19
2964 6628 3.976701 ATGGAAAGGTCCTGCCGCG 62.977 63.158 0.00 0.00 45.22 6.46
2965 6629 2.044946 ATGGAAAGGTCCTGCCGC 60.045 61.111 0.00 0.00 45.22 6.53
2966 6630 1.452108 GGATGGAAAGGTCCTGCCG 60.452 63.158 0.00 0.00 45.22 5.69
2967 6631 0.394899 CTGGATGGAAAGGTCCTGCC 60.395 60.000 0.00 0.00 45.22 4.85
2968 6632 0.394899 CCTGGATGGAAAGGTCCTGC 60.395 60.000 0.00 0.00 45.22 4.85
2969 6633 0.257039 CCCTGGATGGAAAGGTCCTG 59.743 60.000 0.00 0.00 45.22 3.86
2970 6634 0.121197 TCCCTGGATGGAAAGGTCCT 59.879 55.000 0.00 0.00 45.22 3.85
2971 6635 0.548510 CTCCCTGGATGGAAAGGTCC 59.451 60.000 0.00 0.00 45.21 4.46
2972 6636 0.106967 GCTCCCTGGATGGAAAGGTC 60.107 60.000 0.00 0.00 38.35 3.85
2973 6637 0.846427 TGCTCCCTGGATGGAAAGGT 60.846 55.000 0.00 0.00 38.35 3.50
2974 6638 0.554792 ATGCTCCCTGGATGGAAAGG 59.445 55.000 0.00 0.00 38.35 3.11
2975 6639 1.688772 CATGCTCCCTGGATGGAAAG 58.311 55.000 0.00 0.00 40.27 2.62
2976 6640 0.396139 GCATGCTCCCTGGATGGAAA 60.396 55.000 11.37 0.00 43.53 3.13
2977 6641 1.228228 GCATGCTCCCTGGATGGAA 59.772 57.895 11.37 0.00 43.53 3.53
2978 6642 2.760378 GGCATGCTCCCTGGATGGA 61.760 63.158 18.92 0.00 43.53 3.41
2979 6643 2.203451 GGCATGCTCCCTGGATGG 60.203 66.667 18.92 0.00 43.53 3.51
2980 6644 1.528542 CTGGCATGCTCCCTGGATG 60.529 63.158 18.92 0.00 45.68 3.51
2981 6645 2.764737 CCTGGCATGCTCCCTGGAT 61.765 63.158 18.92 0.00 42.32 3.41
2982 6646 2.838436 TACCTGGCATGCTCCCTGGA 62.838 60.000 18.92 2.72 42.32 3.86
2983 6647 2.335092 CTACCTGGCATGCTCCCTGG 62.335 65.000 18.92 16.02 44.47 4.45
2984 6648 1.147824 CTACCTGGCATGCTCCCTG 59.852 63.158 18.92 5.03 0.00 4.45
2985 6649 2.074948 CCTACCTGGCATGCTCCCT 61.075 63.158 18.92 0.63 0.00 4.20
2986 6650 2.512896 CCTACCTGGCATGCTCCC 59.487 66.667 18.92 0.95 0.00 4.30


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

AutoCloner maintained by Alex Coulton.